Home

The ImageJ User Guide – Verson 1.43

1. Distribution Data points 223 Count 223 Min 5 Mean 73 946 Max 1 m OA A StdDev 31 866 Mode g Bins 8 Bin Wid or specify bins 8 5 n and range 0 200 List Copy Log 9 Cancel _ a Area 15 Produces a relative frequency his togram from the data of a chosen column of the Results table C23 Use the List or Copy buttons to save the histogram data Mouse over the histogram bars to read the counts for each bin on the window s lower right corner Analyze gt Histogram h describes in more detail ImageJ s histogram window This command is also available by right clicking on the Results table cf The Results Table Parameter Specifies the parameter in the Results table to be analyzed 128 Data points The number of rows that will be analyzed informative Automatic binning If checked ImageJ will use the method described by Scott D 1979 84 to assess the optimal histogram bin width If unchecked the number of bins can be set with Specify bins and the starting and ending limits of the histogram with range SEE ALSO Distribution Plotter a macro that plots relative and cumulative frequencies on a double Y axis graph 33 5 Label This command labels the active selection with the current measurement counter value i e the number of rows present in the Results table Selection outline and label at the selection centroid are drawn invasively
2. y y a y Help Cancel OK Target Specifies the Java version of the class files created by Plugins Compile and Run Plugins compiled with a Target of 1 6 will not run on earlier version Java A Target of 1 4 should be used to create plugins capable of running on all versions ImageJ Target cannot be set higher than the version of Java ImageJ is currently running on 62 Generate Debugging Info javac g If checked information needed by Java debug gers in the class files will be included Help Opens http rsb info nih gov ij docs menus edit html compiler 30 10 14 DICOM DICOM Options This dialog specifies if ImageJ should open DICOM images as O Open as 32 bit float 32 bit float y SEE ALSO Image Types and Image Formats 30 10 15 Misc Displays a dialog box containing miscellaneous options MC Miscellaneous Options ooo Divide by zero value Specifies the value used when Processt gt Image Calculator detects a divide by zero while dividing one 32 bit real image by another The default is infinity In addition to numeric values infinity posi tive or negative infinity max largest pos itive value and NaN Not a Number can be entered as the Divide by zero value O Use pointer cursor O Hide Process Stack dialog O Require command key for shortcuts O Move isolated plugins to Misc menu O Run single instance listener O Debug mode Cancel
3. SEE ALSO Hyperstack to Stack 31 7 5 Channels Z Opens the Channels window or brings it to the front if it is already open is the keyboard shortcut for this command This tool allows to select the Display mode of composite images In addition several commands hosted in the Image Color gt submenu can easily be accessed through the Mores drop down menu The same drop down menu also provides a convenient list of primary colors additive red green and 88 blue subtractive cyan magenta yellow that can be used to pseudocolor composite channels Composite images are described in more detail on page 17 Channels flybrain tif A selsi 5 A els bit 6 3 2 32 157 256x220 pixels S bit LII Composite 2 Channels Channels e Y Composite i M Channel 1 Composite 4 Grayscale Y Grayscale gt os M Channel 1 O Channel 1 O Channel 1 M Channel 2 M Channel 2 M Channel 2 M Channel 4 E More More More NS Composite Convert to RGB Split Channels Merge Channels Edit LUT Red Green Blue Cyan 31 8 Crop X Crops the image or stack based on the current rectangular selection 31 9 Duplicate D e Duplicate Creates a new window containing a copy of the active image Title Rebinned tif or rectangular selection O a S ge Hold the Alt key down to skip the dialog 31 10 Rename O gt Re
4. If an Options dialog is available for a particular tool it can be accessed by double clicking on the tool icon 16 1 Status bar When the cursor is over an image pixel intensities and coordinates are displayed in the status bar After running a filter elapsed time and processing rate in pixels second 27 is also displayed When clicking on the status bar the ImageJ version the Java version memory in use memory available and percent memory used will be displayed As selec tions are created or resized selection properties e g location width etc are displayed on the status bar Note that clicking on ImageJ s status bar forces the Java garbage collector to run which may help to reclaim unused memory AAO Image Badoj lt rrrzEsa ajo 14 4 0 8 7 8 8 gt Image 1 4305 Java 1 6 0_17 64 bit 3344K of 1166MB lt 1 SEE ALSO Plugins Utilities gt ImageJ Properties Help gt About ImageJ 5 TOGGLING CALIBRATED UNITS If a spatial scale has been defined selection properties are displayed in calibrated units Resizing or moving while holding down forces this information to be displayed in pixels 16 2 Progress bar The progress bar located to the right of the status bar shows the progress of time consuming operations It will not appear if the operation requires less then approxi mately one second 17 Area selection tools 17 1 Rectangular Selection Tool L
5. E Scale Factor Specifies if images should be resized cf Imager Scale E 119 32 12 3 Macro ADD arian Runs a macro over all the images in a specified folder Input Desktop Source ll Input Selects the source folder Output Desktop Destination containing the images io b Output Format TIFF 34 processed Add Macro Code Scale Output Selects the destination seala 1 5 x Add Border J folder where the processed w getWidth scale h getHeight scale Convert to RGB run Size width w height h inter Crop Gaussian Blur images will be stored Output Format Specifies the Invert Label output format that can Measure be set to TIFF 8 bit Pisara TIFF JPEG GIF PNG Show File Info Unsharp Mask PGM BMP FITS Text Image ZIP or Raw cf Image Types and Image Formats and File gt Save Asp submenu Test Open Save t one Cane Add Macro Code This drop down menu contains macro snippets that can be com bined to create the processing macro Other statements can be pasted from the macro recorder or ImageJ s editor while the dialog box is opened C22 Previously written macros can be imported using Open When editing the macro beware of any statements that may interfere with the normal operation of the batch processor such as Close or Open calls Test Tests the macro on the first image of the Input f
6. Creates an RGB copy of the current image and displays a labeled calibration bar on it Location At Selection Fill Color None Label Color Black Number of Labels 5 Decimal Places 2 Font Size 14 Zoom Factor 1 0 O Bold Text Location Defines the position of the bar If there is a selection the bar is initially drawn at the selection Fill Color Defines the bar s background color Label Adjusts the text color Number of Labels Adjusts the total number of values displayed Decimal Places Adjust the number of decimal places present in the labels Font Size Adjusts labels font size labels are drawn bold if Bold Text is checked Zoom Scale Zooms the entire calibration bar The Calibration Bar Macros can be used to add a calibration bar to a stack or to all the images and stacks in a folder SEE ALSO Calibrate 19 147 34 Plugins 34 1 Macros This submenu contains commands for installing running and recording macros as well as any macro commands added by Plugins Macros tInstall Macros contained in a file named StartupMacros txt in the macros folder are automatically added to this submenu when ImageJ starts up 34 1 1 Install Adds one or more macros contained in a file to the bottom of this submenu To install a set of macros and at the same time view their source code open the macro file with File Open and use the editor s Macros
7. M Light Background O Separate Colors M Create Background Don t Subtract O Sliding Paraboloid M Disable Smoothing M Preview Removes smooth continuous backgrounds from gels and other images Based on the rolling ball algorithm by Stanley Sternberg 91 Imagine a 3D surface with the pixel values of the image being the height then a ball rolling over the back side of the surface creates the background If Sliding Paraboloid is checked the command will use a more robust implementation Cancel of the algorithm that uses an approximation of a paraboloid of rotation instead of a ball Rolling Ball Radius The radius of curvature of the paraboloid As a rule of thumb for 8 bit or RGB images it should be at least as large as the radius of the largest object in the image that is not part of the background Larger values will also work unless the background of the image is too uneven For 16 bit and 32 bit images with pixel value ranges different from 0 255 the radius should be inversely proportional to the pixel value range e g for 16 bit images pixel values 0 65535 typical values of the radius are around 0 2 to 5 Light Background Allows the processing of images with bright background and dark objects Separate Colors RGB images only If unchecked the operation will only affect the brightness leaving the hue and saturation untouched Create Background Don t Subtract If checked the output is n
8. SEE ALSO ROI Manager 30 10 Options Use commands in this submenu to change various ImageJ user preference settings 30 10 1 Line Width OOO Displays a dialog box that allows the width of lines generated by Line Width i the Edit Draw d command to be changed This legacy com mand has has been superseded by the Image gt Adjust gt Line Width Cancel OK widget 57 30 10 2 Input Output aQ0 UO Options JPEG Quality 0 100 Specifies the com pression level used by the File gt Save Asp Jpeg command Requesting a higher degree of compression a lower value will result in smaller files but poorer image quality Please note that it is not a good idea to use lossy encoded JPEG formatted images when doing image processing and analysis because it alters the content of the original image and introduces artifacts JPEG Quality 0 100 100 GIF and PNG Transparent Index 1 File Extension for Tables csv O Use JFileChooser to Open Save O Save TIFF and Raw in Intel Byte Order Y Copy Column Headers O Copy Row Numbers A File Extension for Tables Sets the default extension to be used when saving tables e g the Results table Files with txt and xls extensions are saved in tab delimited format and files with csv extensions are saved in comma delimited format Use JFileChooser to Open Save Enables versions of File Open and File Save As that use the Java JFileChoose
9. Virtual Stack From List macro demonstrates how to generate a list of images and then use that list to open the images as a virtual stack 29 6 9 TIFF Virtual Stack Opens a TIFF file as a virtual stack 29 6 10 AVI A AVI Reader Uses a built in version of the AVI reader plugin to open an AVI file JPEG or PNG compressed or uncompressed as a stack or virtual stack one slice per video frame AVI files can also be opened using File gt Open or drag and drop but macros must use this command to gain access to the dialog box options First Frame 1 Last Frame 27 O Use Virtual Stack O Convert to Grayscale O Flip Vertical ae Since version 1 41b a much improved version of the plugin C6 retrieves animation speed from image frame rate adds support for YUV formats the ability to specify the starting and ending frame an option to convert to 8 bit grayscale an option to open the movie as a virtual stack along with many bug fixes Nevertheless ImageJ only supports a restricted number of AVI formats cf plugin source code 29 7 Close w Closes the active image 44 29 8 Close All yOu Close All There are 2 images with unsaved changes If you Closes all open 1mages An alert depicted click OK they will be closed without being saved on the left is displayed if there are unsaved changes 29 9 Save s Saves the active image in TIFF format the default for
10. ROI operations using the Edit gt Selection gt submenu commands SUUS Original Selection Fit Spline Fit Ellipse Convex Hull Create Mask Make Inverse 30 9 1 Select All a Creates a rectangular selection that is the same size as the image 30 9 2 Select None A Deactivates the selection in the active image 30 9 3 Restore Selection E Restores the previous selection to its original position A selection is saved when you 53 Delete the selection by clicking outside of it Draw a new selection De activate the image containing the selection Close the image containing the selection Use a command that deletes or modifies the selection SEE ALSO ROI Manager 11 TRANSFERRING SELECTIONS BETWEEN IMAGES You can transfer a selection from one image to another by activating the image with the selection activating the destination image then pressing the keyboard shortcut for Restore Selection E 30 9 4 Fit Spline Fits a cubic spline curve to a polygon or polyline selection 30 9 5 Fit Ellipse Replaces an area selection with the best fit ellipse The ellipse will have the same area orientation and centroid as the original selection The same fitting algorithm is used to measure the major and minor axis lengths and angle when Fit Ellipse is selected in Analyze p gt Set Measurements SEE ALSO Set Measurements DrawEllipse macro 30 9 6 Convex Hull Replaces a polygon of free
11. Reloads the active image from disk reverting it to its last saved state It is actually a shortcut for closing the window without saving and then reopening it SEE ALSO Undo and Redo 9 LIMITATIONS OF FILED REVERT R The File gt Revert r command currently does not work with stacks 29 12 Page Setup The Page Setup dialog allows you to control the size of MC Page Setu asco printed output plus other printing options Scale 100 Scale Values less than 100 reduce the size of printed im ages and values greater than 100 increase the size O Draw border M Center on page Y Print title 100 corresponds to 72 pixels per inch ppi about U Selection only g E O Rotate 90 the unzoomed screen size of the image The size of the M Print actual size SS ye Print Cancel C ox printed image is determined by the Scale value and the width and height of the image in pixels Spatial calibration is ignored Draw border If checked ImageJ will print a one pixel wide black border around the image 49 IMPROVED Center on page If checked the image will be printed in the center of the page instead of in the upper left corner Print title If checked the title of the image will be printed at the top of the page Selection only If checked current selection will be printed instead of the entire image Rotate 90 If checked the image will be rotated 90 to the left before being printed
12. Terminates animation of the active stack As for the previous command Y can also be used as a shortcut 86 31 6 15 9 Animation Options Alt Use this dialog to set the animation speed in frames per second and the starting and ending frame or to enable oscillating animation Selecting Start Animation animates the stack as soon as the dialog is dismissed Animation Options Speed 0 1 1000 fps 5 First Frame 1 Last Frame 27 This dialog can also be accessed by right clicking on the play pause icon that precedes stack sliders and hyperstack slice sliders cf Stacks O Loop Back and Forth M Start Animation NT ee eee SEE ALSO Properties P File Save Asp Gif Avi 31 7 Hyperstacks gt This submenu contains commands that work with hyperstacks images that have four 4D or five 5D dimensions cf Hyperstacks 31 7 1 New Hyperstack Creates a new hyperstack Hyperstacks have Width Height Channels c dimension Slices z dimen sion and time Frames t dimension Title HyperStack Image Type cf Newb Type and Display Mode cf Width Channels Z can be specified Lo Checking Label Images will draw the channel num E 10 ber slice number and frame number on each image Slices z 5 in the hyperstack Frames t 30 File gt New Hyperstack is an alias of this command M Label Images Cancel C 0K SEE
13. The ImageJ User Guide Version 1 43 April 2010 The ImageJ User Guide Version 1 43 Tiago A Ferreira Wayne Rasband April 20 2010 NOTE This document is highly enriched in hypertext links and was thought as a fully searchable self contained annotatable offline manual cf Using This Guide Given ImageJ s heavy development this guide will always remain an unfin ished draft and should be considered complementary to the remaining ImageJ documentation resources cf Getting Help As such all ImageJ users and developers are encouraged to contribute to future editions of this manual cf About this Guide The latest version of this document can always be obtained from http rsbweb nih gov ij docs user guide pdf Table of Contents Features Implemented in v1 43 Noteworthy Macro Listings I Getting Started 1 What is ImageJ 2 Installation 3 Maintaining ImageJ 4 Using This Guide 5 Getting Help Il Working with ImageJ 6 Shortcuts and Modifier Keys 7 Finding Commands 8 Undo and Redo 9 Image Types and Image Formats 10 Stacks Virtual Stacks and Hyperstacks 11 Color Images 12 Selections 13 The Results Table 14 Settings and Preferences 15 Extending ImageJ III The User Interface ImageJ Window 16 Toolbar LOL Status Darme A A ty Re Be Re GaSe ight e Sh he A od al ddan le a 16 2 Progress DAR Ts e ail soe Bk Sie ae enna ee athe hd te hinted vii viii ix 10 13 15 1
14. The setOption macro function can be used to set this and several other ImageJ options cf Built in Macro Functions Calling this function from the AutoRun macro in the StartupMacros txt file ensures preferences are set each time ImageJ starts So e g to make sure that 1 TIFF tag values are displayed by ImageJ Debug Mode in Edit gt Options gt Misc 2 The name of the measured image name is recorded in the first column of the results table Display Label in Analyze gt Set Measurements 3 Measurements are not restricted to thresholded pixels Limit to Threshold in An alyze gt Set Measurements 4 Binary images are processed assuming white objects on a black background Black background in Process gt Binary gt Options 5 Background color is black and foreground color is white Edit gt Options gt Colors are set properly at startup the following AutoRun macro could be appended to the StartupMacros txt file Macro 3 Ensuring Specific Settings at Launch 1 macro AutoRun 2 setOption DebugMode true 3 setOption Display Label true 4 setOption Limit to Threshold false 5 setOption Black background true 6 setBackgroundColor 0 0 0 7 setForegroundColor 255 255 255 8 run Colors foreground white background black 9 SEE ALSO FAQ s on the ImageJ Documentation Wiki 21 15 Extending ImageJ ImageJ capabilities can be extended by load
15. roi or zip extension Text files txt ijm js and java extensions SEE ALSO Filet gt Import gt Image Types and Image Formats Virtual Stacks 7 38 7 FILED OPEN FILED IMPORTD AND OPEN BY DRAG amp DROP While the File gt Open command opens formats natively supported by ImageJ images and non images files the File gt mport gt submenu provides access to plu gins for additional file types e g reading raw files images in ASCII format or loading images over the network Most of ImageJ s Input Output plugins are installed on this submenu Note that with version 1 43 almost every format known to ImageJ can be opened by dragging and dropping the file into the ImageJ Window E g in the illustration below a remote macro file is opened by dragging its URL directly from a Web browser AAW Image yA Q e 7 ie aE lt lt Drag and NAS phttp rsb info nih gov ij macros FlipSelection txt E hd e A al a gt a alclo 4 4 29 3 Open Next O Closes the current image and opens the next image if any in its directory Modifier keys Opens the previous image if any in its directory 29 4 Open Samples Opens example images hosted on the ImageJ Web site These sample images are useful for creating testing and debugging macros since routines can be applied to the same image regardless of where the macro is run Among all probably the most used i
16. 398 402 May 2009 A M Bell K Parton and E Smith EarthTutor An Interactive Intelligent Tutoring System for Remote Sensing American Geophysical Union 52 08 Dec 2005 c 2005 American Geophysical Union S Bolte and F P Cordeli res A guided tour into subcellular colocalization analysis in light microscopy Journal of microscopy 224 Pt 3 213 32 Nov 2006 K M Brown D E Donohue G D Alessandro and G A Ascoli A cross platform freeware tool for digital reconstruction of neuronal arborizations from image stacks Neuroinformat ics 3 4 343 60 Jan 2005 E Bulut and B Sahin A new method of assessing the size of mandibular cysts on or thopantomograms projection area fraction J Craniofac Surg 20 6 2020 3 Nov 2009 W Burger and M J Burge Digital image processing An algorithmic introduction using Java ISBN 978 1 84628 379 6 Springer Jan 2008 T Carlier L Ferrer J B Berruchon R Cuissard A Martineau P Loonis and O Cou turier Quality controls for gamma cameras and PET cameras development of a free open source ImageJ program Medical Imaging 2005 Physics of Medical Imaging Edited by Flynn 5745 1237 Apr 2005 R Carmona D Macias J A Guadix V Portillo J M P rez Pomares and R Mu oz Ch puli A simple technique of image analysis for specific nuclear immunolocalization of proteins Journal of microscopy 225 Pt 1 96 9 Jan 2007 167 14 15 16 17 18 19
17. 8 bit images 32 6 4 Despeckle This is a median filter It replaces each pixel with the median value in its 3x3 neighbor hood This is a time consuming operation because for each pixel in the selection the nine pixels in the 3x3 neighborhood must be sorted and the center pixel replaced with the median value the fifth Median filters are good at removing salt and pepper noise 101 32 6 5 Remove Outliers Replaces a pixel by the median of the pixels in the sur rounding if it deviates from the median by more than a certain value the threshold Useful for correcting e g hot pixels or dead pixels of a CCD camera A Remove Outliers Radius 2 0 pixels Threshold 50 Which Outliers Bright 54 Radius Determines the area uncalibrated i e in pix M Preview els used for calculating the median See Process gt basaa Cox Filters Show Circular Masks to see how radius J translates into an area Threshold Determines by how much the pixel must deviate from the median to get replaced in raw uncalibrated units Which Outliers Determines whether pixels brighter or darker than the surrounding the median should be replaced SEE ALSO Despeckle 32 7 Shadowsr Commands in this submenu produce a shadow effect with light appearing to come from a direction corresponding to the command name East North Northeast Northwest South Southeast Southwest and West The commands use Convolve 3
18. Bug reporting see also Debug 5 C Calibration 133 Optical density 134 147 Spatial 73 133 146 Calibration bar 147 Caliper length see Feret 131 Canvas 72 Capture image 152 Catmull Rom see Interpolation 71 CCD 15 102 Center of mass 130 Centroid 130 Channels 73 88 CIE Lab 16 70 Circularity 126 131 Clipboard 38 51 CodeBar 25 Color Background 35 75 Balance 68 Blindness 16 Composites 17 Foreground 35 75 Models 15 Settings 60 Threshold 70 Color filter array 15 Color Picker 35 Color quantization 65 Combine 85 Command key 7 Compile 62 154 Concatenate 85 Control Panel 151 Conversions 61 119 Convex hull 54 Convolution 97 102 115 116 Coordinates 27 33 49 98 132 141 Coronal see Orthogonal views 81 Crop 89 121 CSV 20 44 48 CT 67 82 Curve fitting see Curve fitting 142 D Dead pixels 102 Debug 23 63 64 106 Deconvolution see Convolution 97 Delaunay see Voronoi 107 Despeckle 101 Developer resources 156 DICOM 11 63 67 Dilation 104 Dirichlet see Voronoi 106 Display range 65 176 Distance map see EDM 105 Distribution 128 Divide see Math 109 Divide images see Image calculator 121 Dot blot analysis 132 DPI 46 50 Drag amp Drop 39 Duplicate 89 E Editor 22 Elliptical selection 29 Eroded points 106 Erosion 104 Euclidian distance map 105 Exponential transformation 110 Eye dropper 35 F Fa
19. Hose and S MacNeil Automated tracking of migrating cells in phase contrast video microscopy sequences using image registration Journal of microscopy 234 1 62 79 Apr 2009 D Hecker J Kappler A Glassmann K Schilling and W Alt Image analysis of time lapse movies a precision control guided approach to correct motion artefacts J Neurosci Methods 172 1 67 73 Jul 2008 S Hegge M Kudryashev A Smith and F Frischknecht Automated classification of Plasmodium sporozoite movement patterns reveals a shift towards productive motility during salivary gland infection Biotechnol J 4 6 903 13 Jun 2009 J Hegyi V Hegyi G Messer P Arenberger T Ruzicka and C Berking Confocal laser scanning capillaroscopy a novel approach to the analysis of skin capillaries in vivo Skin Res Technol 15 4 476 81 Nov 2009 K M Hewitt and M D Stringer Correlation between the surface area of synovial mem brane and the surface area of articular cartilage in synovial joints of the mouse and human Surg Radiol Anat 30 8 645 51 Nov 2008 A Hii T Bloom D Helling and K J Bloom An algorithm for counting IHC stained nuclei using ImageJ a free image analysis software package Jan 2007 A Hii T Bloom D Helling and K J Bloom Color separation of IHC stained slides using ImageJ a freely available software package Jan 2007 E Iannuccelli F Mompart J Gellin Y Lahbib Mansais M Yerle and T Boudier NEMO a
20. Install Macros command Macros in the file ImageJ macros StartupMacros txt are automatically installed when ImageJ starts up 34 1 2 Run Loads and runs a macro without opening it in The ImageJ Editor To run a macro and at the same time view its source code open it with File gt Open and use the editor s Macros gt Run Macro command 34 1 3 Startup Macros Opens ImageJ macros StartupMacros txt The same file can be opened by holding Shift t while selecting Startup Macros from the drop down menu 34 1 4 Record Opens the ImageJ command recorder To create a macro open the recorder use one or more ImageJ commands then click Create When the recorder is open each menu command you use generates a macro run function call The run function has one or two string arguments The first is the command name The optional second argument contains dialog box parameters Examples Create a rectangular oval or line selection and the recorder will generate a make Rectangle makeOval or makeLine function call Click on Auto or Set in the Image Adjust gt Threshold T window to generate a setThresold call and on Reset to generate a resetThresold call 148 IMPROVED Select an image from the Window menu to generate a selectWindow call Click in the Image Color gt Color Picker K window to generate setForeground Color and setBackgroundColor calls AAP Record
21. No support for batch mode Cannot create tools and toolbar menus Not compatible with Function Finder and CodeBar No debugger CodeBar is a convenient ActionBar that retrieves snippets and common tasks frequently used in macro writing ActionBars provide one or many easy to use button bar s that extend ImageJ s graphical user interface You can read more about the ActionBar plugin here 25 Plugins Plugins are a much more powerful concept than macros and scripts and most of ImageJ s built in menu commands are in fact implemented as plugins Quoting Werner Bailer 3 Plugins are implemented as Java classes which means that you can use all features of the Java language access the full ImageJ API and use all standard and third party Java APIs in a plugin This opens a wide range of possibilities of what can be done in a plugin The most common uses of plugins are filters performing some analysis or processing on an image or image stack and I O plugins for reading writing not natively supported formats from to file or other devices But as you can see when looking at the plugins listed on the ImageJ plugins page there are many other things you can do with plugins such as rendering graphics or creating extensions of the ImageJ graphical user interface Plugins in the plugins folder are listed at the bottom of the Plugins gt menu But only class and jar files in the plugins folder with at least one underscore
22. and M A Wride 3 Dimensional modelling of chick embryo eye development and growth using high resolution magnetic resonance imaging Exp Eye Res 89 4 511 21 Oct 2009 168 31 82 33 34 35 36 37 38 39 40 41 42 43 44 J D Gottsch O H Sundin E V Rencs D G Emmert W J Stark C J Cheng and G W Schmidt Analysis and documentation of progression of Fuchs corneal dystrophy with retroillumination photography Cornea 25 4 485 9 May 2006 A S Green P R Ohmann N E Leininger and J A Kavanaugh Polarization Imaging and Insect Vision The Physics Teacher 48 17 Jan 2010 c 2010 American Institute of Physics D Grewal R Jain G S Brar and S P S Grewal Pentacam tomograms a novel method for quantification of posterior capsule opacification Invest Ophthalmol Vis Sci 49 5 2004 8 May 2008 J C Grochowsky L W Alaways R Siskey E Most and S M Kurtz Digital photogram metry for quantitative wear analysis of retrieved TKA components J Biomed Mater Res Part B Appl Biomater 79 2 263 7 Nov 2006 M Hachet Haas N Converset O Marchal H Matthes S Gioria J L Galzi and S Lecat FRET and colocalization analyzer a method to validate measurements of sensitized emis sion FRET acquired by confocal microscopy and available as an ImageJ Plug in Microsc Res Tech 69 12 941 56 Dec 2006 A J Hand T Sun D C Barber D R
23. bs cx 3 Degree Polynomial y a bg cz da 4 Degree Polynomial y a bz cz dz ex Exponential y a x e Power y ax Log y axln bx Gamma Variate y a x x b x eT Roadboard y at Coe Proposed by David Rodbard NIH Exponential with Offset y a x e c Gaussian y a b a x ae Implemented by Stefan W rz DKFZ Exponential Recovery y ax l e cf FRAP_ Profiler MBF bundle Cf CurveFitter documentation SEE ALSO Profile Plot Options CurveFittingDemo Derivatives macros 143 RodbardSigmoidFit and PlotSigmoid 33 14 5 ROI Manager The ROI Region of Interest Manager is a tool for working with multiple selections The selections can be from different locations on an image from different slices of a stack or from different images All selection types including points lines and text are supported Show All MD mri stack 1 tif 11727 180x226 pixels 8 bit ROI Manager Show All in Edit Mode e O O mri zstack 1 tif Annoaation AR x N ARI aD lt i gt version 1 43p MAP ROI Manager ADT ROI Manager 0013 0057 0051 addi 0026 0175 0067 z p Rename As 0026 0112 0054 Update PS 0026 0186 0141 a 0001 0092 0095 Name z x_ 0024 0098 0156 Rename 7 Stroke Color white 0026 0018 0141 CA Measure m Font Size 16 X coordinate om D
24. if you have an area of constant value dissected by a one pixel wide diagonal line the 8 connected wand will jump over the line and include the other part of that area Legacy In this mode no neighbor is checked and no tolerance is used This is the default mode of the Wand Tool in ImageJ 1 42 and earlier 18 Line Selection Tools Use these tools to create line selections Double click on any line tool to specify the line width by opening the Image Adjust gt Line Width widget The three line selection tools share the same toolbar slot To switch to a different tool right click on the current line tool and select the desired tool from the drop down menu Length and to do are displayed in the status bar 18 1 lt Straight Line Selection Tool Modifier keys Shift 1 Forces the line to be horizontal or vertical Att Keeps the line length fixed while moving either end of the line Forces the two points that define the line to have integer coordinate values when creating a line on a zoomed image Ctrl While moving either end of the line rotates resizes it about its center SEE ALSO Calibration Bar Specify 5 15 18 2 5 Segmented Line Selection Tool Works exactly as described for the Polygon Selection Tool Create a segmented line selection by repeatedly clicking with the mouse Each click will define a new line segment Double click when finished or click in the small box at the starting point Th
25. red green blue 3 or gray 0 299 x red 0 587 x green 0 114 x blue if Weighted RGB Conversions is checked in Edit gt Options Conversions 16 bit Converts to unsigned 16 bit grayscale 32 bit Converts to signed 32 bit floating point grayscale 8 bit Color Converts to 8 bit indexed color using Heckbert s median cut color quanti zation algorithm A dialog box allows the number of colors 2 256 to be specified The active image must be RGB color RGB Color Converts to 32 bit RGB color RGB Stack Converts to a 3 slice red green blue stack The active image must be RGB color HSB Stack Converts to a 3 slice hue saturation and brightness stack The active image must be RGB color 65 31 2 Adjust This submenu contains commands that adjust brightness contrast threshold levels and image size _____ 13 APPLYING AUTO BRIGHTNESS CONTRAST TO ENTIRE STACKS The Process gt Enhance Contrast command can be used to adjust the brightness and contrast of each slice in a stack according to either the optimal for each individual slice if Use Stack Histogram is unchecked or the overall stack if Use Stack Histogram is checked The default behavior of the B amp C tool Imager Adjust gt Brightness Contrast C is to use the overall stack histogram 31 2 1 Brightness Contrast C Use this tool to interactively alter the brightness and contrast of the active image With 8 bit images brightness and contr
26. where white 0 and black 255 This is done by both inverting the pixel values and inverting the LUT Use the Image Lookup Tables Invert LUT command to invert an image without changing the pixel values Double Buffer Selections Reduces flicker when working with complex selections but it also increases memory usage and slows screen updates It is not needed on Mac OSX which has built in double buffering Antialiased tool icons Smooths and darken the tool icons in the ImageJ window Since version 1 43 this option is enabled by default on all operating systems On 60 Windows XP enable Clear Type sub pixel anti aliasing to improve the quality of text in menus Menu font size Specifies the size of the ImageJ window menu font Use a size of 0 zero to use Java s default menu font size The option is ignored on Mac OS X Changing the font size requires a restarting ImageJ Help Opens http rsb info nih gov ij docs menus edit html appearance 30 10 10 Conversions ALDO Conversion Options scale When Converting Use this dialog to set options that control M Weighted RGB Conversions 0 30 0 59 0 11 how images are converted from one type to Y another we a Cancel OK Scale When Converting ImageJ will scale from min max to 0 255 when converting from 16 bit or 32 bit to 8 bit or to scale from min max to 0 65535 when converting from 32 bit to 16 bit Note that Scale When Converting is always checked after ImageJ is resta
27. 000E0 1 41 Clear 61 blobs Clear 468E1 1 280E2 1 280E2 2 480E2 1 790E2 2 518E2 4 238E1 5 666E 1 1 91 Select All A 62 blobs Select All PSO0E1 1840E2 1 280E2 2 160 2 128082 251962 4 956El 4605E 1 2408 63 blobs 880E1 1 360E2 1 280E2 2 480E2 2 348E2 2 522E2 3 556E1 5 268E 1 1 602 Clear Results 64 blobs Clear Results 874E1 1 760E2 1 280E2 2 240E2 7 417E1 2 525E2 3 673E1 4 565E 1 1 7037 Summarize A Summarize ate Distribution Distribution Set Measurements Set Measurements Duplicate Duplicate The ImageJ Results table version 1 43q File gt Save As Exports the measurements as a tab delimited or comma delimited text file File gt Options Alias for the Edit gt Options gt Input Output command In the I O Op Edit Edit Edit Edit Edit tions dialog box a default extension for saved tables can be set With version 1 43 ImageJ tables are saved in CSV format if File Extension for Tables is csv Cus tom extensions e g csv xls or ods allow these text files to be imported seamlessly by spreadsheet applications The same dialog box can be used to specify if Column Headers Row Numbers should be copied when using Edit gt Copy gt Clear Results Alias for the Analyze gt Clear Results command gt Summarize Alias for the Analyze gt Summarize command gt Distribution Alias for the Analyze gt Distribution command gt Set
28. ALSO Straight Line Selection Tool This tool allows you to measure an angle defined by three points The angle is displayed in the status bar while the selection is being created or adjusted Press Analyze gt Measure m to record the angle in the Results window 32 21 jPoint Tool Use this tool to create a point selection to count objects or to record pixel coordinates Modifier keys Shift 1 Shift clicking will add more points Point count is displayed on the Status bar Alt clicking on a point will delete it Alt clicking and dragging with the rectangular or oval selection tool will delete multiple points ONN Point Tool Double clicking on the point tool icon or running Edit gt es eae a aan Options Point Tool displays its configuration dialog box O Auto Measure O Auto Next Slice Mark Width If greater than zero a mark of the spec O Add to ROI Manager ified diameter will be permanently drawn in the M Label Points E 3 current foreground color cf Color Picker K Selection Color magenta Note that marks modify the image it may be a EER wise to work with a copy and color marks are only available with RGB images cf 15 Auto Measure If checked clicking on the image records the pixel location and inten sity Note that if Mark Width is not zero every time a point selection is measured a mark will be painted cf Measure m If unchecked Edit Draw d can be used to
29. DISPLAY RANGE OF DICOM IMAGES With DICOM images ImageJ sets the initial display range based on the Win dow Center 0028 1050 and Window Width 0028 1051 tags Click Re set on the W amp L Imager Adjust gt Window Level or B amp C Imager Adjust gt Brightness Contrast C window and the display range will be set to the mini mum and maximum pixel values As an example the File Open Samples CT 420K 16 bit DICOM image has a Window Center of 50 and Window Width of 500 so the display range is set to 200 to 300 center width 2 to center width 2 Click Reset and the display range is set to 719 to 1402 Press Analyze gt Histogram and you will see that the minimum pixel value in the image is 719 and the maximum is 1402 To display the DICOM tags press EB Image gt Show Info Press R File gt Revert to revert to the initial display range 67 31 2 2 Window Level This command interactively adjusts the Window range of minimum and maxi mum Contrast and Level position of that range in the grayscale intensity space Brightness of the active image in a man ner closer to that implemented on medical image terminals OOO wer OOO Set W amp L Window Center Level 194 Window Width 18 O Propagate to all open imag 4i DIRI Level 94 4i OD lt gt e COK Window 188 Cancel Auto Reset Being redundant with the Brightness Con trast C tool if t
30. Food Agr Immunol 20 1 1 10 Jan 2009 E Y Tong G C Collins A E Greene Colozzi J L Chen P D Manos K M Judkins J A Lee M J Ophir F M Laliberte and T J Levesque Motion based angiogenesis analysis a simple method to quantify blood vessel growth Zebrafish 6 3 239 43 Sep 2009 T Vrekoussis V Chaniotis I Navrozoglou V Dousias K Pavlakis E N Stathopoulos and O Zoras Image analysis of breast cancer immunohistochemistry stained sections using ImageJ an RGB based model Anticancer Res 29 12 4995 8 Dec 2009 T Walter D W Shattuck R Baldock M E Bastin A E Carpenter S Duce J Ellen berg A Fraser N Hamilton S Pieper M A Ragan J E Schneider P Tomancak and J K H rich Visualization of image data from cells to organisms Nature Methods 7 3 Suppl 526 41 Mar 2010 J L West and I D Cameron Using the medical image processing package ImageJ for astronomy arXiv astro ph Jan 2006 J G Wilson Leedy and R L Ingermann Development of a novel CASA system based on open source software for characterization of zebrafish sperm motility parameters Theri ogenology 67 3 661 72 Feb 2007 J Xu and D Chen Desing and Implementation of the Image Format Batch Conversion Software Based on ImageJ Astronomical Research and Technology Publications of Na tional Astronomical Observatories of China ISSN 1672 7673 5 270 Sep 2008 173 D List of Abbreviations and Acr
31. Image Formats Digital Images are two dimensional grids of pixel intensities values with the width and height of the image being defined by the number of pixels in x rows and y columns direction Thus pixels picture elements are the smallest single components of images holding numeric values pixel intensities that range between black and white The characteristics of this range i e the number of unique intensity brightness values that can exist in the image is defined as the bit depth of the image and specifies the level of precision in which intensities are coded e g A 2 bit image has 2 4tones 00 black 01 gray 10 gray and 11 white A 4 bit image has 24 16 tones ranging from 0000 0 to 1111 16 etc In terms of bits per pixel bpp the most frequent types of images that ImageJ deals with are 8 bit Images that can display 256 2 gray levels 16 bit Images that can display 216 65 536 gray levels 32 bit Images that can display 23 4 294 967 296 gray levels These are floating point grayscale images In computing floating point describes a system for representing numbers that would be too large or too small to be represented as integers Indeed in 32 bit images a pixel can have ANY intensity value including NaN Not a Number RGB Color Images that can display 256 values in the Red Green and Blue channel These are 24 bit 2 8 images RGB color images can also be 32 bit color images 24 b
32. ImageJ however will not update any of the plugins you may have installed Plugins are add ons that extend ImageJ s functionality beyond its basic core cf Plugins The 500 freely available plugins the official distribution of ImageJ contains only a subset from independent contributors around the world plays a pivotal role in ImageJ s success 17 You can obtain and know more about plugins on ImageJ s plugins page Help gt Plugins ImageJ Information and Documentation Portal and in all the sites listed on the bottom of ImageJ s plugins page http rsb info nih gov ij plugins more In addition two ImageJ distributions can also be obtained with a pre organized collection of plugins ImageJ Distributions Fiji As above mentioned Fiji is distributed with several plugins and libraries that greatly simplify the use of ImageJ Furthermore Fiji ships with a built in convenient updater that knows whether your files are up to date obsolete or locally modified MBF ImageJ The MBF ImageJ bundle also known as ImageJ for Microscopy is maintained by Tony Collins at MacBiophotonics McMaster University This bundle features a vast collection of plugins related to microscopy and is described in an extensively illustrated online manual Note that you can use multiple distributions simultaneously assemble your own ImageJ distribution by organizing the plugins that best serve your needs probably someone else at your i
33. JPEG Uncom Cancel pressed and PNG are also available Frame Rate 5 fps Frame Specifies frame frequency The proposed value is read from Image Stacks gt Tools gt Animation Options Alt SEE ALSO File gt Import gt AVI 29 10 9 PNG Saves the active image in PNG Portable Network Graphics format All image types except RGB are saved as 8 bit PNGs With 8 bit images the value to be used as the transparent index 0 255 can be set in the Edito Options Input Output dialog box With version 1 43 16 bit images are saved as 16 bit PNGs 29 10 10 LUT Saves the active image s lookup table to a file The 768 byte file consists of 256 red values 256 green values and 256 blue values 29 10 11 Measurements Exports the contents of the Results window as a tab delimited or comma delimited csv text file 48 IMPROVED 29 10 12 Selection Saves the current area selection boundary to a file Use File Open to restore the selection Note that with version 1 43 active selections are saved in the TIFF header by default cf File Save As Tiff 29 10 13 XY Coordinates Exports the XY coordinates of the line selection or area selection boundary as a two column tab delimited text file Coordinates of rectangular oval and straight line se lections cannot be exported Use the Path Writer plugin to save coordinates at evenly spaced one pixel intervals 29 11 Revert r
34. Lists with getHistogram and Plot getValues 1 1 Simple images 2 Ms C251 3 getHistogram values counts 256 4 for i 0 i lt values length i 5 print values i counts i 6 7 PP Entire stacks 8 run OTi Head G AM SAAB 9 mun UH i stograna US ta crio 10 Plot getValues values counts 11 for i 0 i lt values length i 12 print values i counts i 33 11 Plot Profile k AAA blobs gif Displays a two dimensional graph of the intensities of pixels along a line within the image The X axis repre sents distance along the line and the Y axis is the pixel intensity o o Use the List Save or Copy but tons to view and save the profile data 00 Use Edito Options Profile Plot Op Distance pixels tions to adjust how plots are gen erated List Save Copy For rectangular selections or line selections wider than one pixel displays a column average plot where the X axis represents the horizontal distance through the selection and the Y axis the vertically averaged pixel intensity To average horizontally hold down or check Vertical Profile in the Edit gt Options Profile Plot Options dialog box SEE ALSO Plot Z axis Profile Surface Plot Dynamic Profiler Oval Profile Plot Radial Profile Plot Radial Profile Extended plugins StackProfilePlot macro 33 12 Surface Plot Displays a three dimensional graph of
35. Measurements Alias for the Analyze gt Set Measurements command gt Duplicate Creates a new table containing a copy of the data Note that ImageJ will not output measurements to duplicated tables Font gt This menu contains commands to adjust font size A contextual menu listing the majority of these commands can be accessed by right clicking in the Results window Columns width can be adjusted by clicking on and dragging the vertical lines that separate the column headings Selected lines can be deleted by pressing SEE ALSO Summarize Plugins gt New Table 20 IMPROVED 14 Settings and Preferences ImageJ preferences are automatically saved in a preferences file the IJ_prefs txt text file This file is stored in the Library Preferences folder on Mac OSX in the imagej folder on Linux and in the ImageJ folder on Windows Several macros and plugins also write parameters to this file If the IJ_prefs txt is erased ImageJ creates a new one the next time it is opened resetting all parameters to their default values Sometimes it may be useful to override or restore certain settings that may have been changed during a working session For example the Limit to threshold option Analyze gt Set Measurements will affect most measurements performed on thresholded images Thus it may be wise to check the status of this parameter before each analysis specially when working on multiple computers
36. Median at corresponding pixel location Maximum Intensity projection MIP creates an output image each of whose pixels contains the maximum value over all images in the stack at the particular pixel location Sum Slices projection creates a real image that is the sum of the slices in the stack Standard Deviation projection creates a real image containing the standard deviation of the slices Median projection outputs an image wherein each pixel stores median intensity over all images in stack at corresponding pixel location 81 SEE ALSO 3D Project Plot Z axis Profile 31 6 12 3D Project LO 3D Projection Projection Method Brightest Point 3 Axis of Rotation Y Axis Slice Spacing pixels Initial Angle 0 359 degrees Total Rotation 0 359 degrees Rotation Angle Increment Lower Transparency Bound Upper Transparency Bound Opacity 0 100 Surface Depth Cueing 0 100 Interior Depth Cueing 0 100 O Interpolate 1 00 0 360 10 1 255 0 100 50 Cancel Generates an animation sequence by projecting through a rotating 3D data set onto a plane C13 Each frame in the animation sequence is the re sult of projecting from a different viewing an gle To visualize this imagine a field of par allel rays passing through a volume containing one or more solid objects and striking a screen oriented normal to the directions of the rays Each ray projects
37. News section of the ImageJ website 36 3 Documentation Opens the Documentation section of the ImageJ website 36 4 Installation Opens the Installation section of the ImageJ website specifically dedicated to the OS in which ImageJ is running i e either Linux Mac OS 9 Mac OS X or Windows Worth reading are the sections Known Problems and Troubleshooting 36 5 Search Website Opens the Search page on the ImageJ website Use this page to find plugins macros or messages that have been posted to the ImageJ mailing list 36 6 List Archives Opens the ImageJ Interest Group page on the NIH LISTSERV facility Here you can search the mailing list archives post a message to the list join or leave the list or update options 36 7 Dev Resources Opens the Developer Resources section of the ImageJ website 156 36 8 Plugins Opens the Plugins page on the ImageJ website which lists more than 500 ImageJ plugins 36 9 Macros Opens the macros directory on the ImageJ website which contains more than 400 ImageJ macros 36 10 Macro Functions Opens the Macro Functions reference page an indispensable guide to the built in func tions that can be called from the ImageJ macro language 36 11 Update ImageJ Image Updater Upgrades ImageJ to the latest ij jar at es http rsb info nih gov ij upgrade f or down grades to one of the earlier versions at You are currently running v1 430 http rs
38. OK gt Use pointer cursor If checked ImageJ will use an arrow cursor instead of the default cross hair that is sometimes difficult to see on grayscale images in areas of medium brightness This option can also be used to work around a bug on Windows where the text cursor is sometimes used in place of the cross hair Hide Process Stack dialog If checked ImageJ will suppress the dialog that asks Process all xx slices only the current slice will be processed Require control command key for shortcuts If checked requires the Control key Command key on Macs to be pressed when using keyboard shortcuts for menu commands Move isolated plugins to Misc menu This option can reduce the size of the Plu gins menu preventing it from running off the bottom of the screen When this option is enabled plugins that attempt install themselves in a submenu with only one command are instead installed in the Plugins gt Miscellaneous submenu An ex ample of such a plugin is TurboReg which normally creates a Plugins gt TurboReg submenu that contains only one command 63 Run single instance listener If checked ImageJ will use sockets to prevent multi ple instances from being launched On Windows this avoids the problem where another copy of ImageJ starts each time an image is dragged and dropped on the ImageJ icon It also prevents multiple instances when running ImageJ from the command line Note that you may get a security alert
39. Pasquinelli Common tasks in microscopic and ultrastructural image analysis using ImageJ Ultrastruct Pathol 31 6 401 7 Jan 2007 E Picht A V Zima L A Blatter and D M Bers SparkMaster automated calcium spark analysis with ImageJ Am J Physiol Cell Physiol 293 3 C1073 81 Sep 2007 M Pool J Thiemann A Bar Or and A E Fournier NeuriteTracer a novel ImageJ plugin for automated quantification of neurite outgrowth J Neurosci Methods 168 1 134 9 Feb 2008 J Popko A Fernandes D Brites and L M Lanier Automated Analysis of NeuronJ Tracing Data Cytom Part A 75A 4 371 376 Jan 2009 171 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 S Preibisch S Saalfeld and P Tomancak Globally optimal stitching of tiled 3D micro scopic image acquisitions Bioinformatics Oxford England 25 11 1463 5 Jun 2009 R Ropolo O Rampado P Isoardi A Izzo L Savio T Cammarota O Davini R D Lucchi and G Gandini Automated quality control in computed radiography Radiol Med 111 8 1156 67 Dec 2006 J Roszik D Lisboa J Sz llosi and G Vereb Evaluation of intensity based ratiometric FRET in image cytometry approaches and a software solution Cytometry A 75 9 761 7 Sep 2009 J Roszik J Sz llosi and G Vereb AccPbFRET an ImageJ plugin for semi automatic fully corrected analysis of acceptor photobleaching
40. Tagged Image File Format System o Frames Per Second UEPS aces eeri Ultimate eroded points GIF Graphics Tnt r hange URG ocsigen Uniform Resource Locator Format voxel Volumetric pixel GUD ieren morg Graphical User Interface WYSIWYG What You See Is What HDR devs ctode sos High Dynamic Range a HEX ise eee ees Hexadecimal HSB erren pisss Hue Saturation Brightness 174 About this Guide The contents of this guide have been retrieved using html2text from the ImageJ website and updated where necessary using either information posted on the ImageJ mailing list ImageJ Documentation Portal Fiji webpage or Tony Collins ImageJ for Microscopy man ual Nevertheless because there has never been accompanying documentation for some of the 300 described commands some parts of this guide were written from scratch based on the relevant ImageJ source code and or authors own experience Legacy nomenclature that became obsolete with version 1 43 has been intentionally omitted This is a free content guide Thanks to Johannes Schindelin the TEX and LyX source files of this document are available through a Git version control repository at http pacific mpi cbg de guide git Due to ImageJ s heavy development this guide will always remain incomplete You are encouraged to contribute to the ImageJ documen tation resources preferentially by maturing the ImageJ Documentation Portal or by committing changes directly
41. Use Title as Labels If checked image titles without extension will be used as stack labels Keep Source Images If checked original images are kept 31 6 7 Stack To Images Converts the slices in the current stack to separate image windows 78 31 6 8 Make Montage Make Montage AAA Montage x297 pixels 8 bit 164K Columns 7 Rows 3 Scale Factor 0 44 First Slice 1 Last Slice 27 Increment 1 Border Width 1 Font Size 12 M Label Slices O Use Foreground Color Se Produces a single image which contains the images from a stack displayed in a grid format This can be useful for visual comparisons of a series of images stored in a stack and to create panel figures With hyperstacks that are not directly supported instructions are displayed that explain how to create c z or t montages A dialog box allows you to specify the magnification level at which the images are copied and to select the layout of the resulting grid Label Slices If checked images are be labeled in the panel If no slice metadata exists the setMetadata Label string macro function can be used to customize slice labels images are labeled with slice numbers Note that the Label command can also be used to draw labels in stack slices Use Foreground Color If checked borders and labels are drawn in the foreground color and blank areas of the panel are filled with the background colo
42. add the text non destructively to the overlay Use Edit Draw d to permanently draw the text on the image Use Edit Options Fonts or double click on the text tool to specify the type face size and style SEE ALSO TextDemo macro 24 2A Magnifying Glass Click on the image with this tool to zoom in Right click or Alt click to zoom out The current magnification is shown in the image s title bar Double click on the magnifying glass icon to revert to the image s original magnification There are 21 possible magni fication levels 3 1 4 2 6 3 8 3 12 5 16 7 25 33 3 50 75 100 150 200 300 400 600 800 1200 1600 2400 and 3200 percent Modifier keys Shift ft When zooming in will prevent the window from being enlarged Will zoom out right click behavior SEE ALSO Zoom 16 34 25 Scrolling Tool Allows you to scroll through an image that is larger than its window When using other tools except the text tool you can temporarily switch to this tool by holding down the space bar cf 16 26 A Color Picker Sets the foreground drawing color by picking up colors from any open image Colors can also be picked up from the Color Picker CP window Image Colors gt Color Picker K window using any tool In the icon the eye dropper is drawn in the current foreground color while the frame around it is drawn in the current background color Edit gt Draw d and Edito Fill
43. and displays the elapsed time in the ImageJ status bar Additional benchmarks test results and source code are available in the Benchmarks package of plugins SEE ALSO FAQ s on the ImageJ Documentation Wiki 151 34 3 5 Reset ARA Use this command to unlock a locked Image or to reclaim memory used by the clipboard and undo buffers cf Undo and Redo ked Image Cancel Clipboard Undo Buffer 34 3 6 Monitor Memory Displays a continuously updated graph of ImageJ s memory utilization which can be useful for detecting memory leaks OOO Memory 62MB 1 Ideally you should be able to open several images process une alo them close them and the amount of memory used will be the same as when you started Clicking on ImageJ s status bar which forces the Java garbage collector run may help reclaim unused memory cf Status bar Modifier keys Starting the memory monitor with the Alt key down will have it use a 640x480 window that simulates how a frame grabber plugin would work 34 3 7 Search Described in Finding Commands 34 3 8 Capture Screen g Copies the screen to an RGB image and displays that image a new window Modifier keys Ct Shirt 1 Pressing Ctrl Shift 1 will capture the screen while a modal dialog box is active if the dialog is based on ImageJ s GenericDialog class 34 3 9 Capture Image Copies a WYSIWYG version of active imag
44. any open image beyond predefined zoom levels e g 37 4 C15 92 31 14 Overlay gt This submenu contains commands for creating and working with non destructive image overlays An overlay consists of one or more selections arrows lines points shapes and text Press B Add Selection b to add the current selection to the overlay Press Flatten F to create an RGB image with the overlay embedded in it The overlay is preserved when an image is saved in TIFF format cf 4 Outputs from Grid Overlay MakeOverlay and ROI Color Coder macros that exemplify the usage of most Image gt Overlay gt submenu commands Namely how to draw line grids graphics text and particle size heat maps as non destructive image overlays AAA blobs gif ROI Color Coder blobs gif Grid_Overlay blobs gif MakeOverlay 346x280 pixels RGB 378K X pixels it inverting A X pixels 6 bit inverting Area pm PE ur 900 00 y g 00 049 4 9 O 6 9 771 43 Fey 8 Fea 642 86 514 29 00 osi e Es A Da gza th me akii Ri 0 00 31 14 1 Add Selection b O O Add to Overlay Adds the current selection to the overlay displaying the dialog A box depicted on the left Stroke Color Stroke Width and Fill Color to be set Except for text selections the stroke line color and width are ignored if a fill color is specified Modifier keys Skips the Add
45. background foreground color will be painted in equivalent gray levels e g In a 8 bit image if the foreground color is red RGB 255 0 0 intensity of drawn selections will be 255 0 0 3 85 Although this issue can be overcome by converting the image into RGB Imagep Type gt submenu the easiest way to embed true color selections in grayscale images is to use the Image Overlay Add Selection b command followed by Image Overlay gt Flatten F both commands were implemented in version 1 43 31 6 Stacksp This submenu contains commands that work with stacks 76 31 6 1 Add Slice Inserts a blank slice after the currently displayed slice Modifier keys Blank slice is added before the current slice 31 6 2 Delete Slice Deletes the currently displayed slice 31 6 3 Next Slice gt Displays the slice that follows the currently displayed slice Modifier keys Pressing will skip nine slices forward SEE ALSO Arrow Keys 31 6 4 Previous Slice lt Displays the slice that precedes the currently displayed slice Modifier keys Pressing will skip nine slices backward SEE ALSO Arrow Keys 31 6 5 Set Slice O N SetSlice Displays a specified slice The user must enter a slice num ber greater than or equal to one and less than or equal to Cancel the number of slices in the stack Slice Number 1 27 1 TT IMPROVED 31 6 6 Images To Stack ADD EN Creates a new stack
46. can be set Width Height and Depth are automatically converted if Unit of Length is changed from one known unit nm um um micron mm cm meter km or inch to an other With t series stacks the Frame Interval in seconds reciprocal of the frame rate can be viewed and set With version 1 43 setting the Frame Interval sets the frame rate used by Animation Options Alt as long as the unit used is sec Origin always in pixels is the reference point 0 0 of the image coordinate system see also Analyze gt Set Measurements Check Global to make the current settings global i e apply to all images opened during the current session cf 19 SEE ALSO Imager Show Info i Imager Scale E Analyzep Set Scale 31 5 Color This submenu contains commands that deal with color images 31 5 1 Split Channels Splits an RGB image or stack into three 8 bit grayscale images containing the red green and blue components of the original The window names have an appended red green and blue With composite images and or hyperstacks e g the Organ of Corti sample image File Open Samples this command splits the stack into separate channels SEE ALSO Merge Channels 73 IMPROVED 31 5 2 Merge Channels O Color Merge Green c 2 tif e Blue C 3 tif M Create Composite O Keep Source Images Cancel Merge
47. can show only display 256 shades of gray Therefore the data are mapped to 8 bit by windowing The window defines the range of gray values that are displayed values below the window are made black while values above the window are white The window is defined by minimum and maximum values that can be modified using Image Adjust gt Brightness Contrast C It may happen that the initial windowing performed by ImageJ on these high bit depth or HDR images is suboptimal Please note that windowing does not affect image data and ImageJ s automatic adjustments can be easily corrected SEE ALSO Brightness Contrast C HDRexplorerTool Non native Formats When opening a file ImageJ first checks whether it can natively handle the format If ImageJ does not recognize the type of file it calls for the appropriate reader plugin using HandleExtraFile Types a plugin bundled with ImageJ If that fails it tries to open the file using the LOCI Bio Formats library if present a remarkable plugin that supports around eighty of the most common file formats used in microscopy If nevertheless the file cannot be opened an error message is displayed Because both these plugins are under active development it is important that you keep them updated In addition and as of this writing the ImageJ web site lists more than fifty plugins that recognize more exotic file formats The ImageJ Documentation Portal maintains a list of file form
48. commands related to text handling as well as commands for locating text Specially useful are Go to Line I This dialog box enables you to quickly go to a specified line of code Zap Gremlins This command finds and deletes the extraneous non visible charac ters that sometimes appear when cutting and pasting from other sources such as email messages Copy to Image Info This command will copy the selected text or the entire con tents of the editor if no selection is present to the image header being available through the ImageShow Info i command Note that the copied text will sub stitute any other information present in the file header and will only be available in images saved as TIFF cf 4 22 The ImageJ editor version 1 43n Menu Commands Debug Window Debug PIPA Debug Debug Macro 2D Name Value 4 Step E FreeMemory 6878K of 3200MB lt 1 J Trace T nimages 1 Fast Trace OT getTitle blobs gif Run variablel y Run to Insertion Point Main Window variable2 1 43p Macros Abort AOO Untitled txt Run Macro SER variablel 13 7 _ Evaluate Line sey variable2 getVersion Abort Macro showMessage I am running variablel variable2 Install Macros 1 Function Finder unctio de Macros gt Function Finder Edit gt Go to Line Eq Evaluate JavaScript 3 PP cassie ALDO Built in Functions Undo Cmd 2 la Edit gt Find i Cut SEX ARA L Co
49. do not generate virtual stacks will be RAM resident TIFF virtual stacks can usually be accessed faster than JPEG virtual stacks A JPEG sequence can be converted to TIFF by opening the JPEG images as a virtual stack and using File gt Save Asp Image Sequence to save in TIFF format ImageJ appends a V to the window title of virtual stacks and hyperstacks cf Hy perstacks Since version 1 38 cf Virtual Stack Opener several built in ImageJ com mands in the File Import submenu have the ability to open virtual stacks namely TIFF Virtual Stack Image Sequence Raw Stack From List AVI In addition in ImageJ 1 43 TIFF stacks with a tif extension open as virtual stacks when dragged and dropped on the gt toolbar icon cf 6 SEE ALSO Image5D LOCI Bio Formats and RegisterVirtualStackSlices plugins Process Vir tual Stack and VirtualStackFromList macros Hyperstacks mitosis tif V Hyperstacks are multidimensional images extending image Z E 3 stacks to four 4D or five 5D dimensions x width y height z slices c channels or wavelengths and t time frames Hyperstacks are displayed in a window with three la beled scrollbars Similarly to the scrollbar in stacks the frame slider t has a play pause icon cf Virtual Stacks File gt Open Samples gt Mitosis 26MB 5D stack depicted on the left is an example The V on the window title denot
50. either click inside near the right edge or outside to the left of the object To visualize what happens imagine a turtle that starts moving to the right from where you click looking for an edge Once it finds the edge it follows it until it returns to the starting point Note that the wand tool may not reliably trace some objects especially one pixel wide lines unless they are thresholded highlighted in red using Image Adjust gt Threshold T CO Wand Tool Double clicking on the wand tool icon or running Edit gt Options Wand Tool opens the configuration dialog box in which three modes 4 connected 8 connected or Legacy plus a tolerance value can be set C4 gt Mode Legacy Tolerance 0 0 a OEE SEP Cancel OK The WandAutoMeasureTool macro exemplifies how objects can be outlined and measure automatically 30 Tolerance The wand takes the pixel value where you click as an initial value It then selects a contiguous area under the condition that all pixel values in that area must be in the range initial value tolerance to initial value tolerance 4 connected Only the four neighbors of a pixel are considered neighbors E g the wand does not follow a one pixel wide diagonal line because the pixels of that line are not four connected 8 connected Each pixel is considered to have 8 neighbors So the wand follows a diag onal line if you click onto it On the other hand
51. for Each Image O Black Background Y onu i Cancel OK Calculate Threshold for Each Image If checked threshold levels will be calculated for each individual slice otherwise the calculated threshold of the currently dis played slice will be used for all slices 103 Black Background Defines whether the background is black and the foreground is white Note that the value of this checkbox reflects and sets the global Black Background value of Process Binary gt Options SEE ALSO Make Binary Edit Selection gt Convert to Mask 18 18 CREATING BINARY MASKS Four ImageJ commands can be used to create binary masks 1 Edito Selection gt Create Mask 2 Process gt Binary gt Make Binary 3 4 Imagep Adjust Threshold T Apply Process gt Binary gt Convert to Mask By default these commands will produce binary images with inverted LUTs so that black is 255 and white is 0 cf Invert LUT This behavior can be reversed by checking Black Background in Process Binary gt Options before running the above commands i e an inverting LUT will not be used black will be 0 and white 255 This choice can be confirmed when running Make Binary and Convert to Mask on thresholded images or reset globally at startup cf Settings and Preferences 32 8 3 Erode Removes pixels from the edges of black objects Use Filters gt Minimum to perform grayscale erosion SEE ALSO Bina
52. g blobs gif 0339 0163 or blobs gif mySelection Invert Y Coordinates If checked the XY origin is assumed to be the lower left corner of the image window instead of the upper left corner see also Image Properties P Scientif Notation If checked measurements are displayed in scientific notation e g 1 48E2 Redirect To The image selected from this popup menu will be used as the target for statistical calculations done by Analyze Measure m and Analyze gt Analyze Par ticles commands This feature allows you to outline a structure on one image and measure the intensity of the corresponding region in another image 132 Decimal Places This is the number of digits to the right of the decimal point in real numbers displayed in the Results table and in Histogram windows SEE ALSO Feret s Diameter macro 33 8 Set Scale QOD Set Scale Distance in Pixels 1 Pixel Aspect Ratio 1 0 Unit of Length yum M Global Click to Remove Scale Scale 2 999 pixels um mr Known Distance 0 33348 Use this dialog to define the spatial scale of the active image so measurement results can be presented in cali brated units such as mm or pm Before using this command use the straight line selection tool to make a line selection that corresponds to a known distance Then bring up the Set Scale dialog enter the Known Distance and unit of measurement then click ORK ImageJ w
53. in help Note that the final thresholded image type is RGB not 8 bit gray The Color Threshold command C10 implemented in version 1 431 is a built in version of the Threshold Colour plugin and lacks some features that the plugin version is capable of such as being able to record a macro to reproduce the interactive settings and a Selection button that creates ROIs based on the slider settings 70 File gt Open Samples gt Fluorescent Cells 400K Segmentation of DAPI stained nuclei using Image gt Adjust gt Color Threshold AAR FluorescentCells tif RGB 512x512 pixels RGB IMB AAR FluorescentCells tif RGB x5 12 pixels RGB IMB Red Filter type Pass O Stop 0 gt 255 Pass O Stop lt gt 255 O Pass Stop e gt 78 D lt gt ss O Threshold M Black background SEE ALSO 3D Color Inspector Color Histogram 31 2 6 Size AOD Resize Width pixels 186 Height pixels 226 Depth sl OO Resize Time frar Width pixels 128 M Constr Height pixels 300 Interpolaj M Constrain aspect ratio Bilinear S None NOTE Undo is not availabl Y Bilinear Bicubic gt Cancel NOTE Interpolation OK SEE ALSO Imager Scale E 71 Original Filtered Stack Macro Help Sample Hsg O RGB O CIE Lab O Yuv Scales the active image
54. in their name will be installed More information about developing ImageJ plugins and be obtained on Developer Re sources page on the ImageJ website 26 Part ITI The User Interface ImageJ Window Unlike most image processing programs ImageJ does not have a main work area Im ageJ s main window is actually quite parsimonious containing only a menu bar at the top of the screen on the Mac toolbar containing tools for making selections zooming and scrolling etc status bar and a progress bar Images histograms profiles etc are displayed in additional windows Measurement results are displayed in the Results window Most windows can be dragged around the screen and resized The ImageJ Window version 1 43n 2 3 4 5 6 7 8 9 2 A B C D EF GH CEA eTA a x E I Rectangle and Round Rectangle 9 Text tool selection tool 10 Magnifying glass tool 2 Elliptical and Brush selection tool II Scrolling tool 3 Polygon selection tool 12 Color Picker 4 Freehand selection tool 13 Macro toolset switcher 5 Straight Segmented Freehand Line A H Custom tools loaded from Image and Arrow selection tool macros StartupMacros txt 6 Angle selection tool a Status bar 7 Point and Multi point tool b Progress bar 8 Wand tool 16 Toolbar All ImageJ tools share common features The in the bottom right corner of some icons in the toolbar depicts a contextual menu that can be accessed by right clicking on the on the tool icon
55. installed on Mac OSX Troubleshooting information can be found under Compiling Plugins in the Linux and Windows release notes The Edito Options gt Compiler command displays a dialog box that can be used to configure the javac compiler used by Compile and Run 154 35 Window This menu contains four commands plus a list of open ImageJ windows The currently active image will have a checkmark next to its name To activate a window pull down this menu and select the window by name 35 1 Show All Makes all the windows associated with ImageJ visible 35 2 Put Behind tab Displays the next open image Repeatedly press the tab key to cycle through all open images Note that pressing on any image will bring the ImageJ window to the foreground SEE ALSO 1 35 3 Cascade Moves all open images to the left side of the screen slightly offset from each other and displayed in the order they are listed at the bottom of this menu 35 4 Tile Shrinks all open image windows and repositions them to fit on the screen without over lapping 155 36 Help Many of the commands in this menu use ImageJ s BrowserLauncher to open a Web page using the user s default browser On Linux BrowserLauncher looks for netscape firefox konqueror mozilla opera epiphany or lynx and uses the first one it finds 36 1 ImageJ Website Opens the ImageJ home page 36 2 ImageJ News Opens the
56. lines For text files with integer values no larger than 255 use Image Type gt 8 bit to convert to 8 bits Before converting disable Scale When Converting in Edit gt Options gt Conversions to prevent the image from being scaled to 0 255 SEE ALSO Open TextImagesAsStack macro Save Asp Text Image 29 6 5 Text File Opens a text file Note that text files can also be opened using File gt Open or drag and drop 29 6 6 URL OOQ Enter a URL Downloads and displays known for Enter URL of an image macro or web page mats to ImageJ specified by a URL URL http rsb info nih gov ij images clown gif Other URLs ending with or html are opened in the user s default Cancel OK AA MY browser Entered string is saved in the ImageJ preferences file IJ_ Prefs txt Here are some example URLs http rsb info nih gov ij images clown gif http rsb info nih gov ij images ct dcm file Macintosh HD images Nanoprobes tif file D images neuron tif http rsb info nih gov ij opens ImageJ website 43 29 6 7 Results IMPROVED Opens an ImageJ Results table or any tab or comma delimited text file In version 1 43 csv and xls files can also be opened by drag and drop 29 6 8 Stack From List Opens a stack or virtual stack from a text file containing a list of image file paths The images can be in different folders but they must all be the same size and type The
57. pixel val A ues Note that RGB color images do not use 0 255 a lookup table Use the List radio button to export the LUT as a csv file SEE ALSO Edit LUT 31 5 7 Edit LUT EEHEEHE a Opens the ImageJ LUT Lookup Table Editor BEER EEE EEE A lookup table in ImageJ has up to 256 entries EEE EEE EEE EEE One The entry index and the three values red green HH and blue associated with it are displayed in the HHHH pnag ImageJ status bar as you move the cursor over the H H Cse LUT Editor window Click on an entry to edit the HHHH ean red green and blue values for that entry using a HH Color Selector window cf Color Picker K Cancel OK SEE ALSO Show LUT 31 5 8 Color Picker K The Color Picker tool C8 enables the user to select foreground and background colors which affect Edito Fill f Edito Draw d and other color drawing commands It displays current foreground and background colors in the selection boxes at the bottom of the window It has two modes Foreground and Background To change modes click on the desired selection box Clicking on the Foreground Background Switcher button sets the current foreground to the background and vice versa The Black White Reset button sets the foreground to black and the background to white The color palette is based on HSB Hue Saturation and Brightness color model Hue increases as you go down the palette while saturati
58. points that define the line SEE ALSO 31 3 Show Info i OOO Info for tl head tif These comments were added to the TIFF file 7 using this macro info File openAsString setMetadata Info info Title t1 head tif Cut Width 384 00 mm 256 Copy Height 384 00 mm 256 Clear Depth 193 50 mm 129 Select All Edit gt Options gt Line Width and Edit gt Options Fit Spline Opens a text window containing information about the active image For DICOM and FITS images also displays file header information Use the popup menu right click in the Info window to save the information to a text file or copy it to the system clipboard SEE ALSO Image Properties P 72 31 4 Properties P O Global Frames t Voxel Depth Frame Interval Origin pixels ON A organ of corti tif Channels c fa Slices z 15 1 Note c z t must equal 60 Unit of Length Pixel Width Pixel Height um 0 3150001 0 3150001 0 3150001 0 sec 0 0 SSS Se Cancel OK Use this command to display and set various properties of the current image or stack The number of Channels c Slices z and Frames t in the image can be changed as long as the product of c z and t is equal to the number of images in the stack The Unit of Length a string describing the measuring unit Pizel Width Pizel Height and Vozel Depth all in the Unit of Length unit
59. the first time ImageJ starts with this option enabled ImageJ does not require external socket access so it is okay to deny it access in the security alert Debug mode If checked causes ImageJ to display debugging messages in the Log window Close the Log window to disable display of debugging messages Help Opens http rsb info nih gov ij docs menus edit html misc 64 31 Imager 31 1 Type gt Use this submenu to determine the type of the active image or to convert it to another type An attempt to perform an unsupported conversion causes a dialog box to be displayed that lists the possible conversions Supported conversions are listed below 8 bit 16 bit 32 bit 8 bitcolor RGB color RGB stack HSB stack 8 bit LS I S I 16 bit LS gt LS I 32 bit LS LS I LS LS n mn un 8 bit color RGB color IS a IS IS RGB stack I HSB stack I I Conversion is possible in single images S Conversion is possible in stacks 8 bit Converts to 8 bit grayscale ImageJ converts 16 bit and 32 bit images and stacks to 8 bits by linearly scaling from min max to 0 255 where min and maz are the two values displayed in the Image Adjust gt Brightness Contrast C Image gt Show Info i displays these two values as Display range Note that this scaling is not done if Scale When Converting is not checked in Edit gt Options gt Conversions RGB images are converted to grayscale using the formula gray
60. to line number i Dialog addMessage string Copy C exit or exit error message Paste sv OK gt getBoolean message Find 7 et redirectErrorMessages Find oF showMessage message Find Next 8G O Case Sensitive O Whole Words showMessage title message Go to Line L A showMessageWithCancel title message Cancel OK showStatus message Select All SA See waitForUser title message Zap Gremlins Copy to Image Info Font gt This menu contains commands to adjust font size and type Macros gt This menu contains commands that allow you to run install or evaluate macro code Run Macro r Evaluate Line y Runs the line of code that contains the insertion point Runs the macro or the selected line s of code Abort Macro Exits the macro Install Macros i Adds the macro s contained in the editor to Plugins gt Macros gt submenu Plugins gt Macros gt Install command Function Finder F Cert Shitt F C2 Retrieves macro functions in the same way Command Finder retrieves commands Functions are read from the func tions html file stored in the macros folder a local copy of http rsb info nih gov ij developer macro functions html This file is deleted by Help gt Update ImageJ command every time ImageJ is updated to a release version i e not a daily build forcing Function Finder to download a fresh copy the next time it is launched Evaluate JavaScri
61. to temporarily switch to this tool 7 For each peak measure the size by clicking inside the peak with the Wand Tool If necessary scroll the image vertically by holding down the space bar and dragging 140 8 Select Gels gt Label Peaks to label each measured peak with its size as a percent of the total size of the measured peaks SEE ALSO Calibrate SinglePanelGelAnalyzer macro Video tutorial on ImageJ wiki Luke Miller s tutorial Dot Blot Analysis Dot Blot Analyzer toolset 33 14 Tools This submenu provides access to various image analysis plugins 33 14 1 Save XY Coordinates Writes to a text file the XY coordinates and pixel value of all non background pix els in the active image Background is assumed to be the value of the pixel at the upper left corner of the image For grayscale images writes three values per line x y and value separated by spaces For RGB images writes five values per line x y red green and blue The origin of the coordinate system is at the lower left corner of the image BOO Save XY Coordinates This plugin writes to a text file the XY coordinates and pixel value of all non background pixels Backround defaults to be the value of the pixel in the upper left corner of the image Background value 40 O Invert y coordinates off 0 at top of image O Suppress Log output Cancel The number and percentage of non background pixels is printed to the Log wi
62. to the Git repository To reference this document Ferreira T amp Rasband W The ImageJ User Guide Version 1 43 http rsbweb nih gov ij docs user guide pdf Apr 2010 About the Cover The Hartnack microscope ca 1870 depicted on the front page inspired the ImageJ icon for Mac OSX More information about the original picture can be found on the ImageJ website All other images in the guide were created with Grab 1 5 and ImageJ 1 42q 1 43u loaded with G Landini s IJ Robot and J Schindelin s Tutorial Maker plugins Comments and Suggestions Tiago A Ferreira Centre for Research in Neuroscience McGill University Montreal QC Canada tiago ferreiraQGmail mcgill ca 175 Index A ActionBar 25 Add see Math 108 Add images see Image calculator 121 Analyze 125 126 Angle tool 32 Animation 45 87 Annotations 32 34 7 Grayscale images 7 Appearance 60 Area 130 Area under the curve see Definite integral 139 Arrows 32 Aspect ratio 28 29 71 131 AutoRun 21 39 AVI 11 44 48 gt OT N on B Background see Subtract Background 123 Background pixels 141 Batch 118 Benchmark 151 Bicubic interpolation see Interpolation 71 Bilinear interpolation see Interpolation 71 Binary 102 104 Bio7 2 Bio formats see LOCI 12 Bitwise operations 109 Black background 69 104 107 Blend 93 94 Brightness Contrast 12 66 68 100 Brush selection tool 29
63. tool for analyzing gene and chromosome territory distributions from 3D FISH experiments Bioinformatics Oxford England Jan 2010 C Igathinathane L O Pordesimo and W D Batchelor Major orthogonal dimensions measurement of food grains by machine vision using ImageJ Food Res Int 42 1 76 84 Jan 2009 169 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 C Igathinathane L O Pordesimo E P Columbus W D Batchelor and S R Methuku Shape identification and particles size distribution from basic shape parameters using Im ageJ Comput Electron Agr 63 2 168 182 Jan 2008 B A Irving J Y Weltman D W Brock C K Davis G A Gaesser and A Weltman NIH ImageJ and Slice O Matic computed tomography imaging software to quantify soft tissue Obesity Silver Spring 15 2 370 6 Feb 2007 N Jabbour P D Krishna J Osborne and C A Rosen A new approach to geometrical measurements in an animal model of vocal fold scar J Voice 23 1 88 94 Jan 2009 Y Kam A Karperien B Weidow L Estrada A R Anderson and V Quaranta Nest expansion assay a cancer systems biology approach to in vitro invasion measurements BMC Res Notes 2 130 Jan 2009 C Karmonik M York R Grossman E Kakkar K Patel H Haykal and D King An image analysis pipeline for the semi automated analysis of clinical fMRI images based on freely available software Comp
64. where the string was found is displayed In the Log window double click on a file path to open that file in an editor window There is an option to search the macros folder and also an option to search the ImageJ source code if it has been downloaded from rsb info nih gov ij download src and extracted into the ImageJ folder This command runs the macro Search in ij jar SEE ALSO Appendix A Keyboard Shortcuts and SourceCodeRetriever a macro that searches for a menu entry and tries to retrieve the java source file of the respective plugin 8 Undo and Redo Probably the first thing you will notice is that ImageJ does not have a undo redo buffer Undo Edit Undo z is currently limited to the most recent image editing filtering operation With time you will appreciate that this is necessary to minimize memory overhead If you cannot recover from a mistake you can always use File gt Revert r to reset the image lo its last saved state For selections Edit gt Selection gt Restore Selection E can be used to recover any misdealt selection In ImageJ the equivalent to Redo is the Process gt Repeat Command R that re runs the previous used command skipping Edit Undo z and File gt Open commands SEE ALSO Plugins Utilities gt Reset Multi Undo plugin 2 LIMITATIONS OF EDITD UNDO z Edit gt Undo z and File Revert r are not available on operations performed on entire stacks 9 Image Types and
65. x 3 ImageJ s 3x3 convolution function The Shadows Demo command uses all eight kernels to demon strate the speed of Convolve 3 x 3 The illustration below shows four of the Shadows convolution kernels 1 2 1 1 2 1 1 0 1 1 0 1 Original 0 1 0 0 1 0 2 1 2 2 1 2 1 2 1 1 2 al 1 0 1 1 0 1 AA Original tif AAA North tif ADA South tif AAA East tif AON West tif panen bit inverting LUT 64 prana bit inverting LOT 64 256x254 pixels 8 bit inverting LUN 64 256x254 pixels bit inverting LUT 64 256x264 pixels 3 bit inverting T e ADA PA LAD y e F fog O es Ive sas trop to fa ATAN SIENA TA z ob og sss ge ene ARANA e 7 40 0 AN 32 8 Binary This submenu contains commands that create or process binary black and white im ages They assume that objects are black and background is white unless unless Black Background is checked in the Process gt Binary Options dialog box 102 Processp gt Binary gt commands I Original Make Binary Erode Dilate Open Close Outline Skeletonize nageJ ImageJ ImogcJ ImageJ ImageJ ImageJ ImageJ ImageJ Minimum Maximum Erode then Dilate then 1pixel wide 1 pixel wide A Threshold iT grayscale grayscale Dilate Erode outline skeleton 32 8 1 Make Binary ANA Make inane Converts an image to black and white If a threshold has been set using the Image Adju
66. 0 5 1 0 AAA Demonio Blobs gif RON Estado pEdass m AOL Incl de Holes wet AA EEE TUT 64 s i a LAR PA rE Dda A x RUA v p O weed ors A 127 Record Starts This option allows plugins and macros to recreate particle outlines using the doWand x y macro function The CircularParticles macro demonstrates how to use this feature SEE ALSO Particle Remover plugin 4 8 Connected Particle Analysis 33 3 Summarize For each column in the results table calculates and displays the mean standard de viation minimum and maximum of the values in that column This command is also available by right clicking on the Results table cf The Results Table AAA 63 blobs gif 5 300E1 64 blobs gif 4 900E1 Mean 347 547 187 727 203 375 128 SD 217 766 19 042 32 933 0 Min 1 128 128 128 Max 902 219 915 248 128 Label Area Mean Mode Min Max 4 Results 1 884E2 1 360E2 1 280E2 2 480E2 3 556E1 5 268E 1 1 603E1 9 984E3 1 840E2 1 000E2 1 729E2 1 760E2 1 280E2 2 240E2 3 673E1 4 565E 1 1 703E1 8 472E3 1 760E2 1 000E2 230 375 67 902 0 834 24 875 67786 250193 500 100 26 096 26 562 0 144 9 516 44012 2593 111 0 128 2 828 0 406 1 414 128 128 100 a 248 132 225 52 202 178720 240 100 y lt SEE ALSO Analyze Particles Distribution 33 4 Distribution AAA Area Distribution 300x240 pixels 8 bit 70K Parameter
67. 20 21 22 23 24 25 26 27 28 29 30 R Cathelin F Lopez and C Klopp AGScan a pluggable microarray image quantification software based on the ImageJ library Bioinformatics 23 2 247 248 Jan 2007 G Chinga P O Johnsen R Dougherty E L Berli and J Walter Quantification of the 3D microstructure of SC surfaces Journal of microscopy 227 Pt 3 254 65 Sep 2007 B Choi C Nelson Y Tsunashima and P Balter Open source ImageJ based web accessible tool for treatment plan evaluation Jan 2007 T J Collins ImageJ for microscopy Bio Techniques 43 1 Suppl 25 30 Jul 2007 C M Costa and S Yang Counting pollen grains using readily available free image processing and analysis software Ann Bot 104 5 1005 10 Oct 2009 E C Crawford and J K Mortensen An ImageJ plugin for the rapid morphological characterization of separated particles and an initial application to placer gold analysis Computers amp Geosciences 35 347 Feb 2009 S A W G Dello R M van Dam J J G Slangen M C G van de Poll M H A Bemelmans J W W M Greve R G H Beets Tan S J Wigmore and C H C Dejong Liver volumetry plug and play do it yourself with ImageJ World J Surg 31 11 2215 21 Nov 2007 M Doube ImageJ and analysis of correlated confocal and BSE SEM imaging Jan 2006 J N Feige D Sage W Wahli B Desvergne and L Gelman PixFRET an ImageJ plug in for FR
68. 3 31 15 Look pTablesis baaa Booed a e eee ed Ee hE AOE ele ee 96 Process gt 97 32 1 Smooth Sl 2 424 4 8 4 0 seaweed A ee A 97 32 2 NP E Bee Be ee et hh e E A TD de 97 323 Find Edges ii GS He e a a DS Oe ee ee ANA a 97 624 Find Maxima a A A neces ee ede a hed eG 98 32 5 Enhance Contrast 4 4 34 5 AA e AA ae Sete dd Eg 100 3260 NOISED emo as alesse ee Ane Ry oe edn we fete tees ee ed 101 SL DMN AAOWSIS Y 2 og nah shila RA A te Sh RANA AAA A ody le eee S 102 IS Binay Bye aa e NA 102 320 Math sortea bob rotas datada dro BY bbe td Lt Se UA Ad NI Be e 108 BD LONE Pais A A A en A A A A to E 111 E O utd a a a A a a aa a a aa aan a 12 ur ta 115 32 12 Batch e e AES a Go Ra eS a aa a ee a 118 32 1 3mage Calculator A aa ee a te e e 121 32 14 Subtract Backgrounds ee a aani Da Re eee ee 123 32 15 Repeat Command R zastane is o aA E Pe ere es e ah los ld 124 iv 33 34 35 36 Analyze gt 33 Measures Maicao a os SI ee Be 33 2 Analyze PantiCles ise 5 4 00 Pee a A haa es e Ge Rae 330 SUMMAE ci 8st oo at aan cn ap he he ee amp ah hi Buda et ate te o e 33 4 DIStributiont 28 ii a Bd Pre hanes oe ddd 33 5 Label riringa w wa ok Cee er Carlen a a ee a oe wd de RS A at a ee 3390 Clear Results saro dc ch il RR RRS Eee Oe eee e 33 7 Set M asurementsic ii ar DAA Ae A aes 35 0 Det Scalea o arts dk BMA ee a See ee Oe ge ner alist attra ids 339 Calibrate ner A RN 33 10 Histogram h Saa aaa cen Ww Woe oo he BEE No
69. 350 Minimum Y 0 00 Maximum Y 0 00 Plot Width and Plot Height Specify the length in pixels of the X axis Plot Width and Y axis Plot ee j Height UU Fixed y axis scale O Do not save x values r A seers Fixed y axis Scale If checked the Y axis range is fixed O Vertical profile and the specified Minimum Y and Maximum Y O List values values are used otherwise plots are scaled based on M interpolate line profiles Mn the minimum and maximum gray values M Draw grid lines re ee Help Cancel ok gt Do not Save x values If checked List Save and Copy buttons will appear in profile plot win dows Auto close If checked profile plot windows will be automatically closed when List Save and Copy are clicked on Vertical Profile If checked row average plots of rectangular areas or line selections wider than 1 pixel will be generated instead of the default column average plots Note that evoking Plot Profile k with Aft B will generate vertical profiles List values If checked the list of values will be automatically opened If Auto close is also checked the plot is closed and only the list of values remains open Interpolate line profiles If checked profile values will be interpolated along the line selection Draw grid lines If checked gray grid lines will be drawn in the plot Help Opens http rsb info nih gov ij docs menus edit html p
70. 55 x 28 5 4MB Cancel Opens a series of images in a folder as a stack Im ages must all be the same size and type They can be in TIFF JPEG DICOM BMP GIF FITS or PGM format or in a format supported by the HandleEx traFileTypes plugin There are two dialog boxes one to select the folder and one to specify options In the first dialog select ANY of the images in the folder and click Open Use the second depicted on the left to specify which images to open to reduce the image size to convert to a different type or to open the images as a virtual disk resident stack The parameters are Number of Images Specifies how many images to open Starting Image If set to n import will start with the nt image in the folder Increment If set to 2 every other image will be opened If set to 3 to every third image will be opened etc File Name Contains Enter a string into this field and ImageJ will only open files whose name contains that string Enter Pattern Regular expressions regex or regexp can be typed here for advanced filtering Below are some basic examples 1 The following resources provide detailed information on regular expressions http www regular expressions info http java sun com j2se 1 4 2 docs api java util regex Pattern html http www proftpd org docs howto Regex html 40 gray grey matches gray or grey colou r matches both color and colour ab c ma
71. 8 19 21 22 17 Area selection tools 28 17 1 Rectangular Selection Tool a aa aia 4 ee ee wee a 28 17 2 Round Rectangular Selection Tool p p s lt e i a ban a o o o e 29 17 3 Elliptical Selection Tool 2 4 4 rails e e eos eS a i A 29 Lido Brush Selection Tool alt no daa Grated ds 29 175 Polygon Selection Tool ara a A E E E A N 30 17 6 Freehand Selection Tool es 30 LRP Wand Tod api dude rra A e A A ss 30 18 Line Selection Tools 31 18 1 Straight Line Selection Tool i 206066 a a 31 18 2 Segmented Line Selection Tool o ooo e 31 18 3 Freehand Line Selection Tool erica a e a A 32 19 Arrow Tool 32 20 Angle Tool 32 21 Point Tool 33 22 Multi point Tool 34 23 Text Tool 34 24 Magnifying Glass 34 25 Scrolling Tool 35 26 Color Picker 35 27 Macro Toolset Switcher 35 28 Macro Tools 36 IV The User Interface ImageJ Menus 37 29 File gt 37 29 1 NEW tt a To A E Oe en ce oe 37 20 2 OPE a a a Cee ae OB ch tdi IT RE ES a ud ti EE 38 29 3 Open Next Oli nt e A TA a oe or ea ee 39 29 4 Open Samples apre ee td So bed dete phe a Bag 39 29 5 Open Recent pira er diode GA Ae A De Se A Shae fee it le de A ae 40 29 6 MIM PORE Bes ee sole wna a rer ee es Wa a ad A A eae a A 40 29 7 Glosa A AAA A A a et 44 29 8 Elo All a Rh eS Be A Agile e e Ge Gal ee 45 29 9 Save S aoe gc i Sanda amp dee el aE Ree A ae 45 DONO SaVeVAS kd phate ble A oe hs e eee BR Rt bh e Ppl e
72. ALSO Hyperstacks 87 31 7 2 Stack to Hyperstack Converts a stack into a hyperstack RGB stacks are converted into 3 channel hyperstacks Convert to HyperStack Order xyczt defau xyczt default Order is the order of the channels c slices z and frames t within the stack ImageJ hyperstacks are always in czt order Stacks not in czt order will be shuffled to be in czt order The channel Display Mode can be Composite Color or Grayscale cf Channels Z Channels c 1 Slices z 27 Frames t 1 Display Mode Cancel SEE ALSO Hyperstack to Stack 31 7 3 Hyperstack to Stack Converts a hyperstack into a stack in czt order SEE ALSO Stack to Hyperstack 31 7 4 Reduce Dimensionality ADD Reduce C14 This command reduces the dimensionality of an hyperstack by creating a new hyperstack with for example all the channels and time points at a given z position or all the z slices for the current channel and time point Create Image With O Channels 2 M Slices 5 M Frames 51 1x5x51 16MB Uncheck Channels n to delete all but the current channel Slices n to delete all but the current z slice and Frames n to delete all but the current time point Check Keep Source and the original stack will not be deleted Y Keep Source Y The expected dimensions and size of the reduced stack are displayed in the dialog
73. AVI reader and AVI writer plugins were contributed by Michael Schmid The Edit Selection Create Selection command is based on the Threshold_To Selection plugin written by Johannes Schindelin The Color Picker Image gt Color gt Color Picker K was written by Gali Baler a 2003 2004 intern from Bethesda Chevy Chase High School The 16 different thresholding methods available in the Image Adjust gt Threshold T tool were implemented by Gabriel Landini The Image Adjust gt Color Threshold command implements Gabriel Landini s Threshold Colour plugin The Reslice and the ZProject plugin Image gt Stacks Reslice and Z Project com mands were contributed by Patrick Kelly and Harvey Karten of the University of Cali fornia San Diego The Image Stacks gt Orthogonal Views command is based on Dimiter Prodanov s Stack Slicer plugin and Albert Codona s Updater class The Image gt Stacks gt 3D Project was written by Michael Castle and Janice Keller of the University of Michigan Mental Health Research Institute MHRI The Image gt Hyperstacks gt Reduce Dimensionality command is based on J r me Mutterer s Reduce HyperStack macro The Image Zoom Set command is based on Albert Cardona s Zoom Exact plugin The Process gt Find Maxima command is based on a plugin contributed by Michael Schmid The equalization code implemented in Process gt Enhance Contrast was contributed by R
74. Binary gt Watershed which uses the Euclidian distance map Point Selection Displays a multi point selection with a point at each maximum List Displays the XY coordinates of each maximum in the Results window Count Displays the number of maxima in the Results window Exclude Edge Maxima Excludes maxima if the area within the noise tolerance sur rounding a maximum touches the edge of the image edge of the selection does not matter 98 IMPROVED Process gt Find Maxima outputs Single Points Maxima Within Tolerance Segmented Particles Point Selection List and Count LEE pixels e inverting it Y 64 Pe E ixels ae inverting 13 51 fala pixels ye iat ROE pixels yee roi oe tf y a feg gets e s A PARE Above Lower Threshold Thresholded images only Finds maxima above the lower threshold only The upper threshold of the image is ignored If Segmented Particles is selected as Output Type the area below the lower threshold is considered a background This option cannot be used when finding minima image with light background and inverted lut Light Background To be checked if the image background is brighter than the objects to be found as it is in the Cell Colony image in the illustration below Points at maxima Multi point selection Segmented Particles ROIs obtained with Analyze Analyze Particles Output is a binary imag
75. Cmd Key on Macs Modifications Rectangle and Oval selection tools With Alt Current aspect ratio is maintained while resizing Rectangle and Oval selection tools Selection is resized around the center Straight line tool Rotate resize the line about its center A 4 Space Bar Modifications Any Tool Switch to the hand scrolling tool A 5 Arrow Keys Moving Selections The four arrow keys move selection outlines one pixel at a time Resizing Selections Rectangular and oval selections are re sized by holding while using the arrow keys Stacks Navigation The and keys substitute for and for moving through a stack If there is a selection you must also hold Hyperstacks Navigation The and keys change the channel Hold to move through the slices and to move through the frames Zooming The and keys zoom the image in and out If there is a selection you must also hold either or A 6 Keyboard Shortcuts for ImageJ Tools Keyboard shortcuts cannot be used directly to activate tools in the ImageJ toolbar with the exception of the Magnifying Glass and the Scrolling Tool However shortcuts can be assigned to macros that use the setTool function Once copied to the to the ImageJ macros StartupMacros txt file ImageJ will automatically install them at starts up The set of macros listed below taken from the Rename and Save ROI Sets toolset exemplify the use of the setTool function by a
76. Creating MGB Images With the Channels Z Tool 17 Creating MGB Images With the Image Calculator Command 17 Ensuring Specific Settings at Launch s ee cesso sse o coc o 21 Setting File Open Samples for off line usage o e eee eee 39 Obtaining Histogram Lists with getHistogram and Plot getValues 137 Assigning Keyboard Shortcuts to ImageJ Tools o o o 163 Cycling Through ImageJ Tools Using Keyboard Shortcuts 164 ix Part I Getting Started 1 What is ImageJ ImageJ is a public domain Java image processing and analysis program inspired by NIH Image for the Macintosh It runs either as an online applet or as a downloadable application on any computer with a Java 1 5 or later virtual machine Downloadable distributions are available for Windows Mac OS Mac OS X and Linux It can display edit analyze process save and print 8 bit 16 bit and 32 bit images It can read many image formats including TIFF GIF JPEG BMP DICOM FITS and raw It supports stacks and hyperstacks a series of images that share a single window It is multithreaded so time consuming operations such as image file reading can be performed in parallel with other operations It can calculate area and pixel value statistics of user defined selections It can measure distances and angles It can create density histograms and line profile plots It supports stand
77. ET calculation that can accommodate variations in spectral bleed throughs Microsc Res Tech 68 1 51 8 Sep 2005 L Ferrer T Carlier A Lisbona and M Bardies An imageJ plugin to create whole body transmission scan using CT scanner a validation study Jan 2007 L Ferrer Y Grealou D Autret S Gaudaire G Brunet G Delpon A Lisbona B Bridji I Resche C Rousseau T Carlier and M BardiAs A new ImageJ plugin to correct for partial effect volume Eur J Nucl Med Mol I 31 S230 S230 Jan 2004 M G Forero J A Pennack A R Learte and A Hidalgo DeadEasy Caspase Automatic Counting of Apoptotic Cells in Drosophila Plos One 4 5 e5441 Jan 2009 A Fukushima and T Tomita Image analyses of the kinetic changes of conjunctival hyper emia in histamine induced conjunctivitis in Guinea pigs Cornea 28 6 694 8 Jul 2009 S T Gammon W M Leevy S Gross G W Gokel and D Piwnica Worms Spectral unmixing of multicolored bioluminescence emitted from heterogeneous biological sources Anal Chem 78 5 1520 7 Mar 2006 E Gering and C T Atkinson A rapid method for counting nucleated erythrocytes on stained blood smears by digital image analysis J Parasitol 90 4 879 81 Aug 2004 V Girish and A Vijayalakshmi Affordable image analysis using NIH Image ImageJ Indian J Cancer 41 1 47 Jan 2004 N Goodall L Kisiswa A Prashar S Faulkner P Tokarczuk K Singh J T Erichsen J Guggenheim W Halfter
78. Edit gt Options Input Output dialog box 29 10 7 Image Sequence Save Image Sequence Saves a Stack or a hyperstack as an image Taa sequence Format TIFF Save Image Sequence Format Specifies the output format that Name mri s TIFF P 7 romak e EA can be set to either BMP FITS tart At 0 er a Name mitosis FITS GIF JPEG PGM PNG Raw Text Digits 1 8 4 GIF ae Use slice labete Digits 1 8 3 JEG Image TIFF or Zip cf Image sae assay PGM Types and Image Formats Cancel PNG C I ecm P A QA an Name Specifies the leading string that e A F e will be common to all numeric file ZIP names Start At Stacks only Specifies the starting number of the sequence Digits 1 8 The number digits of the incremental sequence Filenames are padded with leading zeroes 47 Use slice labels as filenames Stacks only If checked each slice will be saved with its own label and no numeric sequence will be used With hyperstacks images are saved using Name_t d_zd_cd in which d is the incre mental number of specified Digits t the frame z the slice and c the channel so e g for the depicted snapshot the first image would be saved as mitosis_t001_z001_c001 tif 29 10 8 Avi AO Save as AVI Exports a stack or hyperstack as an AVI file C6 Compression Uncompressed Compression With version 1 43s the de fault compression is
79. FRET images BMC Bioinformatics 9 346 Jan 2008 S Saalfeld A Cardona V Hartenstein and P Tomanc k CATMAID collaborative annotation toolkit for massive amounts of image data Bioinformatics Oxford England 25 15 1984 6 Aug 2009 D Sage F R Neumann F Hediger S M Gasser and M Unser Automatic tracking of individual fluorescence particles application to the study of chromosome dynamics IEEE Trans Image Process 14 9 1372 83 Sep 2005 S M D Santos U Klinkhardt R Schneppenheim and S Harder Using ImageJ for the quantitative analysis of flow based adhesion assays in real time under physiologic flow conditions Platelets 21 1 60 6 Feb 2010 K M Schartz K S Berbaum R T Caldwell and M T Madsen WorkstationJ worksta tion emulation software for medical image perception and technology evaluation research Medical Imaging 2007 Image Perception 6515 49 Mar 2007 R Scorcioni S N Wright J P Card G A Ascoli and G Barrionuevo Point analysis in Java applied to histological images of the perforant pathway A user s account Jan 2008 D Scott Optimal and data based histograms Biometrika 66 3 605 610 Jan 1979 J B Sheffield ImageJ a useful tool for biological image processing and analysis Jan 2007 F Shihana D M Dissanayake N A Buckley and A H Dawson A Simple Quantitative Bedside Test to Determine Methemoglobin Ann Emerg Med Oct 2009 T Shprung and I Gozes A novel
80. Macro setp 1 make border run Select All Name Macro ijm Create run Line Width run Draw Macro JavaScript Plugin setp 2 save saveAs Tiff Desktop blobs tif Recorder Note that you can interact actively with the recorder window by deleting or commenting lines of code or pasting text from the The ImageJ Editor This may be specially useful when writing your own macros or to generate simple Session Logs In this case you would start the Recorder and let ImageJ keep track of the performed actions by gener ating macro code When pertinent you would annotate this output macro with your notes delete irrelevant processing steps etc Once saved this text file could be used as a log book for future reference 34 2 Shortcuts This submenu contains commands for creating keyboard shortcuts and for installing and removing plugins 34 2 1 List Shortcuts This command generates a table with the ImageJ keyboard AAP board z F par UTC E r shortcuts in one column and the commands they call in an j ASave As JPEG j 7 other Commands prefixed by refer to shortcuts created k Plot Profile with Create Shortcuts Commands prefixed by refer to l Find Commands installed macros listed in Plugins gt Macros submenu and m Measure A H Image override default ImageJ hotkeys y open i Note that as mentioned previously you d
81. MakeSelectionBand macro in ij jar Opens a dialog that allows your to define a rectangular or el liptical selection Width and Height are the dimensions of the selection X Coordinate and Y Coordinate define the position of the selection Check Oval to create an elliptical selection If Centered is checked the selection is positioned so X Coordinate and Y Coordinate define the center of the selection otherwise they define the upper left corner This command straightens a curved object in an image The curved object must first be outlined using the segmented line tool Use the Line Width widget opened by double 56 clicking on the line tool icon to adjust the width of the line selection Check Spline Fit in the Line Width widget to fit a cubic spline curve to the points that define the line Drag the points along the line selection to reposition them Alt click on a point to delete it Shift click on a point to duplicate it Press Shift 1 Edit gt Selection gt Restore Selection E to restore accidentally deleted lines Straighten also works with straight line selections In this case the object defined by the line selection is rotated to be horizontal Edit gt Selection gt Straighten a NileBend jpg 300x250 pixels RGB 293K y Y Spline Fit 30 9 16 Add to Manager t Adds the current selection to the ROI Manager If there is no selection then it opens the ROI Manager
82. Print actual size Considers the DPI information in the image header typically 72 cf Jpeg For a higher value use a unit of inch in the Analyze gt Set Scale dialog E g setting Distance in Pixels to 300 Known Distance to 1 and Unit of Length to inch will set the DPI to 300 29 13 Print p Prints the active image The size of the printed image will normally be slightly less its size on the screen unzoomed Use the Page Setup dialog to increase of decrease the size of printed images Images larger than the page are scaled to fit 29 14 Quit Prompts you to save all unsaved images and then exits You can also exit ImageJ by clicking on the close button in its window s title bar 50 30 Edit gt 30 1 Undo z Described in Undo and Redo 30 2 Cut x Copy c Copy to System Paste v Cut x Copy c Paste v Copies the contents of the current image selection to the internal clipboard and fills it with the current background color Copies the contents of the current image selection to the internal clipboard If there is no selection copies the entire active image The amount of image data copied is shown in the status bar Copy to System copies to the system clipboard Inserts the contents of the internal clipboard or from the system clipboard if the internal clipboard is empty into the active image The pasted image is automatically selected allowing it to be dragged with the mouse Clic
83. Selection gt Properties ROI Manager 17 ROI Color Coder and RGBtoHEX macros 17 WORKING WITH HEX COLORS Hexadecimal notation hex is frequently used in computing because it can sum marize binary code in a human friendly manner For example RGB colors that typically range from 0 to 255 can be succinctly represented as two hexadecimal digits ranging from 00 through FF The following table exemplifies some dec hex equivalents Dec 0 1 2 3 4 56 7 8 9 10 11 12 13 14 15 16 17 18 60 100 255 Hex 0 1 23456789A B C D E F 10 11 12 3C 64 FF ImageJ s built in macro function toHex can be used to convert RGB color values into hex color notation The macro RGBtoHEX uses this function to convert current foreground color into a 8 digit hex number 31 14 2 Add Image X location 104 Y location 129 Opacity 0 100 50 selection if any M Create image selection Cancel Properties 94 O O Add image Adds an image to the overlay A blending alpha value Image to add blobs gif 3 can be specified in the Opacity 0 100 field The initial X Y location are based on the existing rectangular Select Create image selection to create overlay images that can be moved around the image Opacity of im age selections can be adjusted using Edit gt Selection gt Image selections behave only partially as regular selections e g can be added to the ROI Manager list but cannot be resiz
84. Sn Default Holding 2 Shift H moves a fixed width aa thresholding window IsoData gt Min Max values Li MaxEntropy gt Intermodes d Red Display mode Mean MinError l O Dark background Minimum Auto Apply Reset Set Over Under Moments Otsu Manual input Percentile Are objects in the image lighter Set Threshold Levels RenyiEntropy than the background Lower Threshold Level 0 Shanbhag Upper Threshold Level 196 Triangle o 31 2 4 Threshold T Use this tool to automatically or interactively set lower and upper threshold values segmenting grayscale images into features of interest and background Use Analyze gt Measure m with Limit to Threshold in Analyze gt Set Measurements checked to measure the aggregate of the selected features Use Analyze Analyze Particles to mea sure features individually Use the Wand Tool to outline a single feature Upper slider Adjusts the minimum threshold value Hold Shift 4 while adjusting the minimum to move a fixed width thresholding window across the range of gray values Lower slider Adjusts the maximum threshold value Method drop down menu Allows any of 16 different automatic thresholding methods to be selected C9 These methods are described on Fiji s Auto Threshold website http pacific mpi cbg de wiki index php Auto_ Threshold The Default method is the modified IsoData method used by ImageJ 1 41 and earlier Display drop
85. W A new feature implemented in ImageJ 1 43 A routine that has been improved since version 1 42q Typically a faster or more precise algorithm a command with better usability or a task that can be applied to more image types A pre existing command that has been moved to a different Menu loca Le tion in ImageJ 1 43 5 Getting Help ImageJ help resources consist of 1 The ImageJ online documentation Can be accessed via the Help gt Documentation command 2 The ImageJ Information and Documentation Portal ImageJ wiki http imagejdocu tudor lu doku php 3 The Fiji wiki http pacific mpi cbg de wiki index php Main_ Page 4 The ImageJ for Microscopy manual http www macbiophotonics ca imagej 5 Several online documents most of them listed at http rsb info nih gov ij links html 6 Mailing lists a ImageJ http rsb info nih gov ij list html General user and developer discussion about ImageJ Can be accessed via the Help List Archives command This list is also mirrored at Nabble and Gmane You may find it easier to search and browse the list archives on these mirrors Specially useful are the RSS feeds and the frames and threads view provided by Gmane b Fiji users http groups google com group fiji users General Fiji user discussion c IJ Macro Support Group http listes inra fr wws info imagejmacro The ImageJ macro support group connects a network of ImageJ users who are sp
86. a value onto the screen or projection plane based on the values of points along its path Three methods are available for calculating the projections onto this plane nearest point brightest point and mean value The choice of projection method and the set tings of various visualization parameters deter mine how both surface and interior structures will appear Projection Method Select Nearest Point projection to produce an image of the sur faces visible from the current viewing angle At each point in the projection plane a ray passes normal to the plane through the volume The value of the nearest non transparent point which the ray encounters is stored in the projection image Brightest Point projection examines points along the rays projecting the brightest point encountered along each ray This will display the brightest objects such as bone in a CT computed tomographic study Mean Value projection a modifica tion of brightest point projection sums the values of all transparent points along each ray and projects their mean value It produces images with softer edges and lower contrast but can be useful when attempting to visualize objects contained within a structure of greater brightness e g a skull Slice Spacing The interval in pixels between the slices that make up the volume Im ageJ projects the volume onto the viewing plane at each Rotation Angle Increment beginning with the volume rotated by Initial Angle and e
87. ability to move through the slices and in ImageJ 1 43 the slider is preceded by a play pause icon that can be used to start stop stack animation Right clicking on this icon runs the Animation Options Alt dialog box Most ImageJ filters will as an option process all the slices in a stack ImageJ opens multi image TIFF files as a stack and saves stacks as multi image TIFFs The Filer Import gt Raw command opens other multi image uncompressed files A folder of images can be opened as a stack either by dragging and dropping the folder onto the ImageJ window or or by choosing File gt Import gt Image Sequence To create a new stack simply choose File gt New gt Image n and set the Slices field to a value greater than one The Imagep gt Stacks gt submenu contains commands for common stack operations Virtual Stacks Virtual stacks are disk resident as opposed to RAM resident and are the only way to load image sequences that do not fit in RAM There are several things to keep in mind when working with virtual stacks 13 IMPROVED Virtual stacks are read only so changes made to the pixel data are not saved when you switch to different slice You can work around this by using macros e g Pro cess Virtual Stack or the Process Batch Virtual Stack command implemented in version 1 43 You can easily run out of memory using commands like Image Crop X because any stack generated from commands that
88. able code modules in the form of macros scripts or plugins 300 macros 500 plugins and 20 scripts are available through the ImageJ web site Below is a short description of these three type of ImageJ add ons Macros Plugins Scripts The easiest way to execute a series of ImageJ commands The ImageJ macro language a Java like language contains a set of control structures oper ators and built in functions and can be used to call built in commands and other macros Macro code is stored in text files txt and ijm extensions Much more powerful flexible and faster than macros most of ImageJ s built in menu commands are actually plugins but harder to write and debug Plugins are written in the Java programming language java source files and compiled to class files ImageJ uses the Mozilla Rhino interpreter to run JavaScripts Similarly to plugins scripts have full access to all ImageJ and Java APIs but do not need to be compiled scripts and macros run interpretively On the other hand scripts lack the simplicity of macro language and feel less integrated in ImageJ The ImageJ Editor Macros Scripts and Plugins can be opened and executed in the ImageJ editor In the Editor commands are organized in five menus File gt Edit gt Font Macros gt and Debug File gt Basic file operations Open Save Print etc are listed in this menu Edit gt Similarly to any other text editor this menu contains
89. ack slices and to have the ROI Manager restore ROIs to the center of the image SEE ALSO Selection gt Properties Add Selection b 17 ROI Color Coder macro 20 SELECTING MULTIPLE ROIs IN MANAGER For most ROI Manager operations Deselect works as a Select All button e g to measure all ROIs in manager one would press Deselect then Measure In ad dition in version 1 43 it is now possible to select contiguous ROIs with a single Shift click in all operating systems cf release notes Non contiguous ROIs can be selected by Ctrl click Command click on Mac OS X 33 14 6 Scale Bar MAX_confocal series tif MGB RGB Draws a labeled spatial calibration bar ScaleBar Plus Width Length of the bar in cali brated units Width in ym 5 are poe 4 J Height Height of the bar in pixels Font Size 16 a Font Size Adjusts the labels font size Background None Location Upper Left 74 Color Adjusts the text color cf 15 Y Bold Text OC Hide Text Serif Font Background Adjusts the filling Cancel color of the label text box 146 Location Adjusts the position of the calibration bar If there is a selection the bar is initially drawn at the selection Bold Text Serif Font Specify if label should be typeset in boldface serif typeface Hide Text If checked the bar is drawn without label SEE ALSO Set Scale 19 33 14 7 Calibration Bar
90. adjusting the contrast of the source image or smoothing it SEE ALSO Plot Profile k Interactive 3D Surface Plot plugin it works with all image types and viewing angle perspective scale lighting and smoothing can be interactively adjusted 3D Color Inspector Color Histogram 138 33 13 Gels gt Use the commands in this submenu to analyze one dimensional electrophoretic gels These commands use a simple graphical method that involves generating lane profile plots drawing lines to enclose peaks of interest and then measuring peak areas i e definite integrals using the Wand Tool Note that this technique cannot be used to compare bands on different gels unless gels are calibrated to known standards OO Lane 1 of gel gif _ 4 z Sok O bit gel gif Uncalibrated O Vertical scale factor 1 0 Horizontal scale factor 1 0 M Uncalibrated OD M Label with percentages O Invert peaks 4820 175 36 631 8338 731 63 369 The commands listed in the Gels gt submenu are Select First Lane 2 Requires a rectangular selection Note that lanes are assumed to be vertical unless the width of the initial selection is at least twice its height Select Next Lane 2 To be used after the first rectangular ROI is moved over the adjacent lanes Note that all selections must have the same dimensions Plot Lanes Generates the lane profile plots ImageJ assumes that only o
91. aining internal holes a O e Composite ROIs are typically originated with the Brush Se O Q lection Tool but they can be defined with any other selection tool using key modifiers such as the ones depicted on the left Modifier keys Shift t Drawing outside current selection while pressing Shift creates new con tent To add a non square rectangle or ellipse the Shift key must be released after adding the selection Drawing inside current selection while pressing Alt creates a hole remov ing content from ROI Note that some operations are not performed properly on these complex ROIs Thus it may be useful to convert a composite into polygon using the Edit gt Selection gt Enlarge command SEE ALSO ROI2PolylineROI macro 13 The Results Table Most of ImageJ analyses are printed to the Results table In this window commands are organized in three menus File Edit gt and Fontb 19 IMPROVED ADA Results Save As Label Area Mean StdDev Mode Min Max XM YM Perim Circ Feret 56 blobs gif 8 580E2 1 973E2 3 012E1 2 320E2 1 280E2 2 480E2 1 805E2 2 302E2 1 137E2 8 334E 1 4 13 Options 157 blobs primicia 082E1 2 160E2 1 280E2 2 320E2 1 385E2 2 337E2 6 277E1 58 blobs M 2 863E1 2 160E2 1 280E2 2 240E2 4 654E1 2 410E2 5 453E1 9 087E 1 1 96 Cut 98x 59 blobs Cut 4 619E0 1 280E2 1 280E2 1 360E2 7 683E1 2 428E2 5 657E0 1 000EO0 2 82 Copy sec 60 blobs Copy OOOEO 1 280E2 1 280E2 1 280E2 1 105E2 2 465E2 2 828E0 1
92. anager Add Name and add selection Plugins gt Utilities gt ImageJ Properties List all Java properties Plugins gt Utilities gt Monitor Memory Simulate 640x480 frame grabber Any user plugin Load using new class loader Area selection tools Subtract this selection from the previ ous one Rectangle and Oval selection tools Current aspect ratio is maintained while resizing Polygon selection tool Alt click on a node to delete it Straight line tool Keeps the line length fixed while mov ing either end of the line Forces the two points that define the line to have integer coordinate values when creat ing a line on a zoomed image Segmented line tool Alt click on a node to delete it Point tool Alt click on a point to delete it Color picker tool Alt click to pick up background color All tools Show location and size in pixels 161 A 2 Shift Key Modifications Image gt Adjust gt Threshold Adjusting Min also adjusts Maz Analyze gt Histogram Display log histogram Installed Macros and Scripts Open instead of run Rectangle and Oval selection tools Forces 1 1 aspect ratio Area selection tool Add this selection to previous one Polygon selection tool Shift click on a node to duplicate it Straight line tool Forces line to be horizontal or vertical Segmented line selection tool Shift click on a node to duplicate it Point selection tool Shift click to add a point A 3 Ctrl Key or
93. ands that match that substring If only a single command matches then that command can be run by pressing If multiple commands match click with the mouse to select a command to run Alternatively pressing the up or down keys will move keyboard focus to the list and the selected command can be run by pressing Enter Pressing switches focus back to the prompt Double clicking on a command will run that command Pressing Esc Esc closes the window If Show full information is checked the Command Finder will display in which menu or jar file the listed command is located Search Plugins gt Utilities gt Search searches recursively for a particular string case sensitive or not contained in the file names or file contents in a chosen folder or in ImageJ macros folder if Search Macros Folder is checked Since most macros txt ijm scripts js and plugins source java files contain cir cumstanced information as commented code you can use this utility to retrieve files not only related to a image processing routine e g background or co localization but also topics related to a certain scientific context such as radiogram cell or histology Indeed the ImageJ source files contain detailed annotations useful to both developers and regular users that want to know more about ImageJ routines and algorithms The results are displayed in the Log window If the Search Contents option is checked the line number
94. ard image processing functions such as contrast manipulation sharpening smoothing edge detection and median filtering It does geometric transformations such as scaling rotation and flips Image can be zoomed up to 32 1 and down to 1 32 All analysis and processing functions are available at any magnification factor The program supports any number of windows images simultaneously limited only by available memory Spatial calibration is available to provide real world dimensional measurements in units such as millimeters Density or gray scale calibration is also available ImageJ was designed with an open architecture that provides extensibility via Java plugins Custom acquisition analysis and processing plugins can be developed using ImageJ s built in editor and Java compiler User written plugins make it possible to solve almost any image processing or analysis problem ImageJ is being developed on Mac OS X using its built in editor and Java compiler plus the BBE dit editor and the Ant build tool The source code is freely available The author Wayne Ras band wsr nih gov is a Special Volunteer at the National Institute of Mental Health Bethesda Maryland USA 2 Installation Detailed information for Linux Mac OS X Mac OS 9 and Windows installation of ImageJ is available at http rsb info nih gov ij docs install index html Specially useful are the platform specific Troubleshooting and Known Problems sections This web
95. ast 10 zd prams bit inverting LUTI 64 paman bit inverting LUT 64 panem bit inverting LUT 64 256x254 pixels 8 bit inverting LUT 64 pran bit inverting LUT Ta Y 5 TV Joz IPL fe Ets 00 074 to 074 oo elt O 0506 o PIDA RRA ORAR ATAR DT DT DN DAT ENTER ALA ARTE 0 2 we 2 we 02 29029 nd pee ee 32 1 Smooth S Blurs the active image or selection This filter replaces each pixel with the average of its 3x3 neighborhood 32 2 Sharpen Increases contrast and accentuates detail in the image or selection but may also accen tuate noise This filter uses the following weighting factors to replace each pixel with a weighted average of the 3x3 neighborhood l i 1 1 12 1 1 1 1 32 3 Find Edges Uses a Sobel edge detector to highlight sharp changes in intensity in the active image or selection Two 3x3 convolution kernels shown below are used to generate vertical and horizontal derivatives The final image is produced by combining the two derivatives using the square root of the sum of the squares 1 2 1 1 0 1 0 0 0 2 0 2 I 2 1 1 0 1 97 32 4 Find Maxima ABE blobs gif al 256x254 pixels 8 bit inverting LUT 64 ar Determines the local maxima in an image and creates a binary mask like image of the same size with the maxima or one seg DOOM Find Maxima Noise Tolerance 50 mented particle per
96. ast are changed by updating the image s lookup table LUT so pixel values are unchanged With 16 bit and 32 bit images the display is updated by changing the mapping from pixel values to 8 bit display values so pixel pixel values are also unchanged Brightness and contrast of RGB images are changed by modifying the pixel values Histogram The line graph at the top of the window which is su perimposed on the image s histogram shows how pixel values are mapped to 8 bit 0 255 display values The two num bers under the plot are the minimum and maximum displayed pixel values These two values define the display range or OLOO B amp G o aas window ImageJ displays images by linearly mapping pixel Minimum values in the display range to display values in the range 0 4 lt gt 255 Pixels with a value less than the minimum are displayed Maximum A Tere T as black and those with a value greater than the maximum Brightness are displayed as white 4 O lt gt Contrast Minimum and Maximum sliders Control the lower and up Auto Reset per limits of the display range YA y a ee Brightness slider Increases or decreases image brightness by moving the display range Contrast slider Increases or decreases contrast by varying the width of the display range The narrower the display range the higher the contrast Holding down ift t will simultaneously adjust all channels of a composite
97. ation will affect the image The background at the edges of the image will be set to 0 SEE ALSO Align Slice and Align RGB_ planes plugins 31 13 Zoom gt This submenu contains commands that control how the current image is displayed The and El are the preferred way to use the In and Out commands 91 31 13 1 In Zooms in to next higher magnification level and if possible enlarges the window There are 21 possible levels shown in title bar 3 1 4 2 6 3 8 3 12 5 16 7 25 33 3 50 75 100 150 200 300 400 600 800 1200 1600 2400 and 3200 Modifier keys SS Shift T Prevents the window from being enlarged 16 SCROLLING ZOOMED IMAGES Hold down the space bar and drag to scroll a zoomed image 31 13 2 Out Zooms out to next lower magnification level and if needed shrinks the window 31 13 3 Original Scale 4 Displays the image at the magnification used when the image was first opened As a shortcut double click on the magnifying glass tool 31 13 4 View 100 5 Displays the image using 100 magnification limage pixel I screen pixel Enable Open Images at 100 in the Edito Options Appearance dialog to have images auto matically opened at 100 magnification 31 13 5 To Selection Zooms in based on the current selection Note that in the absence of a selection this command zooms the image to a Fit to Screen level 31 13 6 Set Sets an exact zoom to
98. ats that are supported by ImageJ SEE ALSO Native Formats Import 4 8 Acquisition plugins Input Output plugins 12 4 IMAGE TYPES Lossy COMPRESSION AND METADATA Two critical aspects to keep in mind when converting images Lossy compression Transcoding an image into a format that uses lossy com pression will alter the original data introducing artifacts This is the case e g for JPEG formats with the exception of some JPEG2000 images that use lossless compression As such these types of data are intended for human interpretation only and are not suitable for quantitative analyses Metadata In ImageJ metadata associated with the image such as scale gray value calibration and user comments is only supported in tiff and zip compressed tiff images In addition with version 1 43 selections and overlays are also saved in the TIFF header cf File gt Save s None of the above is saved in other formats SEE ALSO Native Formats 8 10 Stacks Virtual Stacks and Hyperstacks Stacks ImageJ can display multiple spatially or temporally related images in a single window These image sets are called stacks The images that make up a stack are called slices In stacks a pixel which represents 2D image data in a bitmap image becomes a voxel volumetric pixel i e an intensity value on a regular grid in a three dimensional space All the slices in a stack must be the same size and bit depth A scrollbar provides the
99. awn after each number when the Format chosen is either 0 or Text Label without numeric sequence SEE ALSO Make Montage Stacks gt Tools gt Insert 84 IMPROVED 31 6 15 Tools 31 6 15 1 Combine A Combiner Stack mri stack r tif W Stack2 mrizstack 2 tif 18 O Combine vertically Help Cancel C 0K SEE ALSO Concatenate 31 6 15 2 Concatenate gt Concatenator Stack1 mri stack 1 tif 14 Stack2 mri stack 2 tif Title Concatenated Stacks O Keep Source Stacks Cancel 31 6 15 3 Reduce A Reduce Size Reduction Factor 2 M Reduce in Z Dimension Cancel Combines two stacks Widthx Height x Depth WixH xD and W2xH2xD gt to create a new W W3xmax H H gt xmax D1 D2 stack E g a 256x256x40 and a 256x256x30 stack would be combined to create one 512x256x40 stack If Combine vertically is enabled creates a new max W1 W2 x Hi H2 xmax D1 D2 stack Unused areas in the combined stack are filled with back ground color cf Color Picker K Concatenates two images or stacks that have the same width height and data type SEE ALSO Combine Reduces the size of stacks and hyperstacks by the specified Reduction Factor E g For a 30slices stack and a Reduc tion Factor of 2 the reduced stack will be be composed of 15 slices with every second slice being removed Virtual stacks hyperstacks are
100. b info nih gov ij download jars Se lect daily build from the drop down menu and it will upgrade to the latest daily build at http rsb info nih gov ij ij jar If you click OK Image will quit and you will be running the upgraded version after you restart Image ee Cancel OK _ SEE ALSO Maintaining ImageJ 36 12 Update Menus Use this command to update ImageJ s menus after adding or removing plugins or macros to the plugins folder 36 13 About Plugins gt This submenu displays information about some of the plugins in the ImageJ plugins folder To be included in this submenu a plugin must be packaged as a JAR file There is an example at rsb info nih gov ij plugins jar demo html 157 36 14 About ImageJ AAA About Image 158 Opens an image containing infor mation about the ImageJ version the author the website Java ver sion and memory available Note that clicking in the status bar is a quicker way to show this informa tion SEE ALSO Plugins Utilities gt ImageJ Properties Status bar A Keyboard Shortcuts The following table summarizes the keyboard shortcuts built into ImageJ You can create additional shortcuts or override built in shortcuts by creating simple macros and adding them to the StartupMacros txt You can also assign a function key to a menu command using Plugins gt Shortcuts gt Create Shortcut Except when using the text tool you do no
101. ber of images the resulting stack will get truncated to the actual size Gap Between Images The number of bytes from the end of one image to the be ginning of the next Set this value to widthx height x bytes per pixel x n to skip n images for each image read White is Zero Should be checked if black pixels are represented using numbers that are less than the numbers used for white pixels If your images look like photographic negatives changing this field should fix the problem Little Endian Byte Order Probably needs to be checked when importing 16 bit or 32 bit grayscale images from little endian machines such as Intel based PCs Open All Files in Folder If checked ImageJ will import all the images in the folder as a stack The images must all be the same size and type Use Virtual Stack Images are imported as virtual stacks 42 SEE ALSO Image Types and Image Formats 29 6 3 LUT Opens an ImageJ or NIH Image lookup table or a raw lookup table The raw LUT file must be 768 bytes long and contain 256 reds 256 blues and 256 greens If no image is open a 256x32 ramp image is created to display the LUT Note that lookup tables with file names ending in lut can also be opened using File gt Open or drag and drop 29 6 4 Text Image Opens a tab delimited text file as a 32 bit real image cf illustration on page 47 The image s width and height are determined by scanning the file and counting the number of words and
102. ce The trade off for this increased realism is that data points shown in a depth cued image no longer possess accurate densitometric values Two kinds of depth cueing are available Surface Depth Cueing and Interior Depth Cueing Sur face Depth Cueing works only on nearest point projections and the nearest point component of other projections with opacity turned on Interior Depth Cueing works only on brightest point projections For both kinds depth cueing is turned off when set to zero i e 100 of intensity in back to 100 of intensity in front and is on when set at 0 lt n 100 i e 100 n of intensity in back to 100 intensity in front Having independent depth cueing for surface nearest point and interior brightest point allows for more visualization possibilities Interpolate Check Interpolate to generate a temporary z scaled stack that is used to generate the projections Z scaling eliminates the gaps seen in projections of vol umes with slice spacing greater than 1 0 pixels This option is equivalent to using the Scale plugin from the TransformJ package to scale the stack in the z dimension by the slice spacing in pixels This checkbox is ignored if the slice spacing is less than or equal to 1 0 pixels SEE ALSO Orthogonal Views Z Project and 3D Viewer Volume Viewer plugins 83 31 6 13 Plot Z axis Profile 40 6 Mean 20 8 1 Slice 31 6 14 Label Format 0 Starting value 0 I
103. cify the image title type dimensions and initial content Name Text Image Name is the title that will be used for the Win dow Type is the image type 8 bit grayscale 16 bit grayscale unsigned 32 bit float grayscale or RGB color Fill With White Black or Ramp spec ifies how the image is initialized Width and Height specify the image dimensions in pixels Set Slices to a value greater than one to create a stack Fill With Width 40 pixe Height 40 pixels Slices 1 s SEE ALSO Image Types and Image Formats 29 1 2 Hyperstack Alias for the Image gt Hyperstacks gt New Hyperstack command 29 1 3 Text Window N Creates a new text window with the title Untitled txt SEE ALSO Plugins gt New gt Text Window Macro Table 37 29 1 4 Internal Clipboard Opens the contents of the internal ImageJ clipboard SEE ALSO Edit Cut x Copy c Copy to System Paste v 29 1 5 System Clipboard V Opens the contents of the operating system clipboard SEE ALSO Edit Cut x Copy c Copy to System Paste v I O 29 2 Open Opens an image and displays it in a separate window Image files must be in TIFF GIF JPEG DICOM BMP PGM or FITS format or in a format supported by a reader plugin Also opens ImageJ and NIH Image lookup tables 1ut extension Results tables in tab delimited text format xls or csv extension Selections
104. ck slider to set the frame rate 45 IMPROVED 29 10 3 Jpeg Saves the active image in JPEG format Edit JPEG Quality in Edit gt Options ln put Output dialog box to specify the JPEG compression level 0 100 This value is shown on the title of the save dialog prompt Lower values produce smaller files but poorer quality Larger values produce larger files but better quality Color sub sampling is disabled when the value is set to 100 reducing the likelihood of color artifacts By default the DPI in the JPEG header is set to 72 For a higher value use a unit of inch in the Analyzep Set Scale dialog E g setting Distance in Pixels to 300 Known Distance to 1 and Unit of Length to inch will set the DPI to 300 Since version 1 43 displayed overlays will be embedded on the image cf Flatten F when saving it as Jpeg SEE ALSO 4 8 8 WARNING ON JPEG COMPRESSION The JPEG format uses lossy compression that can result in artifacts This format should not be used if you plan to make measurements on the image or to do further processing 29 10 4 Text Image Saves the active image as a spreadsheet compatible tab delimited text file For calibrated images and floating point images the Decimal Places field in Analyze gt Set Measure ments determines the number of digits to the right of the decimal point For RGB im ages each pixel is converted to grayscale using the formula gray red green blu
105. ctions can be measured Analyze gt Measure m drawn Edit gt Draw d filled Edito Fill f or filtered Process gt Filters gt submenu in the case of area selections In addition with ImageJ 1 43 it is also possible to create non destructive image overlays Image gt Overlay gt submenu Selections can be initially outlined in one of the nine ImageJ default colors Red Green Blue Magenta Cyan Yellow Orange Black and White Once created selections can be contoured or painted with any other color cf Edit gt Selection gt Properties Selection Color can be changed in Edit Options Colors or by double clicking on the Point Tool It is highlighted in the center of the Point Multi point Tool cf illustration on page 27 on which Red is the active selection color Most of commands that can be useful in defining or drawing selections are available in the Edito Selection submenu Listed below are the most frequent manipulations involving selections Deleting Choose any of the selection tools and click outside the selection or use Edit gt Selection gt Select None A Use Edit gt Selection gt Restore Selection E to restore a selection back after having deleted it Moving Selections can be moved by clicking and dragging as long as the cursor is within the selection and has changed to an The status bar displays the coordinates of the upper left corner of the selection or the bounding rectangle for
106. d These tools can be customized by editing the StartupMacros txt file or replaced en tirely using the gt menu The macro language documentation has more information about macro tools SEE ALSO Macro Toolset Switcher Luts Macros and Tools Updater macro Macro Toolsets distributed with version 1 43 C27 Note that you can use Toolset Creator to create toolbar menus for running plugins macros and scripts While StartupMacros txt is located in the ImageJ macros directory all other toolsets must be located in the ImageJ macros toolsets subfolder SON Baco arado dal A Switch to alternate macro tool sets alero Melo v Startup Macros A Arrow Labelling Tools IPOD aAA Drawing Tools GOMA gt Example Icons Lookup Tables Lat E Be lt gt Na Magic Montage aa jono o Plugins 39D A E Fm Js T gt Scale Bar Tools for Microscopes gt lia Stack Tools oo 21 0 0 a Toolset Creator Stk B lt lt lt gt gt 3 Help 36 Part IV The User Interface ImageJ Menus 29 File gt As in any other Image Processing software basic file operations are listed in this menu Most are self explanatory 29 1 New gt Contains commands for creating new images stacks hyperstacks or text windows SEE ALSO Plugins New 29 1 1 Image n Creates a new image window or stack A dialog box depicted on the left allows you to spe
107. djust gt Contrast Shift t C Adjust brightness and contrast Adjust gt Threshold Shite 1 Adjust threshold levels Show Info 0 Display information about active image 159 Command Shortcut Description Properties Color gt Color Picker Stacks gt Next Slice Stacks gt Previous Slice Stacks gt Reslice Stacks gt Animation Hyperstacks gt Channels Hyperstacks Hyperstacks Hyperstacks Hyperstacks Hyperstacks Hyperstacks Crop Duplicate Scale Zoomp In Zoomp Out Zoom Original Scale Zoom View 100 E or or HL HRAM JAM M Nl EEE DM E o HG AAOH iN O Y JE EJE Shift t P Display image properties ift K Open Color Picker Go to next stack slice Go to previous stack slice Reslice stack Start stop stack animation Open the Channels tool Next hyperstack channel Previous hyperstack channel Next hyperstack slice Previous hyperstack slice Next hyperstack frame Previous hyperstack frame Crop active image or selection Duplicate active image or selection Scale image or selection Make image larger Make image smaller Revert to original zoom level Zoom to 1 1 Smooth Repeat Command Measure Histogram Plot Profile Gels gt Select First Gels gt Select Next Gels gt Plot Lanes EROBRBaE HE HA 3x3 unweighted smoothing Repeat previous command Display statist
108. down menu Selects one of three display modes 69 IMPROVED Red Displays the thresholded values in red BEW Features are displayed in black and background in white With version 1 43 this mode respects the Black background flag in Pro cess gt Binary gt Options Over Under Displays pixels below the lower threshold value in blue thresh olded pixels in grayscale and pixels above the upper thresh old value in green These colors can be changed from a macro by calling the ImageProcessor setOverColor and setUnderColor methods example Dark Background checkbox To be checked when features are lighter than the back ground Auto Uses the currently selected thresholding method to automatically set the threshold levels based on an analysis of the histogram of the current image or selection Apply Sets thresholded pixels to black and all other pixels to white For 32 bit float images Apply will also run Process gt Math gt NaN Background Reset Disables thresholding and updates the histogram Set New threshold levels can be entered into a dialog box SEE ALSO 18 31 2 5 Color Threshold Thresholds 24 bit RGB images based on Hue Saturation and Brightness HSB Red Green and Blue RGB CIE Lab or YUV components illustration is depicted below Ranges of the filters can be set manually or based on the pixel value components of a user defined ROI experimental For more information refer to Threshold Color s built
109. draw the ellipse for each particle in a separate window Shape Descriptors Calculates and displays the following shape descriptors Circularity 47 x tics with a value of 1 0 indicating a perfect circle As the value approaches 0 0 it indicates an increasingly elongated shape Values may not be valid for very small particles Uses the heading Circ Aspect Ratio The aspect ratio of the particle s fitted ellipse i e A If Fit Ellipse is selected the Major and Minor axis are displayed Uses the heading AR Roundness 4 x aoe or the inverse of Aspect Ratio Uses the heading Round Solidity cot Note that the Edit gt Selection gt Convex Hull command makes an area selection convex Feret s Diameter The longest distance between any two points along the selection boundary also known as maximum caliper Uses the heading Feret The angle 0 180 degrees of the Feret s diameter is displayed as Feret Angle as well as the minimum caliper diameter MinFeret The length of the object s projection in the X FeretX and Y Feret Y direction is also displayed Integrated Density The sum of the values of the pixels in the image or selection This is equivalent to the product of Area and Mean Gray Value The Dot Blot 131 Analysis tutorial demonstrates how to use this option to analyze a dot blot assay Median The median value of the pixels in the image or selection Skewness The third order moment about the mean The documentation
110. ds de 45 29 Vl Revert If Spy sty yd AR He A A ee ea BN 49 29 12 Page SUDAR OA 49 iii 30 31 32 20 Print plat ek Soe rae Me dh co E a E soe af 50 LITA QUI Se ates Rote cies a aes Se a a E le a cp A Ole Ue Me E AA a Wedd ltd IN 50 Edit gt 51 3055 Uindor Z coc coe eb kaa win ee A A ee A oo eed 51 30 2 Cut x Copy c Copy to System Paste v o ooo 51 30 3 Past Contohi e a e tt 51 BOA Clear ly Aik Bad to MONS A NAAA dd dl di ll 52 30 5 Clear Outside curia a Ad ete e A A A E A 52 SOG ENE apa y ae iS 52 30 7 Driawd iene E i ai n is a Ar 52 30 8 Invert Ile do sucre e Ee SEER OS 53 30 9 SECOND S2 xig yaar arat de E id AE a a Mla lg eee ar oe oe 53 SOLO Options F gin spade ert a DS Ue ee Be Bee ie on 57 Image gt 65 LA ANP A A A Rann eset seeing Re Re a ate ate cae waa ONE 65 B12 Ads a GE een e A lett a a 66 313 Show nfo ill gue Nas AA A ABR RB Bef 72 31 4 Properties Plassa oc eee ee a ae er A A AA D Y 73 GS CO a ld o A e ae Ne 73 a AA TE dh wot da dalle be A hk hh kk lec Ee ed te 76 Shit Hyperstacks S vos PE be AAR REESE SEE ES Be er ee as Bh wd 87 318 Crop Mens er aia ae eee Be deg eis EE a ae 89 31 95 Duplicate a Dl Sica ta a aoe Go A o BEES Aaa 89 SLILO Reames saree A A Sel ee eee eee ye eds OG 89 B11 Seales E cs AER ee PY Lede wee es aa teks 90 SL AQ Tm ee MM A AA 90 SLES ZOOM sso ss Cashed te oe aoe o A AS OER AA 91 Sela rl e Bete ce o ae ae acest ee ee Ree i ee eee e 9
111. e 3 or the formula gray 0 299 x red 0 587 x green 0 114 x blue if Weighted RGB to Grayscale Conversion is checked in Edit gt Options gt Conversions SEE ALSO Import Text Image 29 10 5 Zip Saves the active image or stack as a TIFF file inside a compressed ZIP archive 46 IMPROVED Text Images File gt Import Text Image and File gt Save Asp Text Image AB Text Image txt C2 Cc3 pu A gt N in o om A N o 00 ia wo A e o A H 12 C13 C14 C15 om o o o o La Text Image 1200 16x13 pixels bit OK coooooocoococo lnm E 0 0 0 0 0 255 255 255 255 255 255 0 0 0 0 0 0 0 0 coooooooococooccoc o cooococoococooclclc oooocooocoococec o ooooocooocooococ o o N un un N un un N un un N un un N un un N un un o00000000000Oo ooooocoococoocjeo ooooooocoocoocc so coooooooooocooo y 29 10 6 Raw Data Saves the active image or stack as raw pixel data without a header 8 bit images are saved as unsigned bytes unsigned 16 bit images are saved as unsigned shorts and signed 16 bit images e g File Open Samples gt CT are saved as signed shorts 32 bit images are saved as floats and RGB images are saved in three bytes per pixel 24 bits interleaved format 16 bit and 32 bit float images are saved using big endian byte order unless Export Raw in Intel Byte Order is checked in the
112. e with foreground 255 and background 0 using an inverted or normal LUT depending on the Black Background option in Process Binary gt Options The number of particles as obtained by Ana lyzeb Analyze Particles in the output image does not depend on the selected Output Type Note that Segmented Particles will usually result in particles touching the edge if Exclude Edge Mazima is selected Exclude Edge Maxima ap plies to the maximum not to the particle Find Maxima does not work on stacks but the FindStackMaxima macro runs it on all the images in a stack and creates a second stack containing the output images The FindMaxi maRoiManager macro demonstrates how to add particles found by Find Maxima to the RO Man ager 99 32 5 Enhance Contrast ADO Saturated Pixels 0 4 O Normalize O Equalize Histogram M Normalize All 27 Slices O Use Stack Histogram Enhance Contrast Enhances image contrast by using either histogram stretch ing or histogram equalization Both methods are described in detail in the Hypermedia Image Processing Reference Contrast Stretching and Histogram Equalization This command does not alter pixel values as long as Normal ize Equalize Histogram or Normalize All n Slices in the case of stacks are not checked Cancel Saturated Pixels Determines the number of pixels in the image that are allowed to become saturated Increasing this value will increase c
113. e active image twice Another example is the Image Inverter 153 IMPROVED 34 4 5 Plugin Frame Opens an editor window containing a prototype plugin that extends the PlugInFrame class Plugins of this type displays a window containing controls such as buttons and sliders The prototype opens a window containing a text area Another example is the IP Demo 34 4 6 Text Window gt New Text Window Width 60 characters Height 16 lines Opens a text window of a specified size that macros can write to PrintToTextWindow Clock and ProgressBar are exam ples of macros that write to a text window 4 Menu Bar L Monospaced Font e Cancel OK SEE ALSO Plugins gt New Macro File gt New Text Window N 34 4 7 Table ONON New Table Name Width 350 pixels Height 250 pixels a Noa A Cancel OK Opens a blank table similar to the Results table that macros can write to SineCosineTable2 http rsb info nih gov ij macros SineCosineTable2 txt is an example of such a macro SEE ALSO Plugins gt New Text Window 34 5 Compile and Run Compiles and runs a plugin Runs a plugin if the name of the selected file ends in class Requires that ImageJ be running on a Java Virtual Machine that includes the javac compiler which is contained in the tools jar archive Tools jar is included with the Windows and Linux versions of ImageJ bundled with Java and it is pre
114. e microscopy im ages Cytometry Part A the journal of the International Society for Analytical Cytology 58 2 167 76 Apr 2004 C Messaoudi N G de Loubresse T Boudier P Dupuis Williams and S Marco Multiple axis tomography applications to basal bodies from Paramecium tetraurelia Biol Cell 98 7 415 25 Jul 2006 C Messaoudii T Boudier C O S Sorzano and S Marco TomoJ tomography software for three dimensional reconstruction in transmission electron microscopy BMC Bioinfor matics 8 288 Jan 2007 K Moodley and H Murrell A colour map plugin for the open source Java based image processing package ImageJ Computers amp Geosciences 30 6 609 618 Jan 2004 R L Mort Quantitative analysis of patch patterns in mosaic tissues with ClonalTools software J Anat 215 6 698 704 Dec 2009 C A Myrick A low cost system for capturing and analyzing the motion of aquatic organ isms J N Am Benthol Soc 28 1 101 109 Jan 2009 M L Narro F Yang R Kraft C Wenk A Efrat and L L Restifo NeuronMetrics software for semi automated processing of cultured neuron images Brain Res 1138 57 75 Mar 2007 M Noursadeghi J Tsang T Haustein R F Miller B M Chain and D R Katz Quan titative imaging assay for NF B nuclear translocation in primary human macrophages J Immunol Methods 329 1 2 194 200 Jan 2008 F Papadopulos M Spinelli S Valente L Foroni C Orrico F Alviano and G
115. e points 31 that define a segmented line selection can be moved or deleted and new points can be added Modifier keys Shift 1 Clicking on an existing point with the Shift key down adds a point AI Clicking on an existing point with the Alt key down deletes it SEE ALSO Polygon Selection Tool Freehand Line Selection Tool 5 15 18 3 A Freehand Line Selection Tool Select this tool and drag with the mouse to create a freehand line selection SEE ALSO Freehand Selection Tool 5 15 19 4 Arrow Tool ONNA Arrow Tool Width lt 112 Size gt C lt i gt 10 ry Color blue y Style Filled ry O Double headed Y Filled Notched Open Single NX NX headed Double AA YX X headed 20 A Angle Tool Double clicking on the tool icon opens the Options prompt depicted on the left Because its an annotation tool Color will change foreground color and not selec tion color Width and Size in pixels can be adjusted by dragging the respective sliders or by direct input Apart from the six arrow styles listed on the left a Headless style is also possible As with other tools add arrows to a non destructive overlay using Image Overlay gt Add Selection b or Edit gt Draw d to permanently draw an arrow cf 15 Straight Line Selection Tool key modifiers can be used when creating an arrow e g holding down will force the arrow to be horizontal or vertical SEE
116. e this command to import images ANOO Import that are not in a file format directly supported by ImageJ You will need l Type 8 bit Y a 3 e i N to know certain information about the Width 512 pix oes qu 3 layout of the image file including the PP bit Unsigne A Height 512 PiX 32 bit Signed size of the image and the offset to the Offset to First Image 0 byt 32 bit Unsigned beginning of the image data Number of Images 1 32 bit Real s A 64 bit Real Interleaved RGB images have pixels etween Images is sl 24 bit RGB stored contiguously rgbrgbrgb in a PEI 24 bit RGB Planar O White is Zero 24 bit BGR a single image plane Planar RGB im dc 24 bit Integer ages have the red green and blue im U Open All Files in Folder 32 bit ARCB O Use Virtual Stack SUE ABCR age data stored in separate 8 bit sam Cancer Cd Tbit Bitmap ple planes ImageJ saves RGB images _ both TIFF and raw in interleaved format Image Type There are fourteen choices depicted above 16 bit signed integer images are converted to unsigned by adding 32 768 1 bit Bitmap images are converted to 8 bit Image Width The number of pixel in each row of image data Image Height The number of rows in the image Offset to First Image The number of bytes in the file before the first byte of image data Number of Images The number of images stored in the file If this value is greater than the actual num
117. e to an RGB image and displays that image a new window SEE ALSO Flatten F 152 34 3 10 Find Commands I Described in Command Finder 34 4 New This submenu contains commands that open editor windows that can be used to edit and run macros and plugins It also has a command that opens a text window of a specified size and a command that opens a table that macros can write to The editor windows opened by PlugIn PlugInFilter and PlugInFrame contain prototype Java code for the three types of plugins supported by ImageJ SEE ALSO The ImageJ Editor Extending ImageJ 34 4 1 Macro Opens a blank editor window with the title Macro txt SEE ALSO Macros The ImageJ Editor Text Window File gt New Text Window N 34 4 2 JavaScript Opens a blank editor window with the title Script js SEE ALSO Scripts The ImageJ Editor 34 4 3 Plugin Opens an editor window containing a prototype plugin that implements the Plugln interface Plugins of this type open capture or generate images The prototype displays Hello world in the ImageJ window Press File gt Run Macro to compile and run it Note that the name you choose for the plugin should include at least one underscore Another example is the Step Maker plugin 34 4 4 Plugin Filter Opens an editor window containing a prototype plugin that implements the PlugInFilter interface Plugins of this type process the active image The prototype inverts th
118. eJ 1 41 added support for JavaScript scripting ImageJ uses the Mozilla Rhino interpreter built into Java1 6 for Linux and Windows to run JavaScript Mac users and users of earlier versions of Java must download JavaScript jar into the plugins folder This JAR file is available at rsb info nih gov ij download tools JavaScript jar It is also included with the Mac version of ImageJ 1 41 and later in the ImageJ plugins tools folder Example JavaScript programs are available at rsb info nih gov ij macros js With ver sion 1 43 thread safe JavaScript code can be generated using the Recorder Plugins gt Macros Record Scripts can be opened in the editor as any other macro cf Macros Scripts with the extension js can be run using the Macros gt Run Macro command oth erwise Macros gt Evaluate JavaScript must be used The ImageJ web site has growing documentation on ImageJ JavaScript scripting In addition the Fiji webpage hosts a Javascript tutorial for ImageJ by Albert Cardona SEE ALSO Scripting comparisons on the Fiji website Pros and cons of JavaScript in ImageJ JavaScript Advantages JavaScript Disadvantages Full access to ImageJ and Java APIs Slower especially starting up Richer language objects operator No equivalent of macro sets break continue etc Cannot use most of ImageJ s 360 built in Extensive documentation nacro functions Standardized Requires knowledge of complex ImageJ and Java APIs
119. easurements listed in the Results table will be cleared Summarize If checked the particle count total particle area average particle size area fraction and the mean of all parameters listed in the Set Measurements dialog box will be displayed in a separate Summary table Note that while single images Summaries are output to the same Summary table stack Summaries are printed in dedicated tables named Summary of stack title Also note that descriptive statistics on Results measurements can be obtained at any time using the Summarize command Add to Manager If checked the measured particles will be added to the RO Man ager Exclude on Edges If checked particles touching the edge of the image or selection will be ignored Include Holes If checked interior holes will be included Disable this option to exclude interior holes and to measure particles enclosed by other particles When this option is enabled ImageJ finds the extent of each particle by tracing the outer edge When it is disabled ImageJ finds the extent by flood filling Particle Analyzer Features of thresholded images can be segregated and extracted by specifying suitable Size and Circularity ranges and or choosing if particles should be traced by their outer edge or by flood filling Include Holes checkbox Original Size 0 50 Size 0 00 Size 50 00 Exclud Ed thresholded 7eude on Fages Include Holes eo 6 1 0 Circ 0 0 0 5 Circ
120. ecifically interested in improving their skills in writing macros and plugins for ImageJ The membership base includes experienced programmers and new users who are interested in learning to write their very first macros d Fiji developers http groups google com group fiji devel Fiji developer discussion e ImageJX http groups google com group imagejx Highly technical developer discussion about ImageJ future directions f ImageJDev http imagejdev org mailman listinfo imagej devel For communication and coordination of the ImageJDev project If you are having problems with ImageJ you should inquiry about them in the appropri ated list The ImageJ mailing list is an unmoderated forum subscribed by a knowledge able worldwide user community with 2000 advanced users and developers To have your questions promptly answered you should consider the following 1 Read the documentation files Described earlier in this section before posting Because there will always be a natural lag between the implementation of key features and their documentation it may be wise to check briefly the ImageJ news website Help ImageJ News 2 Look up the Archives Helpb List Archives Most of your questions may already been answered 3 If you think you are facing a bug try to upgrade to the latest version of ImageJ Help Update ImageJ You should also check if you are running the latest ver sion of the Java Virtual Machine f
121. ed in the Set Measurements dialog box Area statistics are calculated for the complete image if there is no selection or for a selected subregion defined by one of the first four tools in the toolbar cf Area selection tools For linear selections Straight Segmented and Freehand lines cf Line Selection Tools length and angle straight lines only are also calculated For Point selections cf Point Tool and Multi point Tool the X and Y coordinates are recorded Note that Measure m will paint invasively a mark over the measured point in foreground color unless Mark Width in the Point Tool options dialog box is set to zero cf Point Tool With RGB images results are calculated using brightness values RGB pixels are converted to brightness values using the formula value red green blue 3 or value 0 299 x red 0 587 x green 0 114 x blue if Weighted RGB Conversions is checked in Edit gt Options Conversions Intensity statistics Mean Modal Median Min amp Max Gray Value Standard Deviation and Integrated Density can be performed on area line and multi point selections With area selections the following parameters can be recorded Area Center of Mass Centroid Perimeter Bounding Rectangle Shape Descriptors Fitted Ellipse Feret s Di ameter Skewness Kurtosis and Area Fraction With line selections the following parameters can be recorded Length Angle straight lines only and Bounding Recta
122. ed or rotated In addition image selections are not saved in the TIFF header SEE ALSO Paste Control ROI Manager 31 14 3 Hide Overlay Causes ImageJ to stop displaying the overlay cf Hide Overlay 31 14 4 Show Overlay Displays an overlay that was hidden by Hide Overlay 31 14 5 From ROI Manager Creates an overlay from the selections on the ROI Manager list cf ROI Manager Note that previously added overlays will be removed 31 14 6 To ROI Manager Copies the selections and images in the current overlay to the ROI Manager where they can be edited moved resized or re colored cf RO Manager Note that previous items in the ROI Manager list will be deleted 31 14 7 Remove Overlay Permanently clears the overlay so that it cannot be restored using Show Overlay 31 14 8 Flatten F Creates a new RGB image that has the overlay rendered as pixel data The RGB image is the same size as the active image unlike Plugins Utilities gt Capture Image which creates a WYSIWYG What You See Is What You Get image that is the same size as its window 95 31 15 Lookup Tables gt This submenu contains a selection of color lookup tables that can be applied to grayscale images to produce false color images If no image is open a 256x32 ramp image is created to display the color table More than 100 additional lookup tables are available at rsb info nih gov ij download luts They are also available as a ZIP arc
123. ee OS a 33 11 Plot Profile ira A Se Oe ela Se odie ce 33 12 SUMACE Plots ors alee seth Beth ReGen de de RG Oh eel a Rs ta a 3310 Gest awit A hk Ae EE BAK ee hot th tit a a a a ieh SOTA TOOISE orau ke Wea a ee ee ae ae ce A ee A A E Rae ee Plugins gt IA Ly Machos gt EAT Bees Ae AE oe Be eee Del SLDS NOUS rara bdo da a A A 343 Utilities 2 2 2 2 ok a eo A e a a a a tE A O ae ot A tee Meath dee te aa a te Ye 34 5 Compile and Runes 4 4 4 4504 Goya he EE OS DED hee Mare Window 30 1 SHOW SAI ll iaa A easier a oo A uaa ty he 35 2 Put Behind tab occ Bee SS Gale eed weed fo E S 35 9 CaSCad Gs 6 am A AA SG i da de Suda Tale 8 a o a a A e A o 0 Help 36 1 Image Website aa Se va eG ea MAS Dy IA a es 36 2 imaged News ooo aaa eee eh RRA Os ee ee A 36 3 Documentations y apollo A be Bon A A LA ta IA 36 4 Installation 00 Search Website Fete Oe A OAS ra ls E oe 9 36 6 Eist ArCHIVeS xc al oe Oe olde ay ae Ue My eR aS GS ke da ee BVA 30 7 DeVs ReSOUNCES lt 2 it A eB AE O LAG ed 30 9 PIU SINS Zs A Ses de Sa aah DA ante SP eet id lg E AAA te A A Ge Be Be tn Se nae auai ea Heme is os ah hh Ads 36 10 Macro Functions 4 4 4 cr cre ese E A A ok ee S 360 11 Update ImageJ e 0 eee ee be See ee ee tia ee Biante td 36 12 Update Men s 30h cco Gaia bee ee ed DEM Ee Ee eee EES UE eS 30 13 About Plugins i 1330 tea ee ee a PDA A Re ee es S614 About Imagekind ne dr dd ee Bee aes A Bee te Soe ee a Keyboard Sho
124. ee Polynomial 2 00 4 5 3rd Degree Polynomial ac se 4th Degree Polynomial 5 00 24 Exponential ALO Formula Power Lo sly reer Formula y a b x cx simplexFitting Options Gamma Variate Function name User defined y a b In x c Formula y a b x c x x Rodbard NIH Image Exponential with Offset Gaussian Exponential Recovery Initial a Initial b Initial c Maximum iterations Number of restarts 2 Error tolerance 1 10A x Cancel 1 00 1 00 1 00 4500 10 AAP y a b x c x x User defined y a D x Cc xx a 0 2107 b 0 4318 c 0 9125 R 2 0 987 Formula y a b x c x x Time 31ms Number of iterations 179 4500 Number of restarts 2 2 0 2 x Sum of residuals squared 5 9469 Standard deviation 1 0906 Save Copy RA2 0 9874 Parameters a 0 2107 b 0 4318 3 Once the Fit button is pressed ImageJ displays a graph of the data with the fitted curve as well as a log window containing information about the fit and the values of the fitted parameters if Show Settings is checked 4 Click Apply to create a 32 bit copy of the current image transformed with the chosen function ImageJ s curve fitter built in functions Function Formula Comments Straight Line y a bx cf Pixel Inverter Calibrate 2 Degree Polynomial y a
125. elected ROIs from the list Deletes all the ROIs if none are selected 144 IMPROVED Rename Rename the selected ROI Measure Measures the selected ROIs or if none are selected all ROIs on the list Use Analyze gt Set Measurements to specify the parameters to measure With a stack you will be given the option to measure all the slices if all ROIs are associated with the first slice have labels like 0001 xxxx yyyy or all have labels in the form XXXX VVVy Deselect Deselects any selected ROIs on the list Delete Measure More gt Save and Mores Combine work with all ROIs on the list when none are selected Properties See Edit gt Selection gt Properties Flatten F See Image Overlay gt Flatten F Show All Displays a non destructive overlay that outlines and labels all ROI Manager selections Click Show All a second time to remove the overlay Click on a label selection number in the overlay to activate the corresponding selection That selection can then be moved or edited and the overlay will be dynamically up dated The color and behavior of the Show All overlay can be changed in the More Options dialog box Edit Mode Disables enables selection labels More gt Displays a drop down menu with several additional commands this drop down menu is also available when right clicking on any listed ROI Open Opens a roi file and adds it to the list or opens a ZIP archive zip file and adds all the s
126. election by pressing to avoid this dialog SEE ALSO Clear Draw d Color Picker 30 7 Draw d Outlines the current selection using the current foreground color and line width The foreground and background colors can also be set using the Edit gt Options gt Colors com mand Use the Edito Options Line Width command or double click on the line tool to change the line width With stacks a dialog is displayed offering the option to draw the selection in all stack images Draw the selection by pressing to avoid this dialog SEE ALSO Label Color Picker 15 10 52 10 DRAWING LINES WIDER THAN ONE PIXEL If the line width is an even number the selection boundary is at the center of the line If the line width is odd 1 3 the center of the line drawn is displaced from the selection edge by 1 2 pixel to the bottom right Thus the line center the line in case of line width 1 is inside the selection at the top and left borders but outside at the bottom and right borders Rectangular selections but not polygonal selections or traced selections that happen to be rectangular are an exception to this rule For rectangular selections one pixel wide outlines are always drawn inside the rectangle Thicker lines are drawn as for the other selection types 30 8 Invert I Creates a reversed image similar to a photographic negative of the entire image or selection SEE ALSO Invert LUT 30 9 Selection
127. elections contained in it to the list Use the Open All macro to add all the roi files in a folder Save Saves the selected ROI as an roi file If no ROIs are selected saves all the ROI Manager selections as a ZIP archive Fill Alias for Edit Fill f Draw Alias for Edit gt Draw d Combine Uses the union operator on the selected ROIs to create a composite selection Combines all the ROIs if none are selected Split Splits the current selection it must be a composite selection into its com ponent parts and adds them to the ROI Manager Add Particles Adds objects segmented by the particle analyzer to the ROI Man ager Requires that Record Starts be checked in the Analyze gt Analyze Particles dialog box Particle analyzer objects can also be added to the ROI Manager by checking Add to Manager in the Analyze Particles dialog box 145 Multi Measure Measures all the ROIs on all images in the stack creating a Re sults table with either one row per image if One Row Per Slice is checked in the dialog or one row per measurement C24 Sort Sorts the list in alphanumeric order Specify See Edit gt Selection gt Specify Remove Slice Info removes the information in the ROI names that associates them with particular stack slices Help Opens http rsb info nih gov ij docs menus analyze html manager Options Displays a dialog box that allows you to set the Show All color to associate Show All ROIs with the st
128. els to remove outliers such as dust and then smoothed to reduce noise average over 3x3 pixels With Disable Smoothing checked the unmodified image data are used for creating the background Check this option to make sure that the image data after subtraction will never be below the back ground Subtract Background This command uses a sliding paraboloid or a legacy rolling ball algo rithm that can be used to correct for uneven illuminated background cf plot profile Analyze gt Plot Profile k displayed below each image The radius should be set to at least the size of the largest object that is not part of the background Original Image Corrected Image SEE ALSO How to correct background illumination in brightfield microscopy by G Landini Auto Local Threshold Background subtractor Rolling Ball Background Subtraction the plugin that implemented this command in versions up to 1 39e 32 15 Repeat Command R Reruns the previous command The Edit gt Undo and File Open commands are skipped SEE ALSO Undo and Redo 124 33 Analyze gt This menu contains commands related to statistical measurements on image data profile and histogram plotting and plugins related to image analysis 33 1 Measure m Based on the selection type calculates and displays on the Results table either area statistics line lengths and angles or point coordinates Performed measurements can be specifi
129. emoves commands added to the Shortcuts submenu by Create Shortcuts Also re moves commands added by Install Plugin and removes plugins installed in the Plugins menu The menus are not updated until ImageJ is restarted 150 34 3 Utilities gt 34 3 1 Control Panel uO O Control Panel a nA i This command C25 opens a window containing Help ImageJ commands in a hierarchical tree structure 4 Show Parent r dea 8 bit Click on a leaf node to launch the corresponding I v in 16 bit ImageJ command or plugin Double click on a gt Bia 32 bR tree branch node folder to expand or collapse it E 8 bit Color y MB Adjust D RGE Color Click and drag on a tree branch node folder to _ Brightness Contrast i 4 Window jewel RGB Stack display its descendants in a separate child win Color Balance _ HSB Stack dow In a child window click on Show Parent _ Threshold Y to re open the parent window SEE ALSO Command Finder 34 3 2 ImageJ Properties This command displays various ImageJ properties Java version OS name and version path separator location of directories screen size etc in a text window Modifier keys Lists all Java properties SEE ALSO Status bar Helpp About ImageJ 34 3 3 Threads This command lists in a text window the currently running threads and their priorities 34 3 4 Benchmark Runs 62 image processing operations on the current image
130. er 45 16 bit images can be saved as 16 bit PNGs o 48 Transparent zero mode now works with 16 bit and 32 bit images 51 Edit gt Options DICOM command ss ers pu ae aea 44 e aa E E ERR a G 63 Image gt Adjust gt Color Threshold command s sao e 70 Imagep gt Stacksp gt Tools gt submenu o 85 Image gt Stacks gt Tools gt Reduce command 2 2 0000 0004 85 Image gt Stacks Tools Insert command 200 50022 eee 86 Image gt Stacks gt Tools gt Montage to Stack command 86 Imager Transforme submenu as a f4e 2 2 bee ee ee ee eR ee 90 Image Transform gt Flip Z command 02 02 eee ee es 90 Non destructive image overlays Image gt Overlay gt submenu 93 Faster Process gt Find Maxima command with List output 98 Binary gt operations with preview e e ee ee es 107 Faster Mathb commands when operating on 16 bit and float images 108 Gamma siders sae 4th A ee E A ee Atak Mo gi 109 Process gt Batehib submentt 2 30 fata eae ha pte eek et Be a 118 Improved and redesigned ROI Manager 02 0050 pe eee 144 The Recorder generates thread safe JavaScript and Java code 148 Improved Command Finder e 153 This list is not extensive Detailed release notes for version 1 43 are available on the ImageJ News web site http rsb info nih
131. ers of the two nearest particles Thus the Voronoi cell of each particle includes all points that are nearer to this particle than any other particle When particles are single points a Voronoi tessellation also known as Dirichlet tessellation is performed 106 The output type Overwrite 8 bit 16 bit or 32 bit of this command can be set in the Process gt Binary gt Options dialog box In the output the value inside the Voronoi cells is zero the pixel values of the dividing lines between the cells are equal to the distance to the two nearest particles This is similar to a medial axis transform of the background but there are no lines in inner holes of particles SEE ALSO Delaunay_ Voronoi plugin Process Binary gt commands II Original Voronoi Ultimate Points Original Distance Map Ultimate Points Watershed Voronoi AAA Original AAA EDM AA N Watershed A OO Voronoi Orig Voronoi UEPs wre ee iv pau pixels Eb Gnverting 200x181 pixels 8 bit inverting Te ee iv 3 pam 8 bit invertin 200x180 pixels EE s 7 s N e 8 X e 8 een af KA e 0 LIA 0 e as pe eve pr p oo W e yrs es Lt Oo Feit tS JS 0 e e 7 9 one A I i JO a 32 8 14 Options Specifies several settings used by Binary gt com mands Binary Options Iterations Specifies the number of times er
132. erties of secondary and tertiary human enteric nervous system neurospheres J Pediatr Surg 44 6 1249 55 discussion 1255 6 Jun 2009 X Ma and M S Hutson Quantifying the intercellular forces during drosophila morpho genesis American Physical Society page 29003 Mar 2006 H M Macdonald D M L Cooper and H A McKay Anterior posterior bending strength at the tibial shaft increases with physical activity in boys evidence for non uniform geo metric adaptation Osteoporos Int 20 1 61 70 Jan 2009 170 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 P Mailly S N Haber H J Groenewegen and J M Deniau A 3D multi modal and multi dimensional digital brain model as a framework for data sharing J Neurosci Methods Dec 2009 P A McAtee I C Hallett J W Johnston and R J Schaffer A rapid method of fruit cell isolation for cell size and shape measurements Plant Methods 5 5 Jan 2009 R B Medeiros K J Papenfuss B Hoium K Coley J Jadrich S K Goh A Elayape rumal J E Herrera E Resnik and H T Ni Novel sequential ChIP and simplified basic ChIP protocols for promoter co occupancy and target gene identification in human embryonic stem cells BMC Biotechnol 9 59 Jan 2009 E Meijering M Jacob J C F Sarria P Steiner H Hirling and M Unser Design and validation of a tool for neurite tracing and analysis in fluorescenc
133. es it c here lt 1 has been opened as a virtual hyperstack cf Stacks 7 4 gt lt gt AME al gt SEE ALSO Image gt Hyperstacks gt submenu 14 IMPROVED 11 Color Images ImageJ deals with color mainly in three ways pseudocolor images RGB images RGB HSB stacks and composite images Pseudocolor images A pseudocolor or indexed color image is a single channel gray image 8 16 32 bit that has color assigned to it via a lookup table or LUT This is literally a table of gray values with matching red green and blue values So instead of displaying a shadow of gray the image displays a pixel with a defined amount of each color Differences in color in the pseudo colored image reflect differences in intensity of the object rather than differences in color of the specimen that has been imaged SEE ALSO ImagebLookup Tables gt submenu True color images As described in Image Types and Image Formats true color images such as RGB images reflect genuine colors i e the green in an RGB image reflects green color in the specimen Color images are typically produced by color CCD cameras in which color filter arrays Bayer mask are placed over the image sensor Color Spaces and Color Separation Color spaces describe the gamut of colors that image handling devices deal with RGB is the most commonly used color space However processing color information stored in the form of RGB images may not be the mos
134. eselectenal A Opti gt Y coordinate p Fill Color__ 77000N22 oe Slice number Properties BOO how All Color Flatten Fi CN Mora Green 4i De Deselect Select All Blue lt gt lt gt 255 M show All Save M Edit Mode Combine Split Add Particles aE Show All with without labels Multi Measure Cancel ok Sort Specify Remove Slice Info More drop down menu Help also available when Options right clicking on list area Add Click Add to add the current selection to the list or press mM T the keyboard shortcut for the Edit gt Selection gt Add to Manager t command The Roi manager creates a three part label The first part stacks only is the slice number the second is the Y coordinate of the selection and the third is the X coordinate Click on a label to restore the associated selection to the current image With stacks the selection is restored to the slice it came from Modifier keys Hold down Shift while clicking Add to Add and Draw Alt Hold down Alt while clicking Add to Add and Rename Install the ROIManagerMacros macro set and you will be able to add a selection by pressing E add and rename by pressing 2 and draw by pressing E and add and advance to the next slice by pressing 4 Update Replaces the selected ROI on the list with the current selection This is usually a modified version of a selection from the ROI Manager list Delete Deletes the s
135. f use the foreground color Edit gt Clear Clear Outside and Cut use the background color Double clicking on the tool icon will display the Color Picker window Modifier keys Alt clicking with the Color Picker Tool on an image will change the background color SEE ALSO Color Picker K Draw d Fill f Image Types and Image Formats 15 27 Macro Toolset Switcher Use this drop down menu to switch to alternative macro tool sets located in the ImageJ macros toolsets folder or to revert to the default ImageJ macros StartupMacros txt IMPROVED toolset C27 Macro toolsets can be obtained at http rsb info nih gov ij macros toolsets or created e g using Toolset Creator Modifier keys Shift 1 Shift clicking on the Toolset Switcher will open the selected toolset file placed in the ImageJ macros toolsets folder 6 OPENING VIRTUAL STACKS BY DRAG amp DROP In ImageJ 1 43 and later TIFF stacks with a tif extension open as virtual stacks when dragged and dropped on the toolbar icon AAO mojej lt lt Open as Virtual Stack gt gt Image asaje z 44 1 y E al gt 35 28 Macro Tools The tools on the right side of the toolbar all slots between lColor Picker and gt Macro Toolset Switcher are defined by macros in the StartupMacros txt file InageJ macros folder which can be opened using the Plugins gt Macrosp Startup Macros comman
136. float images no scaling is done To calculate log g of the image multiply the result of this operation by 0 4343 1 1n 10 32 9 13 Exp Performs a exponential transform on the active image or selection 32 9 14 Square Performs a square transform on the active image or selection 32 9 15 Square Root Performs a square root transform on the active image or selection 32 9 16 Reciprocal Generates the reciprocal of the active image or selection Only works with 32 bit float images 32 9 17 NaN Background Sets non thresholded pixels in 32 bit float images to the NaN Not a Number value For float images the Apply option in Image Adjust gt Threshold T runs this command Pixels with a value of Float NaN 0f 0f Float POSITIVE _ INFINITY 1f 0f or Float NEGATIVE_INFINITY 1 0f are ignored when making measurements on 32 bit float images 110 32 9 18 Abs Generates the absolute value of the active image or selection Works only with 32 bit float or signed 16 bit image images 32 9 19 Macro This command performs image arith metic using an expression specified by the user C18 It can be used to create fully synthetic images or to perform precise pixel manipula tions on existing images The Math MacroDemo macro demonstrates the usage of this command eTe Macro Code v v 50 sin d 10 v pixel value x y amp z pixel coordinates w image width h image height a angle d distance from ce
137. for the Mo ment Calculator plugin explains how to interpret spatial moments Uses the head ing Skew Kurtosis The fourth order moment about the mean Uses the heading Kurt Area Fraction For thresholded images is the percentage of pixels in the image or selec tion that have been highlighted in red using Image Adjust gt Threshold T For non thresholded images is the percentage of non zero pixels Uses the heading Area Stack Position The position slice channel and frame in the stack or hyperstack of the selection Uses the headings Slice Ch and Frame NB For line selections the heading Length is created For straight line selections Angle is recorded even if Fit Ellipse is unchecked Also note that measurements that do not apply to certain selection types may be listed as NaN Infinity or Infinity The second part of the dialog controls measurement settings Limit to Threshold If checked only thresholded pixels are included in measurement calculations Use Imagep Adjust gt Threshold T to set the threshold limits This setting affects only thresholded images cf Settings and Preferences Display Label If checked the image name and slice number for stacks are recorded in the first column of the results table e g mri stack tif 9 For renamed selections Edit gt Selection gt Properties or selections measured via ROI Manager s measure command cf RO Manager the selection label is appended e
138. from images cur rently displayed in separate windows The 2 images differ in size smallest 117x157 largest 256x254 They will be converted o to a stack using the specified method Method If images differ in size a drop down menu allows to choose a conversion method a Method Copy center Copy top left Scale smallest Title Contains Scale largest ANO Images to Stack Name Stack Copy center top left Stack will have the width of the widest open image and the height of the highest open image Smaller images will then be copied either to the center or to the upper left corner of the slice Borders are filled with pixels that have a value of zero O Bicubic Interp M Use Titles as L 5 Name Stack U Keep Source In Title Contains M Use Titles as Labels O Keep Source Images Scale smallest largest Stack will have the dimensions of the smallest largest open image Other images are scaled to the new slice dimensions Bicubic inter polation is used if Bicubic interpolation is checked cf Imageb Size and Image gt Scale E Name Specifies the title of the stack to be created Title Contains Enter a string into this field and ImageJ will only convert to stack images whose name contains that string Bicubic Interpolation If checked bicubic interpolation cf Adjust Size will be used if any of the Scale methods was previously chosen
139. g the folder on the ImageJ win dow Imported sequences are sorted by image number instead of by file name and the tags are preserved when DICOM images are saved in TIFF format ImageJ supports custom DICOM dictionaries such as the one at http rsb info nih gov ij download docs DICOM_ Dictionary txt More information can be found here Flexible Image Transport System image is the format adopted by the astro nomical community for data interchange and archival storage Use Image Show Info i to display the FITS header More information here Portable GrayMap PBM Portable BitMap and PPM Portable PixMap are simple image formats that use an ASCII header More information here Audio Video Interleave is a container format which can contain data en coded in many different ways ImageJ only supports uncompressed AVIs various YUV 4 2 2 compressed formats and PNG or JPEG encoded indi vidual frames Note that most MJPG motion JPEG formats are not read correctly Attempts to open AVIs in other formats will fail Non native Formats 4 8 11 3 BRIGHTNESS CONTRAST OF HIGH BIT DEPTH IMAGES When displayed the intensity of each pixel that is written in the image file is converted into the grayness of that pixel on the screen How these intensities are interpreted is specified by the image type From the ImageJ website 16 bit and 32 bit grayscale images are not directly displayable on computer monitors which typically
140. ges dividing by zero results in Infinity Infinity or NaN 0 0 pixels when the source pixels are positive negative or zero The divide by zero value can be redefined using Edit gt Options Misc 32 9 5 AND Does a bitwise AND of the image and the specified binary constant 32 9 6 OR Does a bitwise OR of the image and the specified binary constant 32 9 7 XOR Does a bitwise XOR of the image and the specified binary constant 32 9 8 Min Pixels in the image with a value less than the specified constant are replaced by the constant 32 9 9 Max Pixels in the image with a value greater than the specified constant are replaced by the constant 32 9 10 Gamma OO Gamma Applies the function f p 2 255 x 255 to each pixel p in the image or selection where 0 1 lt y gt 5 0 For RGB images this function is applied to all three color channels For 16 bit images the image min and max are used for scaling instead of 255 Value 63 1 10 35 Y Preview Cancel OK gt VW _ SEE ALSO GammaCorrection Tool macro 109 IMPROVED 32 9 11 Set Fills the image or selection with the specified value 32 9 12 Log For 8 bit images applies the function f p In p x 255 1n 255 to each pixel p in the image or selection For RGB images this function is applied to all three color channels For 16 bit images the image min and max are used for scaling instead of 255 For
141. gov ij notes html vii Noteworthy 6 1 Frontmost Window and Windows Activation o o o 7 8 2 Limitations of Edit Undo Z 2 44 44h dr 9 9 3 Brightness Contrast of High Bit Depth Images 12 9 4 Image Types Lossy Compression and Metadata 4 13 16 5 Toggling Calibrated Units 42 44 4056 deie e ea Ee ee a 28 27 6 Opening Virtual Stacks by Drag amp Drop 002200020002 e 35 29 7 File gt Open File gt Import gt and Open by Drag amp Drop 39 29 8 Warning on JPEG compression o e o 46 29 9 Limitations of FilebRevertlilovossssm m ocsirraa eee Soe SS ES 49 30 10 Drawing Lines Wider Than One Pixel o e o 53 30 11 Transferring Selections Between Images o e 54 30 12 Converting Composite Selections soaa 0 ee eee eee 56 31 13 Applying Auto Brightness Contrast to Entire Stacks aoaaa 66 31 14 Display Range of DICOM Images e 00002000000 67 31 15 Embedding Color Annotations in Grayscale Images oosa a 76 31 16 Scrolling Zoomed Tmages 20d Re a a a ada 92 31A Working With HEX Colors na 4 41 24 a a ee ee Se a 94 32 18 Creating Binary Masks a yea eri a Ee ee A EA 104 39 19 Global Galibrations irine dd Bote ao a i e ay PGS os BUS OE RA hee 134 33 20 Selecting Multiple ROIs in Manager o e 00202000005 146 viii Macro Listings al w N X 0
142. ground will have negative peaks This setting does not change the analysis cf Invert LUT For practice refer to the video tutorial on the ImageJ wiki page and use the Filet Open Samples Gel sample image 1 D gel to perform the following steps Note that a copy of the gel image with the lane outlines can be created at any point using the Image Overlay gt Flatten F command 1 Use the rectangular selection tool to outline the first lane This should be the left most lane if the lanes are vertical or the top lane if the lanes are horizontal 2 Select Gels gt Select First Lane 1 and the lane will be outlined and Lane 1 selected displayed in the status bar 3 Move the rectangular selection right to the next lane or down if the lanes are horizontal and select Gels gt Select Next Lane 2 The selected lane is outlined and labeled and Lane n selected is displayed in the status bar 4 Repeat the previous step for each remaining lane 5 Select Gels gt Plot Lanes 3 to generate the lane profile plots y 6 Use the Straight Line Selection Tool to draw base lines and or drop lines so that each peak of interest defines a closed area ImageJ will automatically switch to the Straight Line tool Note that you can hold to constrain lines to be either horizontal or vertical To access to all the lanes it may be necessary to scroll the image vertically using the Scrolling Tool Hold down the space bar
143. gs 21 57 Print 49 50 Processing 97 Progress bar 28 Projection 81 82 Proxy 62 Q Quit 50 R RAM 61 Raw 47 58 Reciprocal 110 Record see Macro recorder 148 Rectangular selection 28 Redo 9 Reduce 85 88 Regex 40 Renyi see Threshold 69 Resampling see Interpolation 71 Reset 152 Results 19 Revert 49 RGB 15 70 ROI see Selection 18 ROI Manager 95 Rolling ball 123 Rotate 91 Round rectangle 29 Roundness 131 S Sagittal see Orthogonal views 81 SalsaJ 2 Sample Images 39 Scale 90 Scale bar 146 Scientific notation 132 Screenshot 152 Scrolling 35 Search 8 Segmented Line selection 31 Selection 18 Composite 19 56 Properties 55 Refine 29 Restore 53 ROI Manager 144 Settings 21 57 60 63 107 113 Shadows 102 Shanbhag see Threshold 69 Shape descriptors 131 Sharpen 97 Shortcuts 7 149 159 64 bit 62 Skeleton 105 Skewness 132 Sliding paraboloid see Rolling ball 123 Smooth 97 Sobel edge 97 Solidity 131 Spatial scale 133 Square root transformation 110 Square transformation 110 Stacks 13 Brightness Contrast 66 Export 47 48 From List 44 Hyperstacks 14 87 Labeling 84 86 Montage 79 86 Profile 84 Tools 85 Virtual 13 44 120 StartupMacros 35 36 39 148 Statistics 127 128 Status bar 27 Straight line selection 31 Straighten 56 Subtract see Math 108 Subtract Background 123 Subtract images see Image calcula
144. hand selection with its convex hull which can be thought of as a rubber band wrapped tightly around the points that define the selection SEE ALSO Fit Ellipse ConvexitySolidarity macro Convex_Hull_ Plus plugin 54 30 9 7 Make Inverse Creates an inverse selection What is inside the selection will be outside and vice versa 30 9 8 Create Mask Creates a new 8 bit image called Mask whose pixels have a value of 255 inside the selection and 0 outside By default this image has an inverting LUT so black is 255 and white is 0 unless Black Background in Process Binary gt Options is checked SEE ALSO Process gt Binary gt Convert to Mask 18 30 9 9 Create Selection Creates a selection from a thresholded image or a binary mask C7 30 9 10 Properties Opens a dialog box that allows user to assign a contour color Stroke Color and a contour width Width to the active selection or a filling color Note that selections can be either filled or contoured but not both ALDO Properties Name MySelection Stroke Color magenta width 3 The nine default selection colors black blue cyan Fill Color none green magenta orange red white yellow can be typed as text any other color must be typed in hex notation Y Coon gt Cancel j OK A SEE ALSO Selections Add Selection b ROI Manager 17 30 9 11 Rotate Rotate Selection Rotates the
145. have difficulties recognizing the red component can easily recognize the blue hue The region of double positive becomes white which is easily distinguishable for colorblinds In ImageJ RGB images can easily converted to MGB with a simple macro cf Extend ing ImageJ One possibility of such a macro would make use of the Channels Z tool to recolor the red channel This section is partially extracted from Masataka Okabe and Kei Ito Color Universal Design CUD How to make figures and presentations that are friendly to Colorblind people http jfly iam u tokyo ac jp color accessed 2009 01 15 16 a gt e N oon aw 10 11 12 13 14 MACRO 1 Creating MGB Images With the Channels Z Tool This macro replaces Red with Magenta in RGB images using the Edit gt Color gt Channels tool if bitDepth 24 Tgnore non RGB images exit This macro requires an RGB image setBatchMode true Enter Batch mode title getTitle Retrieve the image title run Make Composite Run Image gt Color gt Make Composite Stack setActiveChannels 100 Select first channel i e Red run Magenta Run Image gt Lookup Tables gt Magenta Stack setActiveChannels 111 Select all channels run RGB Color Run Image gt Type gt RGB Color rename title MGB Rename the image setBatchMode false Restore GUI mode Alternatively Process gt Image Calculator can be
146. he B amp C window is opened it will be closed and the W amp L win dow will be opened at the same location SEE ALSO Brightness Contrast C 31 2 3 Color Balance This panel makes adjustments to the brightness SAT Color and contrast of a single color of a standard RGB image 8 bit per color channel For multi channels stacks and hyperstacks it adjusts each of 7 the color channels independently Use the drop gt lt gt down menu to specify which color channel will be m A A adjusted the histogram is drawn for the selected Maximum color N AE E Mazimum and Minimum sliders Auto Set and Apply work as described for Imagep Adjust gt y x mee Brightness Contrast C Similarly to the Win Auto et Channa 2 dow Level tool if the B amp C window is opened it Channel 3 will be closed and the Color window will be opened Cionna 4 at the same location Channel 5 Channel 6 NB When switching from one color to another the changes made to one color will be lost unless Apply All is clicked before Also note that for 48 bit color images that load as a stack also Brightness Contrast C works on single stack slices i e colors and the color settings of the Color panel are ignored SEE ALSO Brightness Contrast C Color gt submenu 68 Image gt Adjust gt Threshold T Highlighted range Thresholding methods o
147. helm Burger Macro Toolsets distributed with ImageJ have been contributed by Gilles Carpentier Arrow Labelling Tools txt Scale Bar Tools for Microscopes txt J r me Mutterer Example Icons txt Magic Montage txt Tiago Ferreira Toolset Creator txt 166 13 ImageJ Related Publications M Abramoff P Magelhaes and S Ram Image Processing with ImageJ Biophotonics International 11 7 36 42 2004 L Altomare N Gadegaard L Visai M C Tanzi and S Far Biodegradable mi crogrooved polymeric surfaces obtained by photolithography for skeletal muscle cell orien tation and myotube development Acta biomaterialia Dec 2009 W Bailer Writing ImageJ Plugins A Tutorial Upper Austria University of Applied Sci ences Dept of Media Technology and Design Hagenberg Austria http www gm fh koeln de konen WPF BV tutorial ImageJ_ V1 71 pdf Jan 2006 D P Barboriak A O Padua G E York and J R Macfall Creation of DICOM aware applications using ImageJ J Digit Imaging 18 2 91 9 Jun 2005 D J Barry C Chan and G A Williams Morphological quantification of filamentous fungal development using membrane immobilization and automatic image analysis J Ind Microbiol Biotechnol 36 6 787 800 Jun 2009 D S A Beeckman G Meesen P V Oostveldt and D Vanrompay Digital titration automated image acquisition and analysis of load and growth of Chlamydophila psittaci Microsc Res Tech 72 5
148. hive at http rsb info nih gov ij download luts luts zip SEE ALSO Macro Toolset Switcher 31 15 1 Invert LUT Inverts the current lookup table For 8 bit images the value v of each entry in the table is replaced by 255 v With inverted LUTs pixels with a value of zero are white and pixels with a value 255 are black Unlike the Edit gt Invert I command pixels values are not altered only the way the image is displayed on the screen 31 15 2 Apply LUT Applies the current lookup table function to each pixel in the image or selection and re stores the default identity function This modifies the gray values so that when the image is viewed using the default grayscale lookup table it will look the same as it did before This command is equivalent to clicking on Apply in Image Adjust gt Brightness Contrast C For thresholded images it is equivalent to clicking on Apply in Image Adjust gt Threshold T 96 32 Processp This menu lists all commands related to image processing including point operations filters and arithmetic operations between multiple images 11 The File Open Samples gt Blobs 25K B image will be used in most of the illustrations of this section Process gt submenu Smooth S Sharpen Find Edges and Enhance Contrast LA AR blobs gif AA blobs gif Smooth 3x A blobs gif Sharpen 1x blobs gif Find Edges 1x A blobs gif E Contr
149. ichard Kirk The Process gt Math gt Macro command is modeled after Ulf Dittmer s Expression plugin 165 C19 C20 C21 C22 C23 C24 C25 C26 C27 The Process gt FFT gt Bandpass Filter is a built in version of Joachim Walter s FFT Filter plugin The Process Binary gt Fill Holes algorithm was contributed by Gabriel Landini The faster and more accurate version of Process gt Filters gt Gaussian Blur implemented in ImageJ 1 38r and later was contributed by Michael Schmid The NonBlockingGenericDialog class used by Process Batch gt Macro command was added by Johannes Schindelin The Analyze Distribution command was written by Gabriel Landini The ROI Manager Multi Measure command Analyze gt Tools gt ROI Manager is based on Bob Dougherty s Multi_Measure plugin The Control Panel Plugins gt Utilities gt Control Panel was written by Cezar M Tigare Numerous improvements bug fixes in other commands have been contributed by Albert Cardona Adrian Daerr Alden Dima Barry DeZonia Christian Mol Dimiter Pro danov Divakar Ramachandran Erik Meijering Frederic Hessman Gabriel Landini Jay Unruh Joachim Wesner Johannes Hermen Johannes Schindelin Julian Cooper Kai Uwe Barthel Kevin Moll Mark Longair Matt Smith Michael Schmid Norbert Vischer Olaf Freyer Reinhard Mayr Robert Dougherty Shannon Stewman Stephan Saalfeld Stefan Starke Ulf Dittmer Wil
150. ics about active image or selection Display histogram of active image or selection Display density profile plot of current selection Select first gel lane Select next gel lane Plot gel lanes Utilities gt Capture Screen Utilities gt Find Commands ct 9 Grab screenshot List find and launch commands Show All Put Behind ImageJ pe op 5 O Make all windows visible Switch to next image window Bring ImageJ window to front 160 A 1 Alt Key Modifications File gt Open Next Open Previous File gt Revert Don t show dialog Edit gt Copy Copy to system clipboard Image gt Color gt Split Channels Keep original image Image gt Stacks gt Add Slice Insert before current slice Stacks gt Next Slice Skip nine slices Stacks gt Previous Slice Skip nine slices Image Image Stacks gt Start Animation Show options dialog Image Image gt Duplicate Don t show dialog Image gt Overlay gt Add Selection Don t show dialog Process gt Equalize Do classic histogram equalization Analyze gt Histogram Show dialog Analyze gt Plot Profile For rectangular selections generate row average plot Analyze gt Plot Profile For wide straight lines display rotated contents Analyze gt Gels gt Select First Lane Assume lanes are horizontal Analyze gt Tools gt Analyze Line Graph Show intermediate image Analyze gt Tools gt Roi M
151. ill have automatically filled in the Distance in Pixels field based on the length of the line selection Setting Pixel Aspect Ratio to a value other than 1 0 enables support for different horizon tal and vertical spatial scales e g 100 pixels cm horizontally and 95 pixels cm vertically To set the Pizel Aspect Ratio 1 Measure the width and height in pixels of a digitized object with a known 1 1 aspect ratio 2 Enter the measured width in pixels in Distance in Pixels Enter the known width in Known Distance 3 Calculate the aspect ratio by dividing the width by the height and enter it in Pizel Aspect Ratio When Global is checked the scale defined in this dialog is used for all opened images during the current session instead of just the active image cf 19 Click to Remove Scale resets Distance in Pixels field and Know Distance to zero and the Unit of Length to pixel SEE ALSO Three tutorials showing how to use this command Examples of Image Analysis Using ImageJ by Larry Reinking Measuring DNA Contour Lengths and Spatial Calibration Fiji The Copy_ Pixel_ Size plugin 133 19 GLOBAL CALIBRATIONS Calibration settings related to spatial pixel width height and voxel depth tem poral frame interval and luminance brightness information can be set globally i e can be applied to all images opened during the current session instead of just the active image The Global flag can be set
152. ilter Large Structures Down to 40 pixels Filter Small Structures Up to 3 pixels Suppress Stripes one Horizontal Vertical Tolerance of Direction ls M Autoscale After Filtering M Saturate Image when Autoscaling O Display Filter a Cancel OK 113 Removes high spatial frequencies blur ring the image and low spatial frequen cies similar to subtracting a blurred im age It can also suppress horizontal or vertical stripes that were created by scanning an image line by line C19 The Bandpass Filter uses a special algo rithm to reduce edge artifacts before the Fourier transform the image is extended in size by attaching mirrored copies of image parts outside the original image thus no jumps occur at the edges Filter Large Structures Down to Smooth variations of the image with typical sizes of bright or dark patches larger than this value are suppressed background Filter Large Structures Up to Determines the amount of smoothing Objects in the image smaller than this size are strongly attenuated Note that these values are both half the spatial frequencies of the actual cutoff The cutoff is very soft so the bandpass will noticeably attenuate even spatial frequencies in the center of the bandpass unless the difference of the two values is large say more than a factor of 5 or so Suppress Stripes Select whether to eliminate Horizontal or Vertical stripes Removal of horizontal s
153. image e g File Open Samples gt HeLa Cells 1 3 M 48 bit RGB 66 Auto ImageJ will automatically optimize brightness and contrast based on an analysis of the image s histogram Create a selection and the entire image will be optimized based on an analysis of the selection The optimization is done by allowing a small percentage of pixels in the image to become saturated displayed as black or white Each additional click on Auto increases the number of saturated pixels and thus the amount of optimization A run Enhance Contrast saturated 0 35 macro call is generated if the command recorder is running Reset Restores the original brightness and contrast settings The display range is set to the full pixel value range of the image A resetMinAndMax macro call is generated if the command recorder is running Set Allows to enter the minimum and maximum display range values in a dialog box A setMinAndMax macro call is generated if the command recorder is running Check Propagate to all open images to apply these values to the rest of the images currently open Apply Applies the current display range mapping function to the pixel data If there is a selection only pixels within the selection are modified This option currently only works with 8 bit images and stacks and with RGB stacks This is the only B amp C option that alters the pixel data of non RGB images SEE ALSO Window Level Enhance Contrast 13 14 14
154. in three dialog prompts 1 Image Properties P pixel width height voxel depth frame interval 2 Analyzep Set Scale pixel width and height 3 Analyze Calibrate pixel intensity SIDO mitosis tif a TO veh ah Once Global calibration is set a G is dis played in all image title bars until ImageJ is closed A warning message such as the one depicted here is displayed when a calibrated image with conflicting calibration details is opened and the Global option is enabled The calibration of this image conflicts with the current global calibration M Disable Global Calibration O Disable these Messages Cancel Choose Disable Global Calibration to stop using global settings or Disable these Messages to keep respecting global settings ignoring the calibration of the newly open image 33 9 Calibrate Use this dialog box to calibrate an image to a set of density standards for example radioactive isotope standards or a calibrated optical density step tablet ANON Calibrate Function Rodbard NIH ivy Unit pmol mg protein Straight Line 2nd Degree Polynomial 10 02 0 00 3rd Degree Polynomial 1 a 12 218576 69 52 0 13 4th Degree Polynomial b 0 956813 94 23 0 23 Exponential yy Add 118 72 0 36 Power o 130 63 0 50 Log cA bai 179 95 0 69 gt 188 6 0 93 pn 245 93 1 29 amma Variate 252 35 2 10 Y a b In x c Y Rodbard NIH Image 0 00 Exponential wi
155. ing along its boundary will shrink the boundary inwards Brush diameter can be adjusted by double clicking on the tool icon Location width height and aspect ratio are displayed in the status bar during drawing Modifier keys Shift f Brush is always added to the selection Brush is always subtracted from selection SEE ALSO Composite Selections 5 29 17 5 G Polygon Selection Tool Creates irregularly shaped selections defined by a series of line segments To create a polygon selection click repeatedly with the mouse to create line segments When finished click in the small box at the starting point or double click and ImageJ auto matically draws the last segment The points that define a polygon selection edges or vertexes can be moved and modifier keys can be used to delete or add new vertexes to the polygon Modifier keys Shift 1 Clicking on a point with with the Shift key pressed adds a new point Clicking on a point with with the alt key pressed removes it SEE ALSO Segmented Line Selection Tool Enlarge 5 15 17 6 Freehand Selection Tool As with the polygon selection tool ImageJ automatically draws the last segment Lo cation and intensity of starting pixel are displayed in the status bar during drawing SEE ALSO Polygon Selection Tool Freehand Line Selection Tool 5 15 17 7 Wand Tool Creates a selection by tracing objects of uniform color or thresholded objects To trace an object
156. ing the command recorder Plugins gt Macros gt Record A macro is saved as a text file txt or ijm extension and once installed executed by selecting the macro name in the Plugins gt Macros gt submenu by pressing a key or in the case of Macro tools by clicking on an icon in the ImageJ toolbar In addition any macro file placed in the ImageJ plugins folder with an ijm extension will be installed in the Plugins gt menu like any other plugin before version 1 41 only files with an underscore in the name would be listed There are more than 300 example macros on the ImageJ Web site To try one open it in a browser window and drag it directly to the ImageJ Window or copy it to the clipboard Ctri A Ctri C switch to ImageJ and run File gt New System Clipboard V pasting the macro into a new editor window cf The ImageJ Editor Run it using the editor s Macros gt Run Macro command Most of the example macros are also available in the macros folder inside the ImageJ folder The ImageJ web site has excellent tutorials on ImageJ macro language The Built in Macro Functions website Help Macro Functions is thoroughly documented and constantly updated These resources are indispensable guides to macro writing In 24 addition there is also a PDF version of the ImageJ macro language documentation as of version 1 38m created by Uwe Walschus SEE ALSO Scripts IJ_ ED plugin Scripts Imag
157. is already open it will activated when its opening command is re run e g if the B amp C window is already opened pressing its keyboard shortcut will activate it In addition Pressing on any image will bring the ImageJ window to the foreground 7 Finding Commands There are two expedite ways of finding your way through the extensive list of ImageJ commands macros and plugins Pluginsp Utilities gt Find Commands I and Plugins gt Utilities gt Search Plugins gt Utilities gt Find Commands l AAA Command Finder Adaptive3 DThreshold 14 Colocalisation Threshold y Color Threshold DynamicThreshold 1d a Entropy Threshold ly 1 Show full information m Close when running ALO S I Run Export Close 4 O Search Contents Y Ignore Case 4 Search Macros Folder ImageJ macros AutoThresholdAndSegment txt Search Source Folder ImageJ macros examples AutoThresholdingDemo txt YM ao Cancel OK gt lmageJ macros examples SetOverUnderThresholdColors txt Plugins gt Utilities gt Search Command Finder The quickest way to find a command without having to navigate through all the menus is using the built in Command Finder C1 Plugins gt Utilities gt Find Commands I com mand Evoke the prompt by pressing E as in command Launcher Locator or List If you type part of a command name the list will only show comm
158. it color images with additional eight bits coding alpha blending values i e transparency SEE ALSO Color Images Native Formats Natively i e without the need of third party plugins ImageJ opens the following for mats TIFF GIF JPEG PNG DICOM BMP PGM and FITS Many more formats are supported with the aid of plugins These are discussed in Section Non native Formats TIFF Tagged Image File Format images can be 1 bit 8 bits 16 bits unsigned 32 bit real or RGB color TIFF files with multiple images of the same type and size open as a stack Tiff tags are printed to the log window when Debug Mode is enabled Edit gt Options gt Misc cf Settings and Preferences 1A numeric variable is signed if it can represent both positive and negative numbers and unsigned if it can only represent positive numbers 10 DICOM FITS PGM AVI SEE ALSO ImageJ opens LZW and PackBits compressed TIFF files and TIFF files can be opened and saved as ZIP archives TIFF is the default format of ImageJ cf File gt Save s Digital Imaging and Communications in Medicine is a standard popular in the medical imaging community Support in ImageJ is limited to un compressed DICOM files DICOM files containing multiple images open as a stack Use Imagep Show Info i to display the DICOM header in formation A DICOM sequence can be opened using File gt Import gt Image Sequence or by dragging and droppin
159. k outside the selection to terminate the paste Select Edit gt Undo z to abort the paste operation 30 3 Paste Control SOL Paste Control After pasting use the Paste Control pop up menu Transfer Mode Y Copy J to control how the image currently being pasted is Seng transferred to the destination image Difference Basane Except for Blend and Transparent the Paste Con AND trol transfer modes are the same as those listed OR in the description of Process gt Image Calculator Pe The Blend mode is the same as the Image Calculator Subtract Average mode In Transparent mode white black ae pixels are transparent and all other pixels are Min copied unchanged With version 1 43 Transparent Max zero mode works with all image types SEE ALSO Image gt Overlay gt Add Image 51 IMPROVED 30 4 Clear Erases the contents of the selection to the current background color and keys are shortcuts to this command With stacks a dialog is displayed offering the option to clear the selection in all stack images Clear by pressing to avoid this dialog SEE ALSO Clear Outside Fill f Color Picker 30 5 Clear Outside Erases the area outside the current image selection to the background color SEE ALSO Clear Fill f Color Picker 30 6 Fill f Fills the current selection with the current foreground color With stacks a dialog is displayed offering the option to fill the selection in all stack images Fill the s
160. lly explicit models 3 Maintaining ImageJ Once installed updating ImageJ consists only of downloading the latest ij jar file This file is installed in the ImageJ folder on Linux and Windows or inside the ImageJ app on Mac OSX The easiest to perform this task is to use the built in command Help gt Update ImageJ Note that the installation packages may not contain the latest bug fixes so straight after a first installation it is recommended to upgrade the ij jar file Releases and Updates As mentioned the Help Update ImageJ command can be used to upgrade or down grade the ij jar file to other versions including release updates and daily builds Re lease updates are announced frequently and are labeled alphabetically e g v 1 43m Typically these releases contain several new features and bug fixes described in de tail on the top of ImageJ News page Daily builds on the other hand are labeled with numeric sub indexes e g v 1 43n4 and are often released without documenta tion Nevertheless if available release notes for daily builds can be found at http rsb info nih gov ij source release notes html When a release cycle ends v 1 41 ended with 1 410 v 1 42 with 1 42q etc an instal lation package is created downloadable from http rsb info nih gov ij download html Typically this package bundles a selected list of add ons macros tools and toolsets scripts and plugins Running Help Update
161. lor spaces Several other plugins related to color processing can be obtained from the ImageJ website Conveying Color Information AAN confocal series tif RGB People see color with significant variations ALO A confocal series tif MGB Indeed the popular phrase One picture is worth ten thousand words may not apply to certain color images specially those that do not follow the basic principles of Color Uni versal Design Citing Masataka Okabe and Key Ito from the Color Universal Design Organization CUDO in Japan Colorblind people can recognize a wide ranges of colors But certain ranges of colors are hard to distinguish The frequency of colorblindness is fairly high One in 12 Caucasian 8 one in 20 Asian 5 and one in 25 African 4 males are so called red green colorblind There are always colorblind people among the audience and readers There should be more than TEN colorblinds in a room with 250 people as suming 50 male and 50 female There is a good chance that the paper you submit may go to color blind reviewers Supposing that your paper will be reviewed by three white males which is not unlikely considering the current population in science the probability that at least one of them is colorblind is whopping 22 One practical point defined by the Color Universal Design is the use of magenta in red green overlays Magenta is the equal mixture of red and blue Colorblind people that
162. lot options 30 10 5 Arrow Tool See Arrow Tool 30 10 6 Point Tool See Point Tool 59 30 10 7 Wand Tool See Wand Tool 30 10 8 Colors BL00O Colors Foreground black Displays a dialog box that allows you to set Foreground Background white E Color Background Color and Selection Color Selection magenta Y Se A Cancel OK SEE ALSO Color Picker K Point Tool Point Tool 30 10 9 Appearance This dialog contains options that control how images are displayed an option to display better looking toolbar icons and an option to set the menu font size Appearance O Interpolate zoomed images O Open images at 100 O Black canvas O No image border O Use inverting lookup table M Antialiased tool icons Menu font size fo points Help Y Cancel OK Interpolate zoomed images Uses interpolation in stead of pixel replication when displaying zoomed images Open Images at 100 Newly open images are dis played using 100 magnification 1 image pixel 1 screen pixel y Black Canvas Causes the image canvas white by default to be rendered in black This is useful when looking at X ray images in order to avoid high contrasting intensities at the image edges No image border Displays images without the default one pixel wide black border Use inverting lookup table Causes newly opened 8 bit images to have inverted pixel values
163. mat of ImageJ cf 4 To save only a selected area create a rectangular selection and use the Image Duplicate D command Save s and File gt Save As gt Tiff are redundant commands 29 10 Save Asp Use this submenu to save the active image in TIFF GIF JPEG or raw format Can also be used to save measurement results lookup tables selections and selection XY coordinates 29 10 1 Tiff Saves the active image or stack in TIFF format in redundancy with File gt Save s TIFF is the only format other than raw that supports all ImageJ data types 8 bit 16 bit 32 bit float and RGB and the only format that saves spatial and density calibration In addition with version 1 43 selections and overlays are also saved in the TIFF header By default 16 bit and 32 bit images are saved using big endian byte order Check Save TIFF and Raw in Intel Byte Order in the Edit gt Options gt Input Output dialog box to save using little endian byte order SEE ALSO Native Formats 4 8 29 10 2 Gif Saves the active image in GIF format RGB images must first be converted to 8 bit color using using Image gt Type gt 8 bit Color The value to be used as the transparent index 0 255 can be set in the Edito Options gt Input Output dialog box Stacks are saved as animated GIFs Use Image gt Stacks gt Tools Animation Options Alt or right click on the on the play pause icon that precedes the sta
164. maximum marked C16 Output type Single Poin Maxima Within Tolerance Segmented Particles Point Selection O Exclude Edge Maxima Y Above Lower Threshold Y Light Background M Preview Point Selection Analysis is performed on the ex isting rectangular selection or on List eet A P a the entire image if no selection is 65 Maxima present Cancel OK For RGB images maxima of luminance are selected with the luminance defined as weighted or unweighted average of the colors depending on how Weighted RGB to Grayscale Conversion is set in Edit gt Options gt Conversions Noise Tolerance Maxima are ignored if they do not stand out from the surroundings by more than this value calibrated units for calibrated images In other words a threshold is set at the maximum value minus noise tolerance and the contigu ous area around the maximum above the threshold is analyzed For accepting a maximum this area must not contain any point with a value higher at than the maximum Only one maximum within this area is accepted Output Type Can be cf illustration on the next page Single Points Results in one single point per maximum Mazima Within Tolerance All points within the Noise Tolerance for each max imum Segmented Particles Assumes that each maximum belongs to a particle and segments the image by a watershed algorithm applied to the values of the image in contrast to Process
165. method for analyzing mitochondrial movement inhibi tion by paclitaxel in a pheochromocytoma cell model J Mol Neurosci 37 3 254 62 Mar 2009 S Sieuwerts F A M de Bok E Mols W M de Vos and J E T van Hylckama Vlieg A simple and fast method for determining colony forming units Lett Appl Microbiol 47 4 275 278 Jan 2008 A Sol J Mas and I Esteve A new method based on image analysis for determin ing cyanobacterial biomass by CLSM in stratified benthic sediments Ultramicroscopy 107 8 669 73 Aug 2007 D Stepensky FRETcalc plugin for calculation of FRET in non continuous intracellular compartments Biochem Biophys Res Commun 359 3 752 8 Aug 2007 S Sternberg Biomedical image processing IEEE Computer January 1983 172 92 93 94 95 96 97 98 99 100 101 J R Swedlow and K W Eliceiri Open source bioimage informatics for cell biology Trends in Cell Biology 19 11 656 60 Nov 2009 P Th venaz U E Ruttimann and M Unser A pyramid approach to subpixel registration based on intensity IEEE Trans Image Process 7 1 27 41 Jan 1998 P Th venaz and M Unser User friendly semiautomated assembly of accurate image mosaics in microscopy Microsc Res Tech 70 2 135 46 Feb 2007 Z Tian L Q Liu C Peng Z Chen and C Xu A new development of measurement of 19 Nortestosterone by combining immunochromatographic strip assay and ImageJ software
166. n upside down y mirror 31 12 3 Flip Z Reverses the order of the slices in a stack z mirror 90 IMPROVED 31 12 4 Rotate 90 Degrees Right Rotates the entire image or stack clockwise 90 31 12 5 Rotate 90 Degrees Left Rotates the entire image or stack counter clockwise 90 31 12 6 Rotate Use this dialog to rotate the ac tive image or selection clockwise the specified number of degrees LO Rotate Angle degrees 8 0 Grid Lines 3 Interpolation Bicubic M Fill with Background Color Y Enlarge Image to Fit Result Set Grid Lines to a value greater than zero to superimpose a grid on the image in Preview mode Pere Two resampling methods are Cancel possible Bilinear and Bicubic interpolation cf Image Size With 8 bit and RGB images check Fill with Background Color to fill with the back ground color instead of zero cf Color Picker K Check Enlarge to Fit Result and the image will be enlarged as needed to avoid clipping 31 12 7 Translate Vere EE Translates moves the image in the x and y directions by a specified number of pixels With stacks you can translate either the current image or all the images in the stack Two resampling methods are possible Bilinear and Bicubic interpolation cf Image Size X Offset pixels 15 0 Y Offset pixels 15 0 Interpolation None 4 M Preview Cancel Check Preview to see how the transl
167. name Title mri stack tif SA Renames the active image Cancel Cok 89 31 11 Scale E ADD Scal X Scale 1 0 Y Scale 1 0 ZScale 1 0 Width pixels 186 Height pixels 226 Depth images 27 Interpolation Bicubic 34 O Fill with Background Color Process entire stack M Create new window Title mri stack 1 tif a tae LlC mne Cancel OK SEE ALSO Image Size 31 12 Transformer Resizes the image or current area selection by scale factors entered into a dialog box As with Image Size two resampling methods are possible Bilinear and Bicubic interpolation Use integer scale factors 2 3 5 etc for the best look ing results particularly with graphics and text With scale factors less then 1 0 smoothing the source image prior to scaling may produce better looking results Scaled image selection are copied to a new image named Title if Create new window is checked If scaling a selection that will not be copied to a new image check Fill with Background Color to fill with the background color instead of zero Entire stacks or hyperstacks in the Z Dimension will be scaled if Process entire stack is checked This submenu contains commands that perform geometrical image transformation on the active image or stack 31 12 1 Flip Horizontally Replaces the image or selection with a x mirror image of the original 31 12 2 Flip Vertically Turns the image or selectio
168. nding once the volume has been rotated by Total Rotation Lower Upper Transparency Bound Determine the transparency of structures in the volume Projection calculations disregard points having values less than the 82 lower threshold or greater than the upper threshold Setting these thresholds per mits making background points those not belonging to any structure invisible By setting appropriate thresholds you can strip away layers having reasonably uni form and unique intensity values and highlight or make invisible inner structures Note that you can also use Image Adjust gt Threshold T to set the transparency bounds Opacity Can be used to reveal hidden spatial relationships specially on overlapping ob jects of different colors and dimensions The surface Opacity parameter permits the display of weighted combinations of nearest point projection with either of the other two methods often giving the observer the ability to view inner structures through translucent outer surfaces To enable this feature set Opacity to a value greater than zero and select either Mean Value or Brightest Point projection Surface Interior Depth Cueing Depth cues can contribute to the three dimensional quality of projection images by giving perspective to projected structures The depth cueing parameters determine whether projected points originating near the viewer appear brighter while points further away are dimmed linearly with dis tan
169. ndow if Suppress Log output is not checked 33 14 2 Fractal Box Count 000 Plot This command is used to estimate the fractal dimension D of a binary image D can be used as a measure of pattern complexity cell shape vascularization textures etc and is specially relevant in cases in which Euclidean measures such as diameter or length are not good descriptors of complexity o log count The command counts the number of boxes of an increasing size needed to cover a one pixel binary object boundary and implements the method described in T G Smith Jr G D Lange and W B Marks Fractal Methods and Results in Cellular Morphology J Neurosci Methods 69 1123 126 1996 p log box size Save Copy 141 A plot is generated with the log of size on the X axis and the log of count on the Y axis and the data is fitted with a straight line The slope S of the line is the negative of the fractal dimension i e D slope Size S and count C are printed to the Results table Refer to the source code for additional information SEE ALSO Fractal Dimension and Lacunarity 33 14 3 Analyze Line Graph AAA Line Graph ImageJ can be used to recover numeric coordinate bie data from scanned line graphs using the following procedure Steps 2 and 3 are not necessary for binary black and white graphs For practice use the File Open Samples Line Graph sample image 1 O
170. ne plot is created per analysis As a consequence re running this command more than once within the same analysis will cause a You must first use the Select First Lane command error message To recreate plotted profiles use the Re plot Lanes command Re plot Lanes Recreates the lane profile plots If Plot Lanes has not yet been run a The data needed to re plot the lanes is not available error message is displayed Reset Resets the analysis Label Peaks Uses the area measurements obtained with the Wand Tool to label lane peaks cf Gel Analyzer Options 139 IMPROVED Gel Analyzer Options Use this dialog to control the behavior of the Gel Analyzer Vertical Horizontal scale factor Specify the scale factor at which the lane profile plots are displayed Uncalibrated OD If checked ImageJ will convert gray values to uncalibrated optical density values using the function Unc OD log p 255 pizel value Note that images can be calibrated to e g a calibrated optical density step tablet using the Calibrate command Label With Percentages If checked the Label Peaks command will print to the Results table the peak percentage and use it to label the plot The percentage value is obtained by dividing the area of each peak by the sum of all measured peaks from all lanes Invert Peaks If checked peaks will be inverted i e bands darker than back ground will have positive peaks bands lighter than back
171. ngle The mean standard deviation etc are calculated from the values of the pixels along the line SEE ALSO The Results Table Analyze Particles Summarize Distribution Set Measure ments Batch gt Measure 125 33 2 Analyze Particles This command counts and measures ob jects in binary or thresholded images Image gt Adjust gt Threshold T Analy MC Analyze Particles Size umA2 0 Infinity sis is performed on the existing area se O Pixel Units lection or on the entire image if no selec Circularity 0 00 1 00 tion is present It works by scanning the image or se lection until it finds the edge of an ob Show Nothin Nothing Outlines M Display Results MExclude on Ed asks ject It then outlines the object using the M Clear Results Include Holes Elli ee P y pa lt p ipses Wand Tool measures it using the Mea M Add to Manager Count Manan Cancel sure m command fills it to make it invisible then resumes scanning until it reaches the end of the image or selection Press to abort this process Size Particles with size area outside the range specified in this field are ignored Values may range between 0 and Infinity For spatial scaled images cf Set Scale values are expressed in physical size square units or in pixels if Pixel Units is checked Enter a single value and particles smaller than that value will be ignored Circularity Par
172. non rectangular selections as it is being moved To move the contents of a selection rather than the selection itself Edit gt Copy c Edit gt Paste v and then click within the selection and drag Adjusting Area selections can be adjusted with the Brush Selection Tool In addition vertexes of polygon selections can be adjusted by Alt Shift clicking cf Polygon Selection Tool Nudging Selections can be nudged one pixel at a time in any direction using the arrow keys Managing A selection can be transferred from one image window to another by acti vating the destination window and using Edit gt Selection gt Restore Selection E Selections can be saved to disk using File gt Save Asp Selection and restored using File gt Open Use the ROI Manager Analyze gt Tools gt RO Manager to work with multiple selections 18 Three type of area selections Notice the cursor changes to an arrow when it is within the selection to a cross hair when outside the selection to a hand when over a selection handler Notice also the filled handler in the polygon selection and the absence of point handlers in composite selections Rectangular Polygon Composite Cursor outside selection Sti Rh Selection can be moved Ls Selection can be resized di Edge can be moved deleted or added Composite Selections Composite selections are non contiguous ROls containing more than one cluster of pixels and or cont
173. nstitute university already started one or create symbolic links to share plugins between ImageJs installed on your computer SEE ALSO Luts Macros and Tools Updater a macro toolset that performs live updating of macros listed on the ImageJ web site http rsb info nih gov ij macros Certain plugins however provide self updating mechanisms e g ObjectJ and the LOCI Bio Formats library 4 Using This Guide In this guide hypertext links to either document sections or external URLs are typed in gray e g Section Undo and Redo the ImageJ website ImageJ commands are typed in sans serif typeface with respective shortcut keys flanked by square brackets e g Image Duplicate D Shortcuts and modifier keys are ex plained in detail on page 7 Macro functions and filenames are typed in monospaced font e g resetMinAndMax StartupMacros txt Example macros and macro snippets are inserted in grayed listings e g Macro on page 17 A similar syntax highlighting can be obtained within ImageJ using J r me Mutterer s J ED plugin or Fiji s Script Editor The full list of macro listings is available on page ix Noteworthy tips tricks and reminders are placed in Noteworthy boxes cf 1 on page 7 The full list of these information notes is available on page viii Selected highlights of version 1 48 are listed on page vii and flagged with colored marginal notes These should be interpreted as NE
174. nter v Preview aS eee Cancel OK SEE ALSO Expression plugin 32 10 FFT gt The commands in this submenu support frequency domain display editing and process ing They are based on an implementation of the 2D Fast Hartley Transform FHT contributed by Arlo Reeves the author of the ImageF FT spinoff of NIH Image The frequency domain image is stored as 32 bit float FHT attached to the 8 bit image that displays the power spectrum Commands in this submenu such as Inverse FFT op erate on the 32 bit FHT not on the 8 bit power spectrum All other ImageJ commands only see the power spectrum Two FFT dedicated tutorials are available on the ImageJ website FFT Measurements and FFT Filtering 32 10 1 FFT Computes the Fourier transform and displays the power spectrum Polar coordinates of measured point selections are recorded by Analyze gt Measure m If the mouse is over an active frequency domain FFT window its location is displayed in polar coordinates The angle is expressed in degrees while the radius is expressed in pixels per cycle p c The radius is expressed in units per cycle e g mm c if the spatial scale of the image was defined using Analyzep Set Scale Bob Dougherty s 3D Fast Hartley Transform plugin performs 3D FHTs 111 32 10 2 Inverse FFT Computes the inverse Fourier transform You can filter or mask spots on the transformed frequency domain image and do an i
175. nterval 1 X location 5 Y location 20 Font size 18 Range 1 36 Text FLIM M Preview Help Cancel 0 PET stack tif 63 57 i Gone Gone xX m Save Copy X 25 Y 27 0 Plots the ROI selection mean gray value versus slice number Requires a point or area selection Coordinates of the upper left corner of the selection or the bounding rectangle for non rectangular selections are displayed in the graph title SEE ALSO Profile Plot Options Plot Profile k Adds a sequence of numbers e g timestamps and or a label to a stack Numbers and label are drawn in the current foreground color cf Image Colors gt Color Picker K The initial X Y location and Font size of the label are based on the existing rectangular selection if any Slices outside the Range are not affected Currently this com mand does not work with single time point hyperstacks Format Specifies the structure of the label 0 Un padded sequence 0000 Pads each number with leading zero s 00 00 Converts the label into a Minutes Seconds timestamp 00 00 00 Converts the label into a Hours Minutes Seconds times tamp Text Stamps only the contents of the Text field Starting value and Interval Specifiy the first value and the numeric steps to be ap plied Note that with timestamps metric time values must be used e g an Interval of 3600 will create 1 hour increments Text The string to be dr
176. nverse transform to produce an image which only contains the frequencies selected or which suppresses the frequencies selected Use Im ageJ s selection tools and fill clear commands to draw black or white areas that mask portions of the transformed image Black areas pixel value 0 cause the correspond ing frequencies to be filtered removed and white areas pixel value 255 cause the corresponding frequencies to be passed It is not however possible to both filter and pass during the same inverse transform Note that areas to be filtered in the frequency domain image must be zero filled and areas to be passed must be filled with 255 You can verify that this is the case by moving the cursor over a filled area and observing that the values displayed in the status bar are either 0 or 255 FFT Creating masks that remove or pass the low frequencies of an image et Power spectrum with mask that passes low frequencies Power spectrum with Original mask that filters low frequencies Result of inverse transform Result of inverse transform With off center selections the same spatial frequency appears twice in the power spec trum at points opposite from the center It is sufficient to fill clear only one of these FFT Cleared selections in the upper half of the power spectrum have been automatically mir rored to the lower half as shown in the power spectrum of the filtered image courtesy of Arlo Reeves Edi
177. ny measurement of OD standards Uncalibrated OD Causes ImageJ to convert gray values from 8 bit images to uncali brated optical density values using the function Unc OD log p 255 Pixel value Pixel Inverter Linear function defined by Inverted pixel Bit depth 1 Pixel value with Bit depth being 255 for 8 bit images or 65535 for 16 bit images SEE ALSO 19 Image Types and Image Formats Curve Fitting 135 33 10 Histogram h OOO Histogram of Cells Calculates and displays a histogram of the distribution of gray values in the active image or selection is a con venient shortcut for this command The X axis represents the possible gray values and the Y axis shows the number of pixels found for each Bins 256 M Use min max or 0 l ae Cao rene X Min 0 00 gray value The total pixel Count ount in O p i Mean 76 448 Max 252 X Max 255 00 is also calculated and displayed as StdDev 61 524 Mode 5 284 mano well as the Mean standard deviation a StdDev minimum Min maximum List Copy Log SRE arere Maz and modal Mode gray value 7 eee coun Cancel OK gray Use the List or Copy buttons to save the histogram data Click on Log to display a log scaled version of the histogram overlaid in gray Value Count pairs i e grayscale value corresponding to the X axis cursor position the number of pixels that have that intensity a
178. o sion dilation opening and closing are per formed Iterations can be aborted by press ing Esc Iterations 1 100 1 Count 1 8 1 M Black background O Pad edges when eroding Count Specifies the number of adjacent back ground pixels necessary before a pixel is re moved from the edge of an object during erosion and the number of adjacent fore ground pixels necessary before a pixel is added to the edge of an object during di lation Black background If checked binary images will be created without using an inverted LUT cf 18 and commands in the Process gt Binary gt submenu will assume that images contain white objects on a black background Macros can set this option using the setOption black background true macro function cf Settings and Preferences 107 IMPROVED Pad edges when eroding If checked Binary gt Erode does not erode from the edges of the image This setting also affects Binary gt Close which erodes from the edges unless this checkbox is selected EDM output Determines the output type for the Binary gt Distance Map Ultimate Points and Voronoi commands Set it to Overwrite for 8 bit output that overwrites the input image 8 bit 16 bit or 82 bit for separate output images 32 bit output has floating point subpixel distance resolution Do This drop down menu allows to test the chosen settings by previewing each binary operation Erode Dilate O
179. o not have to hold p Print 4 es r Revert A down Ctrl to use a keyboard shortcut E g to open an image press o File gt Open SEE ALSO Keyboard Shortcuts Create Shortcuts 149 CHANGE 34 2 2 Create Shortcuts ALDO Create Shortcut Command Add reference frame Shortcut fri A ib Y Cancel OK 34 2 3 Install Plugin Plugin Bleach_Correction B Menu Shortcuts h Command AntiBleach Shortcut F4 Argument 34 2 4 Remove Y Shortcuts Plugins Import Save As Filters Tools Utilities cc Assigns a keyboard shortcut to an ImageJ menu command and lists the shortcut in the Shortcuts submenu Select the command from the popup menu and enter the shortcut in the text field A shortcut can be a lower or uppercase letter or F1 through F12 Use Plugins Utilities gt List Shortcuts to get a list of shortcuts that are already being used Installs a plugin in a user specified submenu Plugins with a showAbout method are also automatically added to the Help About Plug ins gt submenu Use the first popup menu to select the plugin and the second to select the submenu it is to installed in The command must be different from any existing ImageJ command Shortcut optional must be a single letter or F1 through F12 Argument optional is the string that will passed to the plugin s run method R
180. ocation width height and aspect ratio are displayed in the status bar during drawing Modifier keys Shift t Selection is constrained to a square Alt Width height are changed with arrow keys one pixel at a time E Ctrl Selection is resized around the center Ctrl Alt Current aspect ratio is maintained while resizing SEE ALSO Round Rectangular Selection Tool Specify 5 15 28 17 2 O Round Rectangular Selection Tool NEw This tool shares the same toolbar slot and the same modifier keys with the Rectangular Selection Tool Corner arc size can be adjusted by double clicking on its icon Because its an annotation tool the round rectangle is displayed in foreground color instead of selection color cf Selections Color Picker K SEE ALSO Rectangular Selection Tool 15 I O 17 3 O Elliptical Selection Tool Location width height and aspect ratio are displayed in the status bar during drawing Modifier keys Shift T Selection becomes circular Alt Width height are changed with arrow keys one pixel at a time Ctrl Selection is resized around the center Ctrl Alt Current aspect ratio is maintained while resizing SEE ALSO Specify 5 15 17 4 la Brush Selection Tool Adjusts the shape of any area selection using a circular brush Clicking inside the area selection and dragging along its boundary will expand the boundary outwards Clicking outside the area selection and dragg
181. older the processed image will be displayed Open Imports previously written macros Save Saves the assembled macro SEE ALSO Batch Virtual Stack 32 12 4 Virtual Stack This command that shares the same interface of Batch gt Macro cf BatchProcesser java allows virtual stack manipulations E g Cropping a virtual stack can be performed by executing the following steps 120 1 Open a virtual stack 2 Run Processp Batch gt Virtual Stack 3 Select an Output folder and Output format 4 Select Crop from the Add Macro Code drop down menu 5 Edit the macro code as needed and press the Test button to verify the macro 6 Click Process to create the cropped virtual stack Note that cropped images are not loaded into memory but are saved to disk as they are cropped cf Virtual Stacks 32 13 Image Calculator Image Calculator Performs arithmetic and logical operations between two images selected from popup menus Imagel mri stack 1 tif 4 Operation Image2 mri stack 2 Subtract Image1 or both Image1 and Image2 can be Multiply ES Create New Window Divide stacks If both are stacks they must have O 32 bit float Result e the same number of slices Image1 and Im A OR age2 do not have to be the same data type E or the same size Max Average Operation Selects one of the 13 available Difference Copy operators Transparent zero C
182. on and brightness values are split horizontally The left half of the palette varies only in brightness while the right half varies only in saturation At the center of the color ramp are enlarged red green blue 79 IMPROVED The Color Picker K tool oTo eT Color Ramp Algorithm t Red H Color Selectors 4B s gt A v Yellow Foreground Color Background Color AA 255 Green Red lt gt lo 5551 Green 4 gt i gt 255 lo Black White Cyan Blue p Ramp o M DK Cancel OK Magenta NAS Foreground Color gt Foreground Background Switcher Black White Reset Background Color cyan magenta and yellow colors for quick selection To the left of the color palette is a grayscale ramp that goes from pure black to pure white Double clicking on a color brings up one of the Color Selectors shown on the right in the illustration Use the sliders to specify the RGB values of the foreground or background color To get precise colors manually change the values in the text boxes The title of the Color Selector window Foreground Color or Background Color indicates the current selection mode SEE ALSO 15 Draw d Fill f Clear Clear Outside Image Types and Image Formats 15 EMBEDDING COLOR ANNOTATIONS IN GRAYSCALE IMAGES Color marks are only available with color images or grayscale images that have been converted to RGB For non RGB images
183. on of Java Mac users must be running OS X 10 5 or later and may need to use the Java Preferences utility in Appli cations Utilities Java to select a 64 bit version of Java They may also need to switch to the ImageJ64 application Linux users need to be running 64 bit ver sions of Linux and Java The title of the Memory amp Threads dialog box changes to Memory 64 bit when ImageJ is running on a properly configured 64 bit system Parallel Threads for Stacks Defaults to the number of available processors deter mines the number of parallel threads used by commands in the Process Filters gt and the Process Math submenus when processing stacks Help Opens http rsb info nih gov ij docs menus edit htmlf memory SEE ALSO FAQ s on the ImageJ Documentation Wiki 30 10 12 Proxy Settings Proxy Settings Use this dialog to modify the proxy settings of the TAS CN Java Virtual Machine This may be required for Im i ageJ to connect to the internet in certain machines Port 8080 running behind HTTP proxies that otherwise e g wouldn t be able to open the example images File gt Open Samples submenu Settings are saved in the ImageJ preferences file IJ_ Prefs txt O Authenticate LlC ny Cancel OK 30 10 13 Compiler Compile and Run Target 158 Displays a dialog box with options for the Plugins gt O Generate debugging info javac g Compile and Run command
184. ontrast This value should be greater than zero to prevent a few outlying pixel from causing the histogram stretch to not work as intended Normalize If checked ImageJ will recalculate the pixel values of the image so the range is equal to the maximum range for the data type or 0 1 0 for float images The contrast stretch performed on the image is similar to the Auto option in the Brightness Contrast C window except that with stacks each slice in the stack is adjusted independently according to the optimal for that slice alone if Use Stack Histogram is unchecked The maximum range is 0 255 for 8 bit images and 0 65535 for 16 bit images With stacks another checkbox Normalize All n Slices is displayed If checked normalization will be applied to all slices in the stack Note that normalization of RGB images is not supported and thus this option will not be available on RGB images Equalize Histogram If checked ImageJ will enhance the image using histogram equal ization C17 Create a selection and the equalization will be based on the his togram of the selection Uses a modified algorithm that takes the square root of the histogram values Hold Att to use the standard histogram equalization algo rithm The Saturated Pixels and Normalize parameters are ignored when Equalize Histogram is checked Use Stack Histogram If checked ImageJ will use the overall stack histogram instead of individual slice histograms
185. onyms Alt Libs aenent sha Alt Option or Meta key IJ ImageJ O Application Programming Java ARchive Intertace JPEG Joint Photographic ASCII American Standard Code Experts Group for Inf ti na ONGS LUT asterrais Lookup table nterchange AVI ceciserrssves Audio Video Interleave DENY passes Sea Lempel Ziv Welch bit 2 Binary digit MIP secre 263 Maximum Intensity Projection DPD mesitas Bits per pixel Ed A MJPG asses cs Motion JPEG COD nssnmsnpriss Charge coupled device NAN ias Not a Number CP ree rihi Color Picker Oir eii Operating System CS ess Comma separated values DiC igre bg Pixels per cycle OT Computed Tomography PBM eves eeeecse Portable Bit Map CUE pac cesper gs Control key In this document also the POM isis Portable Gray Map Command key in Apple pixel Picture element keyboards PNG lamentos Portable Network DICOM Digital Imaging and Graphics Communications in Medicine PPL Bede danke Pixels per inch DPI Dots Per Inch PEM feces bh eats Portable PixMap EDM catas Euclidian Distance Map RAM Random access memory FAQ 0 eee Frequently Asked TEPER A Regular expression Questions RGB encase Red Green Blue BET goss hor esere Fast Fourier Transform ROL rd Region of interest BAD reste Fast Hartley Transform Shift Shift key FIPS muii setts Flexible Image Transport TIFF
186. or selection to a specified Width and Height in pixels Check Constrain aspect ratio and Im ageJ will adjust either the Height or the Width to maintain the original aspect ra tio When applicable other dimensions can also be resized Depth images in stacks Depth slices and Time frames in hyperstacks Two resampling methods are possible Bi linear and Bicubic interpolation The implementation of the bicubic method Catmull Rom interpolation is derived from Burger and Burge 2009 11 IMPROVED 31 2 7 Canvas Size C N Resize Image Canvas _ Width pixels Height 172 pixels mee Center Position Top Center Top Right Center Left Y Center Center Right Bottom Left Bottom Center Bottom Right O Zero Fill 31 2 8 Line Width E 4 gt 1 O Spline Fit Changes the canvas size of an image or stack without scaling the actual image Width and Height may be either expanded or contracted If the canvas size is increased the border is filled with the current background color or if Zero Fill is checked the border is filled with pixels that have a value of zero The position of the old image within the new canvas may also be specified SEE ALSO Size Color Picker K 15 This widget is opened more easily by double clicking on the line tool icon and its used to adjust the width of line selections Checking Spline Fit fits a cubic spline curve to the
187. or your operating system Detailed instructions on how to submit a bug report are found here 4 Remember that in most cases you can find answers within your own ImageJ instal lation without even connecting to the internet In the latest versions the heuristics for finding commands or writing macros have been significantly improved cf Sec tions Finding Commands and Extending ImageJ 5 As with any other mailing list you should always follow basic netiquette namely a USE DESCRIPTIVE SUBJECT LINES Re Problem with Image gt Set Scale com mand is much more effective than a general Re Problem b STAY ON TOPIC Do not post off topic messages unrelated to the message thread c BE CAREFUL WHEN SENDING ATTACHMENTS Refrain from attaching large files Use e g a file hosting service instead d EDIT REPLIES You should include only the minimum content that is nec essary to provide a logical flow from the question to the answer i e quote only as much as is absolutely necessary and relevant Part II Working with ImageJ For a detailed description of all ImageJ menus and toolbar buttons most are self explanatory have a look at Parts III on page 27 and IV on page 37 6 Shortcuts and Modifier Keys There are three modifier keys in ImageJ Control Command Key on Apple keyboards Denoted by Ctrl or in this document Although a control key is typically present on Apple keyboards on a Macintosh computer
188. ot the image with the background subtracted but rather the background itself This option is useful for examining the background created in conjunction with the Preview option Create Background can be also used for custom background subtraction algorithms where the image is duplicated and filtered e g removing holes in the background before creating the background and finally subtracting it with Process gt Image Cal culator Sliding Paraboloid If checked the rolling ball is replaced by a paraboloid that has the same curvature at the apex as a ball of that radius This option allows any value of the radius gt 0 0001 The rolling ball algorithm requires a radius of at least 1 The sliding paraboloid typically produces more reliable corrections since the rolling ball a legacy algorithm is prone to edge artifacts E g to reduce the computing time the rolling ball algorithm downscales the image in a way that is not really consistent The sliding paraboloid algorithm does not use downscaling and thus produces no downscaling artifacts Nevertheless the sliding paraboloid is also an approximation since it does not really use a paraboloid an exact imple mentation would require a great computing effort but it rather slides parabolae in different directions over the image 123 Disable Smoothing For calculating the background rolling the ball images are maximum filtered 3x3 pix
189. page can also be opened using the Help Installation command Other software packages based on ImageJ Fiji Fiji Fiji Is Just ImageJ was presented publicly for the first time on the ImageJ User and Developer Conference in November 2008 Fiji tar gets image registration stitching segmentation feature extraction and 3D visualization among others It also supports many scripting languages BeanScript Clojure Jython Python Ruby For users Fiji is easy to install and update bundles a set of plugins in a coherent menu structure bundles a Java runtime and Java3D and has a lot of comprehensive doc umentation For developers Fiji has these benefits it comes with the complete source it is properly version controlled it bundles many useful libraries and it has a comprehensive build system pManager Manager is a software package for control of automated microscopes It lets you execute common microscope image acquisition strategies such as time lapses multi channel imaging z stacks and combinations thereof uManager works with microscopes from all four major manufacturers most scientific grade cameras and many peripherals used in microscope imaging SalsaJ SalsaJ is a software dedicated to image handling and analysis in the class room It is particularly adapted to professional astronomy images Bio Bio7 is an integrated development environment for ecological modelling with a main focus on individual based modelling and spatia
190. paint the mark Mark Width diameter at the location of each point Auto Next Slice If checked ImageJ will automatically advance to the next stack slice Note that this feature will only allow one point per slice Add to ROI Manager If checked points will be automatically added to the RO Man ager Label Points If checked each point selection will be displayed with an accompanying numeric label Selection Color Specifies the selection color chosen from one of the nine ImageJ de fault colors Red Green Blue Magenta Cyan Yellow Orange Black and White Note that the selection color is highlighted in the center of the Point MultiPoint Tool cf Selections SEE ALSO Multi point Tool 33 22 E Multi point Tool The Multi point Tool selects multiple points behaving as the Point Tool when Shift is pressed Label Points is checked and Auto Measure and Auto Next Slice are deselected As described for the Point Tool Att can also be used to remove points Similarly when using Edit gt Draw d marks are painted with the diameter of Mark Width Double clicking on the tool icon runs the Image Overlay gt Add Selection b command SEE ALSO Point Tool 23 A Text Tool Use this tool to add text to images It creates a rectangular selection containing one or more lines of text Use the keyboard to add characters to the text and the backspace key to delete characters Use Image Overlay gt Add Selection b to
191. ped vertically Rotate 90 Degrees If checked each slice in the output stack will be rotated 90 Avoid interpolation If checked no interpolation will be done SEE ALSO Dynamic Reslice and Radial Reslice plugins 80 31 6 10 Orthogonal Views O_O t1 head tif A A yz 109 Provides an orthogonal view display of the x pixels 16 x pixels 16 current stack or hyperstack C12 E g if a stack displays sagittal sections coronal YZ projection image and transverse XZ pro jection image will be displayed through the data set The two extra planar views are displayed in sticky panels next to original image The intersection point of the three views follow the location of the mouse click with its XY coordinates being displayed in the title of projection panels Voxel dimensions can be adjusted in Image gt Properties P SEE ALSO 3D Project and 3D Viewer Vol ume Viewer Stack Slicer Dis play3_ TP plugins 31 6 11 Z Project ODO ZProjection Projects an image stack along the axis per Start slice 1 pendicular to image plane the so called z Stop slice 27 axis C11 Five different projection types are supported eae Intensity Max Intensity K n A Canc Min Intensity Projection Type Average Intensity projection outputs an image wherein each pixel stores aver Sum Slices orale RE age intensity over all images in stack
192. pen Close on the active image This option is only available when the active image is binary 32 9 Math gt The commands in this submenu add subtract multiply etc a constant to each pixel in the active image or selection A Preview option is available for most operations LO esrrocessistacia With stacks the dialog depicted on the left is dis j played Choose Yes to process entire stack or No Process all 27 images There is 5 5 5 no Undo if you select Yes to process only the active slice The dialog is not dis 3 a played if Hide Process Stack dialog is checked in No Cancel Yes A eree Edit gt Options Misc SEE ALSO Memory amp Threads 32 9 1 Add Adds a constant to the image or selection With 8 bit images results greater than 255 are set to 255 With 16 bit signed images results greater than 65 535 are set to 65 535 32 9 2 Subtract Subtracts a constant from the image or selection With 8 bit and 16 bit images results less than 0 are set to 0 32 9 3 Multiply Multiplies the image or selection by the specified real constant With 8 bit images results greater than 255 are set to 255 With 16 bit signed images results greater than 65 535 are set to 65 535 108 IMPROVED 32 9 4 Divide Divides the image or selection by the specified real constant Except for 32 bit float images attempts to divide by zero are ignored With 32 bit ima
193. pen the image containing the graph Y pixels 2 Open the Threshold T tool Shift ff MT Adjust the threshold so the graph is highlighted in red 0 X pixels 132 3 Click on Apply make sure foreground is black Save Copy and background is white 4 Use the Elliptical Selection Tool as an erasor press to erase to isolate a single curve NB background color must be white cf Color Picker K 5 Select the curve by clicking to the left of it with the Wand Tool 6 Use Edit gt Clear Outside to erase everything but the curve 7 Use Analyze Toolsp Analyze Line Graph to get the XY coordinates 33 14 4 Curve Fitting ImageJ s curve fitter provides a very simple tool for fitting various functions to X and Y data The typical usage of this command is listed below 1 Tabular data is entered or copied in the input window or alternatively a two column text file is opened by clicking on the Open button Values may be separated by spaces tabs commas or semicolons 2 The function to be fit is selected from the drop down menu 14 built in functions are available User defined functions are also possible by choosing User defined In this case Formula and Fitting Options must be specified by the user 142 Analyze gt Tools gt Curve Fitting DA Curve Fitter User defined Fit Open Apply M Show settings 0 00 0 0 Straight Line 1 00 0 9 2nd Degr
194. played not the actual FHT data Therefore editing an image with swapped quadrants for filtering or masking may lead to undesired results 32 11 Filters gt This submenu contains miscellaneous filters including those installed by the Plugins gt Utilities gt Install Plugin command More information on image filters can be obtained by looking up related keywords con volution Gaussian median mean erode dilate unsharp etc on the Hypermedia Image Processing Reference index SEE ALSO Memory amp Threads 115 32 11 1 Convolve OO Convolver Does spatial convolution using a kernel entered into a text area 0 0 0 1 1 1 o 0 o 1 a a 3 3 a 1 0 A kernel is a matrix whose center corresponds o a 3 3 a a 3 a 0 f 133 618 633 41 to the source pixel and the other elements cor a 3 1 13 24 133 1 3 4 ats r n neighboring pixels Th tination Htt eha ear espond to eighboring p els e destinatio o a 3 3 1 3 3 1 0 pixel is calculated by multiplying each source o 1 a 3 3 3 a a 0 i f ol ol ol alala o o pixel by its corresponding kernel coefficient and adding the results If needed the input image is effectively extended by duplicating edge pixels outward There is no arbitrary limit to the size of the kernel but it must be square and have an odd width 4 gt y Open Save Sa eee Mi Normalize Kernel M Preview Rows in the text area mu
195. pression 12 46 LUT 15 43 48 96 LZW compression 11 M Macro functions 23 157 Macro recorder 148 Macro Tools 36 Macro Toolset Switcher Macros 22 24 111 120 148 Install 148 Magenta Green Blue MGB 16 Magnifying Glass Tool 34 Mailing lists see Help resources 5 Mask 55 102 104 118 Math 108 Max 109 MaxEntropy see Threshold 69 Maxima 98 MBF ImageJ 3 4 15 Measure 118 125 Measurements 130 Median cut algorithm see Color quantization 65 Memory 28 61 152 Metadata 12 72 pManager 2 Min 109 MinError see Threshold 69 Minima 99 MIP see Projection 81 MJPG 11 Modifier Keys 7 159 Modifier keys 159 Moments see Threshold 69 Montage see Stacks Montage 79 Multiply see Math 108 Multiply images see Image calculator 121 Multi point tool 34 wo al N NaN 110 Noise 97 98 101 116 123 Non background pixels 141 O Optical density see Calibration Optical density 134 Options see Settings 21 57 177 Orthogonal views 81 Otsu see Threshold 69 Outliers 102 Outline 105 Overlay 93 P PackBits compression 11 Panel figures see Stacks Montage 79 Paste 51 Perimeter 131 PGM 11 Pixel size 73 Planar views see Orthogonal views 81 Plot profile 59 84 137 Plugins 3 22 26 157 PNG 11 48 Point tool 33 Polar coordinates 111 Polygon selection 30 Power spectrum 113 PPI 49 Precision 133 Preferences see Settin
196. pt j Runs JavaScript code in the editor window Note that Run Macro runs JavaScript code if the title of the file ends with js Debug gt This menu contains seven commands related to the macro debugging You can debug a macro using the commands in the Debug menu You start a debugging 23 session initiating Debug Macro You can then single step through the macro code by repeatedly running Step Debug Macro d Starts running the macro in debug mode and opens the Debug window which initially displays the memory usage number of open images and the active image s title The macro stops running at the first exe cutable line of code which is highlighted Use one of the following commands to continue execution Step e Executes the highlighted statement and advances to the next The variable names and values in the Debug window are updated Trace t Runs the macro displaying variable names and values in the Debug window as they are encountered Fast Trace T Ctrl Shift A T Same as above but faster Run Runs the macro to completion at normal speed similarly to Macros Run Macro Run to Insertion Point Runs the macro to a statement that was previously defined by clicking the mouse on an executable line of code Abort Exits debug mode Macros A macro is a simple program that automates a series of ImageJ commands The easiest way to create a macro is to record a sequence of commands us
197. r SEE ALSO Stacks Tools Montage to Stack command RC Montage plugin Magic Montage a macro toolset to reorder and manipulate images in the montage a video tutorial can be found here 79 31 6 9 Reslice CIO Reslice l C11 Reconstructs one or more orthogonal slices through the image volume represented by the cur rent stack or hyperstack Slice Spacing um 3 00 Start At Top A dialog allows you to specify the spacing of the re constructed slices The estimated size of the output stack and the amount of available memory are dis played at the bottom of the dialog O Flip Vertically O Rotate 90 Degrees O Avoid Interpolation use 1 0 for spacings Voxel Size 3x3x3 um Output Size 1MB 3174MB free Cancel Increase Slice Spacing to reduce the size of the out put stack Slice Spacing Determines the number of orthogonal slices that will be reconstructed Increasing Slice Spacing reduces the size of the output stack Slice Spacing is replaced by Slice Count if there is a line selection With lines selections a stack is created by shifting by Slice Spacing the line down and to the left to generate additional slices for the output stack In this case the size of the output stack in determined by Slice Count Start At Determines the image edge top bottom left or right from which reconstruc tion starts Flip Vertically If checked each slice in the output stack will be flip
198. r instead of the native OS file open and save dialogs The main advantage of JFileChooser is the ability to open multiple files by shift clicking to select multiple contiguous files and control clicking to select more than one individual file On the other hand it is slower uses more memory and does not behave like the file open and save dialogs used in other applications Save TIFF and Raw in Intel Byte Order Specifies the byte order used when sav ing 16 bit and 32 bit images using File Save Asp Raw Data or File Save Asp Image Sequence when Raw is chosen as the format Check this option to export images using the order used by Intel x86 based processors little endian This Wikipedia article has more information Copy Column Headers Row Numbers Specifies if Column Headers Row Numbers should be copied from ImageJ tables such as the Results and Summarize windows cf The Results Table 30 10 3 Fonts Opens a small window with three pop up menus for specifying the type face size and style of the font used by the Text Tool AOO Fonts SansSerif 3 M Smooth 58 IMPROVED 30 10 4 Profile Plot Options Use this dialog to control how plots generated by ImageJ are displayed e g Image gt Stacksp Plot Z axis Profile Analyze gt Plot Profile k Analyze gt Calibrate Analyze gt Tools gt Curve Fitting etc Profile Plot Options Width pixels 350 Height pixels
199. r than 255 are labelled as 255 105 32 8 11 Ultimate Points Generates the ultimate eroded points UEPs of the EDM Requires a binary image as input The UEPs represent the centers of particles that would be separated by segmentation The UEP s gray value is equal to the radius of the inscribed circle of the corresponding particle The output type Overwrite 8 bit 16 bit or 32 bit of this command can be set in the Process gt Binary Options dialog box SEE ALSO Binary Options 32 8 12 Watershed Watershed segmentation is a way of automatically separating or cutting apart particles that touch It first calculates the Euclidian distance map EDM and finds the ultimate eroded points UEPs It then dilates each of the UEPs the peaks or local maxima of the EDM as far as possible either until the edge of the particle is reached or the edge of the region of another growing UEP Watershed segmentation works best for smooth convex objects that don t overlap too much Enable debugging in Edit gt Options gt Misc and the Watershed command will create an animation that shows how the watershed algorithm works cf online example Original Segmentation Movie Watershed in Debug mode Watershed result amp Y tl we gt Y 4 _ v w er pa AS amp gt a y SEE ALSO Find Maxima 32 8 13 Voronoi Splits the image by lines of points having equal distance to the bord
200. re displayed on the bottom right while mousing over the histogram window With RGB images the histogram is calculated by converting each pixel to grayscale using the formula gray red green blue 3 or gray 0 299 xred 0 587 x green 0 114xblue if Weighted RGB Conversions is checked in Edit gt Options Conversions With 16 bit images the range of gray values between the Min and Maz values is divided into 256 bins With 32 bit images the number of bins is specified in the depicted dialog box With any image type this dialog can be called with or O Histogram by holding while clicking on Histogram h 255 Bins Specifies the number of bins M Use min max or X Min 0 00 Use min max If checked the X axis range is determined by X Max 255 00 the minimum and maximum values in the image or selec O tion If unchecked X Min and X Maz values can be or ax ma specified to fix the X axis range Cancel Y Maz Fixes the Y axis range Type type Auto to have the range determined by the largest bin count The getHistogram and Plot getValues macro functions can be used to get the 2This shortcut is not listed on Mac OS X because it conflicts with the system wide shortcut for the Hide command It is shown on Windows and Linux and the shortcut without holding down Cmd does work on OS X 136 value and Count data displayed when you click the List button cf MACRO 5 MACRO 5 Obtaining Histogram
201. reate New Window If checked a new image or stack will be created to hold the result Otherwise the result of the operation replaces some or all of Image1 32 bit float Result If checked the source images will be converted to 32 bit floating point before the specified operation is performed With 32 bit float images pixels resulting from division by zero are set to Infinity or to NaN Not a Number if a zero pixel is divided by zero The divide by zero value can be redefined in Edit Options Misc 121 Image Calculator operations On these examples source and destination images 8 bit grayscale are displayed with inverted LUTs White 0 Black 255 cf Lookup Tables sub menu Note that calculations between images can also be performed using Copy amp Paste and the Edit gt Paste Control command Source image imgl Destination image img2 Operator at Result Operator Result Add imgl imgl img2 Subtract imgl imgl img2 Multiply imgl imgl x img2 Divide imgl imgl img2 AND imgl imgl1 Aimg2 OR imgl imgl V img2 XOR imgl imgl img2 ole ll DSI 122 Min imgl min imgl img2 Max imgl max imgl img2 Average imgl imgl im92 2 Difference imgl limgl img2 Copy imgl img2 Transparent zero e 32 14 Subtract Background Subtract Background Rolling Ball Radius 50 0 Pixels
202. rtcuts Avi Alt key Modifications cc ati rica il eit A ee A 2 Shift Key Modifications aooaa ee A 3 Ctrl Key or Cmd Key on Macs Modifications o o o 125 125 126 128 128 129 129 130 133 134 136 137 137 139 141 148 148 149 151 153 154 155 155 155 155 155 156 156 156 156 156 156 156 156 157 157 157 157 157 157 158 159 161 162 162 A 4 Space Bar Modifications lt m mai 2a aa ee ee a ee 162 ADT ATOW REYS E teeter ad ee Oe A oR eh es a 162 A 6 Keyboard Shortcuts for ImageJ Tools o CRER E ES 163 B Credits 165 C ImageJ Related Publications 167 D List of Abbreviations and Acronyms 174 About this Guide 175 Index 176 vi New Features Implemented in 1 43 Improved dimension sliders in stacks and hyperstacks 13 TIFF virtual stacks can be opened by drag and drop 2 44 14 Round rectangular selection tool y 2 422 4 643 ew A EY he 29 Improved constrained shift key down elliptical selection tool 29 4 8 Conmected wand tool s 2 23 Ak oe bok eee ER ORES ESE SE Oe 30 Arrow tool sane dag A wont oe oS Bote pe AAA ee 32 Multizpoint tool ti Hoek Ah Pel ee ai osteo Zan a 34 Improved ColorPicker n 2 ee Aes Be BS ee SA ee Be SSS 35 Improved Drag amp Drop Support ne pee Be a ke Hae ee A ee eae a 38 Files Close All command eii a eee ee a es 45 Selections and overlays are saved in the TIFF head
203. rted Weighted RGB Conversions 0 30 0 59 0 11 When checked the formula gray 0 299 x red 0 587 x green 0 114 x blue is used to convert RGB images to grayscale If it is not checked the formula gray red green blue 3 is used The default weighting factors 0 299 0 587 0 114 which are based on human perception are the ones used to convert from RGB to YUV the color encoding system used for analog television The weighting factors can be modified using the setRGBWeights macro function 30 10 11 Memory amp Threads Use this dialog to specify the maximum amount of memory available to ImageJ and to specify the number of threads used by filters when processing stacks gt Memory 64 bit Maximum Memory MB Parallel Threads for Stacks 2 N Java applications such as ImageJ will only use the memory allocated to them but this dialog allows the Help Y Cancel OK user to allocate more than the default typically 640 MB Note that specifying more than 75 of real RAM could result in virtual RAM being used which may cause ImageJ to become slow and unstable Also note that this dialog cannot be used to set the memory allocation if ImageJ is run from the command line or by double clicking on ij jar 61 Maximum Memory 64 bit OS and a 64 bit version of Java are required to use more than 1700 MB of memory Windows users must be running a 64 bit version of Windows and must install a 64 bit versi
204. ructures as in the input image This is equivalent to adding a high pass filtered image and thus sharpens the im age O Preview f a ae 117 Radius The standard deviation o blur radius cf Gaussian Blur of the Gaussian blur that is subtracted Increasing the Gaussian blur radius will increase contrast Mask Weight Determines the strength of filtering whereby MaskWeight 1 would be an infinite weight of the high pass filtered image that is added Increasing the Mask Weight value will provide additional edge enhancement 32 11 8 Variance Highlights edges in the image by replacing each pixel with the neighborhood variance 32 11 9 Show Circular Masks Generates a stack containing examples of the circular masks used by the Median Mean Minimum Maximum and Variance filters for various neighborhood sizes 32 12 Batch This submenu allows the execution of commands in a series of images without manual intervention Batch gt commands are non recursive i e they are applied to all the images of the chosen Input folder but not its subfolders Nevertheless a directory hierarchy can be transversed using ImageJ macro language cf BatchProcessFolders macro Three critical aspects to keep in mind when performing batch operations that modify processed images Files can be easily overwritten since the batch processor will silently override ex isting files with the same name The destina
205. running ImageJ the Command key replaces the functionality of the control key of other operating systems For sake of simplification Ctrl will always refer to both throughout this document Shift Denoted by Shift or Shift in this document Alt Denoted by Alt or in this document This is also the Option or Meta key on many keyboards You ll learn more and more shortcut keys as you use ImageJ because almost all short cuts are listed throughout ImageJ menus Similarly in this this guide each command has its shortcut key listed on its name flanked by square brackets Please note that the notation for these key bindings is case sensitive i e shift modifiers are not explic itly mentioned a capital A means Shift A and assumes that Require control key for shortcuts in Edit gt Options Misc is unchecked i e except when using the text editor page 22 you won t have to hold down the Control key to use menu shortcuts For example the command Edit Invert I can be evoked by Shift ft 1 or Ctrl Shift 1 if Require control key for shortcuts is checked The full list of ImageJ shortcuts can be retrieved at any time using the Plugins Utilities gt List Shortcuts command This list is also available on page 159 1 FRONTMOST WINDOW AND WINDOWS ACTIVATION In ImageJ all operations are performed on the active frontmost image which has its title bar highlighted If a window
206. ry Options 32 8 4 Dilate Adds pixels to the edges of black objects Use Filters gt Maximum to perform grayscale dilation SEE ALSO Binary Options 104 32 8 5 Open Performs an erosion operation followed by dilation This smoothes objects and removes isolated pixels SEE ALSO Binary Options 32 8 6 Close Performs a dilation operation followed by erosion This smoothes objects and fills in small holes The command has a tailing hyphen to differentiate it from File Close w SEE ALSO Binary Options 32 8 7 Outline Generates a one pixel wide outline of foreground objects in a binary image The line is drawn inside the object i e on previous foreground pixels 32 8 8 Fill Holes This command fills holes 4 connected background elements in objects by filling the background C20 32 8 9 Skeletonize Repeatably removes pixels from the edges of objects in a binary image until they are reduced to single pixel wide skeletons topological skeletons SEE ALSO Skeletonize3D plugin 32 8 10 Distance Map Generates a Euclidian distance map EDM Each foreground pixel in the binary image is replaced with a gray value equal to that pixel s distance from the nearest background pixel The output type Overwrite 8 bit 16 bit or 32 bit of this command can be set in the Process gt Binary Options dialog box Note that when selecting Overwrite or 8 bit output distances large
207. s when smoothing with very high blur radius the output will be dominated by the edge pixels and especially the corner pixels in the extreme case with a blur radius of e g 107 the image will be replaced by the average of the four corner pixels 116 For increased speed except for small blur radii the lines rows or columns of the image are downscaled before convolution and upscaled to their original length thereafter SEE ALSO Accurate Gaussian Blur plugin AnimatedGaussianBlur macro 32 11 3 Median Reduces noise in the active image by replacing each pixel with the median of the neigh boring pixel values 32 11 4 Mean Smooths the current image by replacing each pixel with the neighborhood mean 32 11 5 Minimum This filter does grayscale erosion by replacing each pixel in the image with the smallest pixel value in that pixel s neighborhood SEE ALSO Binary gt Erode 32 11 6 Maximum This filter does grayscale dilation by replacing each pixel in the image with the largest pixel value in that pixel s neighborhood SEE ALSO BinarybDilate 32 11 7 Unsharp Mask Sharpens and enhances edges by subtracting a blurred version of the image the unsharp mask from the original Unsharp Mask Radius Sigma 1 0 pixels Mask Weight 0 1 0 9 0 60 Unsharp masking subtracts a blurred copy of the image and rescales the image to obtain the same contrast of large low frequency st
208. s blobs gif Open Samples Blobs 25K B Sample images can be downloaded from http rsb info nih gov ij images or in bulk from http rsb info nih gov ij download sample images zip The AutoRun macro in the StartupMacros txt file can be used to change the default path of sample images allowing a complete off line usage of the File Open Samples submenu cf MACRO 4 MACRO 4 Setting File gt Open Samples for off line usage 1 This macro calls the Prefs setImageURL method to change the 2 default location of IJ s Sample Images http rsb info nih gov 3 ij images to a subfolder of IJ s directory named samples 4 Note that Fiji provides this feature by default 6 macro AutoRun 7 fldr getDirectory imagej samples 8 path replace fldr 20 9 call vuig Prers set lmagesUR Ils ep ata ADE 1 39 29 5 Open Recent gt The submenu shows a list of the 15 recently opened files Click on a filename to open it 29 6 Import gt This submenu lists the installed image reader plugins SEE ALSO Non native Formats Acquisition plugins Input Output plugins VirtualStackFrom List macro 7 29 6 1 Image Sequence Sequence Options Number of Images 28 Starting Image 1 Increment 1 Scale Images 100 File Name Contains or Enter Pattern png O Convert to 8 bit Grayscale O Convert to RGB M Sort Names Numerically O Use Virtual Stack 198 x 2
209. s 1 4 grayscale images or stacks into an RGB image or stack Select None to keep a channel empty filled with 0 Check Create Composite to convert 2 4 grayscale images or stacks into a composite image or hyperstack Check Keep Source Images if you wish to keep the originals SEE ALSO Channels Z 31 5 3 Channels Tool Z Alias for Image Hyperstacks gt Channels Z 31 5 4 Stack to RGB Converts a two or three slice stack into an RGB image assuming that the slices are in R G B order The stack must be 8 bit or 16 bit grayscale Also converts composite images e g the HeLa Cells sample image File Open Samples into RGB 31 5 5 Make Composite Converts an RGB image a 2 7 image stack or a 2 7 channel hyperstack into a composite color image Use Composite the Channels Z tool Shift to enable and disable the channels of a composite image Use Bright Grayscale ness Contrast C Shift C to adjust the brightness and contrast of the current channel ALO Make Composite Display Mode SEE ALSO Channels Z 74 31 5 6 Show LUT Displays a plot of the active image s lookup ta A e o ble LUT The lookup table or color table 255 describes the color that is displayed for each of the 256 possible pixel values For 16 and 32 bit images the range of displayed pixel values is mapped to 0 255 A bar under the plot dis plays the color representation of the
210. selection by the specified number of de Angle 15 dearend grees negative number indicate cone clockwise rota tion This command runs the RotateSelection macro in Enter negative angle to rotate counter clockwise Cancel OK ij jar SEE ALSO FlipSelection macro 59 30 9 12 Enlarge Enlarge Selection Enlarge by fis pixels Enter negative number to shrink a Cancel OK Grows an area selection by a specified number of pix els Enter a negative value to shrink the selection This command runs the EnlargeSelection macro in ij jar ShrinkSelection is a variation of this macro that does not shrink from the image edges SEE ALSO EnlargeSelection and ShrinkSelection macros 12 CONVERTING COMPOSITE SELECTIONS Enter zero in the Edito Selection gt Enlarge dialog box to convert a composite selection into a polygon selection 30 9 13 Make Band Make Band Band Size fis pixels AAA Cancel OK 30 9 14 Specify OLO Specify Width 119 Height 9 X Coordinate 1124 Y Coordinate 96 O Oval O Centered Cancel 30 9 15 Straighten Takes an area selection and creates a band with a thickness of the specified number of pixels If you imagine the band as a doughnut shape then the original selection corresponds to the hole i e the band is made by growing out the original selection This command runs the
211. ssigning the numeric keys 1 4 to the first four Area selection tools The macro Refine selection activates temporarily the brush selection tool when is pressed Once the mouse is released the previously selected tool is restored Macro 6 Assigning Keyboard Shortcuts to ImageJ Tools This set of macros exemplify how to use the setTool function to assign hotkeys to ImageJ tools Append this file to the Startup Macros and ImageJ will automatically install them at start up macro Rectangle 1 setTool rectangle macro Ellipse 2 setTool elliptical 0 0 JD NM F WN HB macro Polygon 3 setTool polygon 11 macro Freehand 4 setTool freehand 13 macro Refine Area Selection 5 14 if nImages 0 4 15 tool IJ getToolName 16 setTool brush 17 while true 18 getCursorLoc x y z flags 19 if flags amp 16 0 setTool tool exit 20 21 22 BP This approach however requires the user to memorize as many shortcuts as the number of tools in the toolbar In addition it may be difficult to assign so many hotkeys without conflicting with previously defined ones cf List Shortcuts Probably a more efficient way to control the toolbar using the keyboard is to create macros that can cycle through all the tools in the ImageJ toolbar The example on the next page demonstrates such an approach It is composed of two macros activated by and that iterate thro
212. st Fourier transform 111 Fast Hartley Transform 111 Feret 131 Fiji 2 4 17 25 39 Filters 113 115 117 118 Find see Search 8 Fit Cubic spline 54 56 Curve 142 Ellipse 54 130 131 FITS 11 Flatten 95 Fractal box count 141 Frame interval 73 Freehand area selection 30 Freehand line selection 32 Frequency domain 111 G Gamma correction 109 Gaussian Blur 116 1 D Gel analysis 139 GIF 45 Global calibration see Calibration 133 Graph see also Plot profile 59 137 142 Grayscale morphology 104 H HandleExtraFileTypes 40 Heckbert s median cut algorithm see Color quantization 65 Help resources 4 5 156 Hexadecimal Hex colors 93 94 Histogram 136 Histogram measurements 128 Holes 105 127 Hot pixels 102 HSB 15 70 Huang see Threshold 69 Hyperstacks 87 I Image calculator 121 Image formats Native 10 Non native 12 Image sequence 40 47 Image types 10 15 65 ImageJ for Microscopy see MBF ImageJ 3 Import 40 Installation 157 Integrated density 132 Interpolation 71 IsoData see Threshold 69 J Java 2 22 26 58 61 62 151 JavaScript 22 25 JFileChooser 58 JPEG 11 14 46 JPEG2000 12 k Kurtosis 132 L Lanes see 1 D Gel analysis 139 Layers see Image overlays 94 Levels see Brightness amp Contrast 66 68 Li see Threshold 69 LOCI Bio Formats 3 12 Log 110 Lossless compression see LZW and PackBits 11 Lossy com
213. st all have the same number of coefficients the rows must be terminated with a carriage return and the coefficients must be separated by one or more spaces Kernels can be pasted into the text area using Cer Vv Checking Normalize Kernel causes each coefficient to be divided by the sum of the coefficients preserving image brightness The kernel shown is a 9x9 Mexican hat which does both smoothing and edge detection in one operation Note that kernels can be saved as a text file by clicking on the Save button displayed as an image using File gt Importp gt Text Image scaled to a reasonable size using Image gt Adjust gt Size and plotted using Analyze gt Surface Plot SEE ALSO ConvolutionDemo macro 32 11 2 Gaussian Blur Gaussian Blur This filter uses convolution with a Gaussian function for a smoothing C21 Sigma Radius 2 00 Sigma is the radius of decay to e709 61 i e the standard deviation of the Gaussian this is the same as in Adobe Photoshop but different from ImageJ versions till 1 38q in which radius was 2 5xo cf GaussianBlur java O Scaled Units um M Preview Cancel Like all ImageJ convolution operations it assumes that out of image pixels have a value equal to the nearest edge pixel This gives higher weight to edge pixels than pixels inside the image and higher weight to corner pixels than non corner pixels at the edge Thu
214. stt gt Threshold T tool the depicted dia log is displayed The value of the Black fore ground white background checkbox reflects and sets the global Black Background value of Pro cess gt Binary gt Options Y Thresholded pixels to foreground color Y Remaining pixels to background color M Black foreground white background a e TAT Cancel OK If a threshold has not been set Make Binary will analyse the histogram of the current selection or of the entire image if there is no selection is present and set an automatic threshold level to create the binary image Auto thresholding is displayed in the Status bar cf Threshold T With stacks the Convert to Mask dialog box is displayed Note that for non thresholded images and stacks Make Binary and Convert to Mask behave similarly SEE ALSO Convert to Mask Edit gt Selection gt Convert to Mask 18 32 8 2 Convert to Mask Converts an image to black and white er Convert to Mask The mask will have an inverting LUT white is 0 and black is 255 unless Black Background is checked in the Process Binary gt Options dialog box If a threshold has not been set automatic threshold lev els will be calculated cf Make Binary Note that for non thresholded images and stacks Make Binary and Convert to Mask behave similarly With stacks the depicted dialog is displayed Convert all images in stack to binary M Calculate Threshold
215. supported With Hyperstacks the default reduction is performed in the T Dimension but a choice is available to Reduce in Z Dimension instead SEE ALSO Hyperstacks Reduce Dimensionality 85 CHANGE 31 6 15 4 Reverse Alias for the Image Transform gt Flip Z command 31 6 15 5 Insert Ow Stack Inserter i ooo Inserts an image or stack into a stack ource image or Stack 34 at the specified X and Y Location The Destination Stack mri stack tif Source Image or Stack must be of the X Location 0 same type as the Destination Stack Y Location 0 SEE ALSO Stacksp Label Cancel 31 6 15 6 Montage to Stack Stack Maker Converts a montage image to an image stack based on the specified number of rows and columns This is the oppo site of what the Image Stacks gt Make Montage command does Images Per Row 2 Images Per Column 2 Cancel SEE ALSO Stacksp gt Make Montage Demontager plugin 31 6 15 7 Start Animation Animates the active stack by repeatedly displaying its slices frames in sequence Use Stop Animation Y or click with the mouse to stop The frame rate is displayed in the status bar Open the Animation Options Alt dialog box to specify the animation speed More than one stack can be animated at a time Modifier keys Pressing while holding down Alt opens the Animation Options dia log 31 6 15 8 Stop Animation
216. t need to hold down the control key to use a keyboard shortcut Note that this listing was obtained from http rsb info nih gov ij docs shortcuts html A similar list can be obtained at any time using the Plugins gt Shortcuts gt List Shortcuts command SEE ALSO Shortcuts and Modifier Keys Finding Commands Macro Tools Command New Image Newb Text Window Shortcut m Description Create new image or stack Create new text window New System Clipboard Shift 11 M Create image from system clipboard Open TO Open TIFF GIF JPEG BMP DICOM FITS etc Open Next Shift 7 o Open next image in folder Open Samples gt Shift 1 B Opens Blobs example image Close W Close the active window Save Ss Save active image in Tiff format Revert R Revert to saved version of image Print P Print active image Undo z Undo last operation Cut X Copy selection to internal clipboard and clear Copy Tc Copy selection to internal clipboard Paste VJ Paste contents of internal clipboard Clear E Erase selection to background color Fill TF Fill selection in foreground color Draw D Draw selection Invert Shift 7 1 Invert image or selection Selection gt Select All A Select entire image Selection gt Select None Shift A Remove selection Selection gt Restore Shift T ia Restore previous selection Selection gt Add to Manager IT _ Add selection to ROI Manager A
217. t efficient method There can be significant advantages in processing colors stored in other formats such as HSB Hue Saturation Brightness In the HSB color space Hue describes the attribute of pure color and therefore dis tinguishes between colors Saturation characterizes the shade of color i e how much white is added to the pure color Brightness also know as Value HSV system or Lightness HSL systems describes the overall brightness of the color In terms of digi tal imaging processing using the HSB system over the traditional RGB system may be This section is partially extracted from the MBF ImageJ online manual The original section Colour Image Processing can be found at http www macbiophotonics ca imagej colour_image_ processi htm 2Cf Wootton R Springall D R Polak J M Image Analysis in Histology Conventional and Confocal Microscopy ISBN 0521434823 Cambridge University Press June 1995 15 advantageous E g since the Brightness component of an HSB image corresponds to the grayscale version of that image processing only the brightness channel in routines that require grayscale images is a significant computational gain You can read more about the HSB color model here In ImageJ conversions between image types are performed using the Image Type gt sub menu In addition the Color Threshold command implemented in version 143 performs segmentation on the HSB RGB CIE Lab and YUV co
218. tches ac abc abbc abbbc and so on ab c matches abc abbc abbbc and so on but not ac Scale Images Setting a value less than 100 will reduce memory requirements E g entering 50 reduces the amount of memory needed to open a stack by 75 Convert to 8 bit Grayscale When checked reduces memory requirements by 50 for 16 bit images and by 75 for 32 bit and RGB images Convert to RGB Allows a mixture of RGB and grayscale images to be opened Sort Names Numerically When checked the stack will be opened in NUMERIC file name order e g namel tif name2 tif namel0 tif instead of alphanumeric order e g namel tif name10 tif name2 tif DICOM files in the same series tag 0020 0011 are always sorted by the image number tag 0020 0013 The List Stack Tags macro part of the List DicomTags macro set lists the values of the image number and image series tags Use Virtual Stack When checked images are opened as a read only virtual disk resident stack using a version of the Virtual Stack Opener plugin This allows image sequences too big to fit in RAM to be opened but access time is slower and changes are lost when switching to a different image in the stack cf Virtual Stacks Information widthx height x depth size of the stack that will be created is displayed at the bottom on the dialog box and is updated dynamically SEE ALSO OpenSeriesUsingFilter macro Al 29 6 2 Raw Us
219. ted power spectrum Power spectrum after Inverse transform filtering Original 112 32 10 3 Redisplay Power Spectrum Recomputes the power spectrum from the frequency domain image 32 bit FHT This command allows you to start over after mis editing the 8 bit power spectrum image 32 10 4 FFT Options Displays the FFT Options dialog box The first group of Display M FFT Window O Raw Power Spectrum O Fast Hartley Transform O Complex Fourier Transform O Do Forward Transform Cancel AO FFT Options checkboxes specifies which image s are created by the FFT command Display FFT Window The standard output It con sists of an 8 bit image of the power spectrum and the actual data which remain invisible for the user The power spectrum image is displayed with loga rithmic scaling enhancing the visibility of compo nents that are weakly visible The actual data are used for the Inverse FFT command Display Raw Power Spectrum The power spectrum without logarithmic scaling Display Fast Hartley Transform The internal format used by the command which is based on a Hartley transform rather than Fourier transform Display Complex Fourier Transform A stack with two slices for the real and imag inary parts of the FFT Do Forward Transform If checked the current image is transformed immediately when closing the FFT Options dialog 32 10 5 Bandpass Filter FFT Bandpass Filter F
220. ter point of the selection This is the average of the x and y coordi nates of all of the pixels in the image or selection Uses the X and Y headings Center of Mass This is the brightness weighted average of the x and y coordinates all pixels in the image or selection Uses the XM and YM headings These coordinates are the first order spatial moments 130 Perimeter The length of the outside boundary of the selection Uses the heading Perim Bounding Rectangle The smallest rectangle enclosing the selection Uses the headings BX BY Width and Height where BX and BY are the coordinates of the upper left corner of the rectangle Fit Ellipse Fits an ellipse to the selection Uses the headings Major Minor and Angle Major and Minor are the primary and secondary axis of the best fitting ellipse Angle is the angle between the primary axis and a line parallel to the X axis of the image The coordinates of the center of the ellipse are displayed as X and Y if Centroid is checked Note that ImageJ cannot calculate the major and minor axis lengths if Pixel Aspect Ratio in the Set Scale dialog is not 1 0 There are several ways to view the fitted ellipse 1 The Edit gt Selection gt Fit Ellipse command replaces an area selection with the best fit ellipse 2 The DrawEllipse macro draws destructively the best fit ellipse and the major and minor axis 3 Select Ellipses from the Show drop down menu in the particle analyzer and it will
221. th Offset pixel value Gaussian Open Exponential Recovery Save Copy Y X 187 6 Y 0 41 M Global Calibration aie Uncalibrated OD Cance remy 134 Note that to create a calibration curve the left column must contain a list of measured mean pixel values and the right column must contain the same number of calibration standard values The ImageJ web site has a tutorial on Optical Density Calibration explaining how to calibrate an image to an optical density step tablet 1 Before using this command use Analyzep Clear Results to reset the measurement counter and use one of the selection tools and Analyzeb Measure m to record the mean gray value of each of the standards 2 When finished making the measurements select Analyzep Calibrate to display the Calibrate dialog box To calibrate the image enter the known standard values in the right column The left column will be already populated with the measured mean gray values Select a curve fitting method from the popup menu enter the unit of measurement and click OK ImageJ will then display the calibration function on a separate window 3 If the calibration function is not satisfactory bring up the Calibrate dialog box again and select a different curve fitting method In addition to the fourteen functions that can be chosen from the drop down menu described in Curve Fitting two other functions are available that do not require a
222. that allow optimal adjustments for each slice alone This option may be specially relevant when performing enhancements based on a ROI SEE ALSO Brightness Contrast C 13 100 32 6 Noise Use the commands in this submenu to add noise to images or remove it Process gt Noise gt submenu Salt and Pepper Despeckle Add Noise and Remove Outliers ADA Original MMM Salt amp Peppel Salt Pepper gt Despecle tif QOD Add Noi QOD Add Ne gt Remove Ou 256x254 dE xels 8 1 ee A LUT 64 FTF ier ng E wy 256x254 pixels 8 bit inverting LUT 64 250x254 pixels Ett efit ng LUT 64 256x251 pixels be inverting ote 64 Sl 0 gt sie p te AA e 4 oes by e tee we SEE ALSO RandomJ package Binomial Exponential Gamma Gaussian Poisson and Uni form a Java package for image randomization by Erik Meijering 32 6 1 Add Noise Adds random noise to the image or selection The noise is Gaussian normally dis tributed with a mean of zero and standard deviation of 25 32 6 2 Add Specified Noise Gaussian Noise Standard Deviation 30 Adds Gaussian noise with a mean of zero and a chosen standard deviation Cancel C 0K 32 6 3 Salt and Pepper Adds salt and pepper noise to the image or selection by randomly replacing 2 5 of the pixels with black pixels and 2 5 with white pixels This command only works with
223. the intensities of pixels in a grayscale or pseudo color image non RGB images The plot is based on the existing rectangular selection or on the entire image if no selection is present 137 A stack of plots can be produced when the source image is a stack or hyperstack In this case closing the plot stack window will abort the plotting process AO Surface Plot 438x380 pixels RGB 650K 2738 0 119 0 lt ALDO Surface Plotter Polygon Multiplier 10 200 100 M Draw Wireframe M Shade M Draw Axis O Source Background is Lighter O Fill Plot Background with Black M One Polygon Per Line Smooth casi Polygon Multiplier Adjusts the number of profiles used to generate the plot Draw Wireframe If checked the outline of each profile will be drawn in black Shade If checked a shaded plot will be generated using the LUT of source image Draw Axis If checked the three axis will be drawn and labeled Source Background is Lighter If checked lighter areas in the source image will rep resent lower elevations valleys while darker areas in the source image will repre sent higher elevations peaks Fill Plot Background with Black If checked the plot is drawn with a black back ground otherwise white will be used One Polygon Per Line If checked all polygons will be drawn Smooth If checked sharp fluctuations will be smoothed Note that some plots can be further improved by
224. ticles with size circularity values outside the range specified in this field i i Area are also ignored Circularity 47 x Perimeter cf Set Measurements ranges from 0 infinitely elongated polygon to 1 perfect circle Show This drop down menu specifies which image should ImageJ display after the analysis Nothing No image will be displayed Outlines 8 bit image containing numbered outlines of the measured particles graylevels Outlines 0 Labels 1 Background 255 Masks 8 bit binary image containing filled outlines of the measured particles Ellipses 8 bit binary image containing the best fit ellipse of each measured par ticle Count Masks 16 bit image containing filled outlines of the measured particles painted with a grayscale value corresponding to the particle number Display Results If checked the measurements for each particle will be displayed in the Results table 126 Original thresholded Outlines Masks Ellipses Count Masks blol ANN Outlines of blobs gif AAA Masks of ALO N Ellipses of blobs gif A Count Masks e blobs gif a bs gif 256x254 pix DEBA vo i 256x a xels 8 bit blobs gif 256x254 pixels 8 bit inverting LUT 64 256x254 pixels 8 bit 6 256x254 pixels 16 bit ey oA o enc ERs Cea TAT 2 Se 00 oY SS E tee we Clear Results If checked any previous m
225. tifacts can occur For some examples see the FF TCustomFilterDemo and FFTRemoveStreaks macros 114 32 10 7 FD Math This command correlates convolves or deconvolves SNQ FFT Math two images Imagel FFT of Original SD re Operation Deconvolve 4 Image2 FFT Filter 05 06 tif Result Result It does this by converting Image1 and Image2 to the frequency domain performing conjugate multi plication or division then converting the result back to the space domain These three operations in the frequency domain are equivalent to correlation con volution and deconvolution in the space domain M Do Inverse Transform Cancel Refer to the DeconvolutionDemo and MotionBlur Removal macros for examples 32 10 8 Swap Quadrants This command transforms between the user friendly dis play of Fourier transforms with the lowest frequencies at the center and the native form with the lowest frequencies at the four corners Original A ed Swap Quadrants swaps quadrants I with III and II with IV E D F E a counter clockwise starting from Northeast so that points rigina appe i i li T near the center are moved towards the edge and vice versa Another way to see this command is to imagine that the T image is periodically repeated and the origin is shifted by width 2 in x and by height 2 in y direction For Fourier transforms Swap Quadrants affects only the image dis
226. tion Output folder should have adequate disk space to receive the cre ated images In the case of non native formats batch operations will be influenced by the be havior of the reader plugin or library cf Non native Formats 32 12 1 Measure This command measures all the images in a user specified folder by running the Ana lyze gt Measure m command in all images of the chosen directory 118 In the case of TIFF images saved with active selections Measure m will be performed on a ROI and not the whole image Note that measurements are performed on non thresholded images SEE ALSO Analyzep Set Measurements Batch gt Macro 32 12 2 Convert POO Batch Convert Batch converts and or resizes multiple images from a specified folder Input Desktop Raw Lee A Output Desktop Converted Output Format TIFF red Interpolation Bilinear Scale Factor 1 00 Input Selects the source folder con taining the images to be processed Output Selects the destination folder where the processed images will be stored Cancel Convert Output Format Specifies the output format that can be set to TIFF 8 bit TIFF JPEG GIF PNG PGM BMP FITS Text Image ZIP or Raw cf Image Types and Image Formats and File gt Save As gt submenu Interpolation The resampling method to be used in case Scale Factor is not 1 00 cf Image Size and Image Scale
227. to Overlay dialog Stroke Color red Width 1 Fill Color none O New Overlay Use the alt b shortcut to skip this dialog Cancel Hex color codes must be given as either a 6 digit hexadecimal number in the form RRGGBB opaque colors or a 8 digit number in the form AARRGGBB where AA specifies the alpha blending value RR the intensity of red GG the intensity of green and BB the intensity of blue The table below provides the conversion of some RGB color triplets into hex notation Colors are specified using the name of one of the eight de fault colors black blue cyan green magenta red white and yellow or using hex notation 93 Hexadecimal equivalents of RGB colors As for RGB triplets alpha values range from 0 fully transparent to 255 solid color Opacity values are thus obtained using 100 x 255 a 255 Alpha values can be omitted for fully opaque colors RGB Color R G B Blue Cyan Green Magenta Red Orange Yellow 0000FF 00FFFF 00FF00 FF00FF FF0000 FFC800 BF0000FF BFOOFFFF BFOOFFOO BFFFOOFF BFFF0000 BFFFC800 7F0000FF 7FOOFFFF 7FOOFFOO 7FFFOOFF 7FFFOO00 7FFFC800 25 3F0000FF 3FOOFFFF 3FOOFFOO 3FFFOOFF 3FFFO000 3FFFC800 Opacity ante oa o 5 FFFF00 BFFFFF00 7FFFFF00 3FFFFF00 Table generated with RGBtoHEX using ImageJ default selection colors Previously added overlays are removed if New Overlay is checked SEE ALSO
228. tor 121 Surface 137 Syntax highlighting 4 Synthetic images 111 T Tesselation see Voronoi 106 Text 34 Threads 151 3D Projection 82 3D viewer 81 Threshold 69 110 132 Binary images 102 Color 70 TIFF 10 45 Time stamper 84 Tolerance Wand Tool 31 Toolbar 27 Tools Angle 32 Area Selection Brush 29 Ellipse 29 Freehand 30 Polygon 30 Rectangle 28 Round Rectangle 29 Wand 30 Color Picker 35 178 Line Selection Arrow 32 Freehand Line 32 Segmented Line 31 Straight Line 31 Macro Tools 36 Macro Toolset Switcher 39 Magnifying Glass 34 Multi point 34 Point 33 Scrolling 35 Text 34 Toolset 35 Tracing see Wand tool 30 Transform 55 56 90 Translate 91 U Undo 9 49 Unsharp mask 117 Updates 2 3 157 NA Variance 118 Virtual stacks see Stacks Virtual 13 Voronoi 106 Voxel depth 73 W Wand tool 30 Watershed 106 Web browser 156 Window management 155 Y Yen see Threshold 69 YUV 11 16 70 Z ZIP 38 46 145 Compressed TIFF 11 46 Zoom 34 91 Fit to Screen 92 Z Profile 84 This document was typeset with TRXLive 2009 on Mac OS 10 6 3
229. tripes is similar to subtracting an image that is only blurred in the horizontal direction from the original Tolerance of Direction This is for Suppress Stripes higher values remove shorter stripes and or stripes that are running under an angle with respect to the hori zontal vertical direction Autoscale After Filtering If checked puts the lowest intensity to 0 and the highest intensity to 255 preserving all intensities Saturate Image when Autoscaling If checked allows some intensities to go into sat uration and produces a better visual contrast Saturate Image when Autoscaling only has an effect when Autoscale After Filtering is enabled Display Filter If checked shows the filter generated Note that this disables Undo of the filter operation on the original image 32 10 6 Custom Filter SIOO FFT Filter This command does Fourier space filtering of the active image using a user supplied spatial domain non FFT image as the filter Filter FFT Filter 05 06 tif 4 TT N This image will be converted to 8 bit For pixels that have a value of 0 the corre sponding spatial frequencies will be blocked Pixel with values of 255 should be used for passing the respective spatial frequencies without attenuation Note that the filter should be symmetric with respect to inversion of the center Points that are opposite of the center point defined as x width 2 y height 2 should have the same value Otherwise ar
230. ts table cf The Results Table O Invert Y Coordinates L Scientific Notation Redirect To None rg The dialog contains two groups of checkboxes The first group controls the type of measure ments that are printed to the Results table The second group controls measurement set tings Decimal Places 0 9 3 f sy O The eighteen checkboxes of the first group are Area Area of selection in square pixels or in calibrated square units e g mm pm etc if AnalyzebSet Scale was used to spatially calibrate the image Mean Gray Value Average gray value within the selection This is the sum of the gray values of all the pixels in the selection divided by the number of pixels Reported in calibrated units e g optical density if Analyze gt Calibrate was used to calibrate the image For RGB images the mean is calculated by converting each pixel to grayscale using the formula gray red green blue 3 or gray 0 299 x red 0 587 x green 0 114 x blue if Weighted RGB Conversions is checked in Edit gt Options gt Conversions Standard Deviation Standard deviation of the gray values used to generate the mean gray value Uses the Results table heading StdDev Modal Gray Value Most frequently occurring gray value within the selection Corre sponds to the highest peak in the histogram Uses the heading Mode Min amp Maz Gray Level Minimum and maximum gray values within the selection Centroid The cen
231. ugh the toolbar items from left to right forward cycle and right to left reverse cycle 163 oN OO FPF WN 23 Macro 7 Cycling Through ImageJ Tools Using Keyboard Shortcuts Ui Ui dll Vv vV These two macros loop through the all the tools listed in the tools array using Fi and F2 forward and reverse cycling respectively Append this file to the StartupMacros txt file and ImageJ will automatically install them at start up ar tIndx 0 ar tools newArray rectangle elliptical brush polygon ecc AMG pola Mir eTe e vandi Mco Errores ane e Morley ala MAS macro Cycle Tools Fwd F1 4 setTool tools tIndx tIndx if tIndx tools length tIndx 0 macro Cycle Tools Rwd F2 4 tmd if tIndx lt 0 tIndx tools length 1 setTool tools tIndx 164 Cl C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 C17 C18 Credits The Command Finder was written by Mark Longair The macro editor s Function Finder Macrosp Find Functions was written by J r me Mutterer The Brush Selection Tool is based on the ROI Brush Tool plugin from Tom Larkworthy and Johannes Schindelin Michael Schmid added 4 connected and 8 connected tracing with tolerance to the Wand Tool The File gt Import gt Results command is based on J r me Mutterer s Import Results Table macro The improved versions of the
232. used to mirror the red channel on the top of the blue channel by adding the red component to the blue an gt N o 0 3 aw 10 11 MACRO 2 Creating MGB Images With the Image Calculator Command This macro replaces Red with Magenta in RGB images using the Process gt Image Calculator command setBatchMode true tater set Tastes ig 4 titlen ol ye liniers acc e y SS Yeager Mimo run Split Channels imageCalculator Add b r run Merge Channels red amp r green amp g blue b rename title MGB setBatchMode false In ImageJ you can simulate color blindness on your images using the Vischeck plugin or in Fiji using the Image Color gt Simulate Color Blindness command Color Composites In a composite image colors are handled through channels The advantages with this type of image over plain RGB images are 1 Each channel is kept separate from the others and can be turned on and off using the Channels tool Image gt Hyperstacks gt Channels Z This feature allows e g to perform measurements on a specific channel while visualizing multiple 2 Channels can be 8 16 or 32 bit and can be displayed with any lookup table 3 More than 3channels can be merged or kept separate 17 12 Selections Although ImageJ can display simultaneously several selections or regions of interest ROIs only one selection can be active at a time Sele
233. using current foreground background colors As for Edit gt Draw d Use the Edit Options Line Width command or double click on the line tool to change the width of selection s outline Selections can be labelled if they were previously analyzed Analyze Particles or Mea sure m commands and the parameter Centroid cf Set Measurements extracted in the Results table SEE ALSO Color Picker 15 33 6 Clear Results Erases the results table and resets the measurement counter This command is also available by right clicking on the Results table cf The Results Table 129 33 7 Set Measurements Use this dialog box to specify which mea surements are recorded by Analyze gt Measure ANO Set Measurements m ROI Manager s Measure command cf Y Area Mean Gray Value ROI Manager and Analyzep Analyze Parti U Standard Deviation LU Modal Gray Value E Min amp Max Gray Value Y Centroid cles Measurements are performed on the O Center of Mass O Perimeter current selection the entire active image if no Y Bounding Rectangle Fit Elipse selection is present For thresholded images Shape Descriptors Feret s Diameter y i O Integrated Density O Median measurements can be restricted to highlighted O Skewness O Kurtosis pixels if Limit to Threshold is checked Area Fraction Stack Position B This command is also available by right U Limit to Threshold L Display Label clicking on the Resul
234. uters in biology and medicine Jan 2010 S Kerner D Etienne J Malet F Mora V Monnet Corti and P Bouchard Root coverage assessment validity and reproducibility of an image analysis system J Clin Periodontol 34 11 969 76 Nov 2007 G Kilimnik A Kim J Jo K Miller and M Hara Quantification of pancreatic islet distribution in situ in mice Am J Physiol Endocrinol Metab 297 6 E1331 8 Dec 2009 Y J Kim B F M Romeike J Uszkoreit and W Feiden Automated nuclear segmenta tion in the determination of the Ki 67 labeling index in meningiomas Clin Neuropathol 25 2 67 73 Jan 2006 A Kirilova G Lockwood M Math P Choi N Bana M A Haider K K Brock C Eccles and L A Dawson Three dimensional motion of liver tumors using cine magnetic resonance imaging Jan 2008 A Kobayashi T Fujigaya M Itoh T Taguchi and H Takano Technical note a tool for determining rotational tilt axis with or without fiducial markers Ultramicroscopy 110 1 1 6 Dec 2009 D Lau A Seibert D Gandara L Laptalo E Geraghty and C Coulon Computer assisted image analysis of bronchioloalveolar carcinoma Clin Lung Cancer 6 5 281 6 Mar 2005 C A Lessman R Nathani R Uddin J Walker and J Liu Computer aided meiotic maturation assay CAMMA of zebrafish danio rerio oocytes in vitro Mol Reprod Dev 74 1 97 107 Jan 2007 R M Lindley D B Hawcutt M G Connell D H Edgar and S E Kenny Prop

The ImageJ User Guide – Verson 1.43

Contents

Download Pdf Manuals

Related Search

Related Contents

The ImageJ User Guide &ndash; Verson 1.43

Contents

Download Pdf Manuals

Related Search

Related Contents

The ImageJ User Guide – Verson 1.43