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1. Activate Deactivate Quick amp Dirty Scaling menu determines the quality and speed of the reduction algorithm Before quick amp dirty scaling is activated like in Figure 11 the reduced tiles show good fidelity to the full size tiles Once quick amp dirty scaling is activated the menu switches to Deactivate Quick amp Dirty Scaling In this condition the reduction is performed faster albeit with a lesser quality Help Menu Image File Edit Object Scale Credits Status Figure 12 Help menu The menu Credits is always active Its purpose is to present the text of Figure 13 AOO Mosaic This Mosaic version is dated July 6 2011 H This work is based on the following paper P Th venaz M Unser User Friendly Semiautomated Assembly of Accurate Image Mosaics in Microscopy Microscopy Research and Technique vol 70 no 2 pp 135 146 February 2007 This paper is available on line at http bigwww epfl ch publications thevenaz0701 htm Other relevant on line publications are available at http bigwww epfl ch publications Additional help available at http bigwww epfl ch thevenaz mosaicj You ll be free to use this software for research purposes but you should not redistribute it without our consent In addition we expect you to include a citation or an acknowledgment whenever you present or publish results that are based on it Figure 13 Credits The menu Status is always active Its purpose i2. existing files of the same name in the temporary directory may be silently overwritten V Conditions of Use You ll be free to use this software for research purposes but you must not transmit and distribute it without our consent In addition you undertake to include a citation or acknowledgment whenever you present or publish results that are based on it EPFL makes no warranties of any kind on this software and shall in no event be liable for damages of any kind in connection with the use and exploitation of this technology
3. obtrude once tiles are moved to the gridded area Color Images When color images are provided the registration proceeds on a grayscale version that is built as a weighted sum of the red green and blue components even when the stack is pseudo color The weights can be made to correspond to the BT 709 norm but by default they depend on the whole stack and are determined by a principal component analysis in such a way as to provide the maximum possible contrast The colors are restored upon completion of the interaction and automatic registration stages so that the created mosaic is in full color when at least one input tile is colored File Menu Edit Object Open Image 0 Open Image Sequence CHO Deactivate Smart Color Conversion Scale Help Create Mosaic S Deactivate Blending Deactivate Rotation Activate Log File Save Pre Mosaic TES Load Pre Mosaic CR Previous Pre Mosaic Z Reset Mosaic Abort ob W Figure 3 File menu The menu Open Image will allow access to one file at a time it is always available so that more tiles can be added to the mosaic at will If the file contains a stack all slices will be considered as independent tiles The menu Open Image Sequence will allow access to every file inside a folder directory except to the files that start with the character a leading dot To access the folder select any file within but please note that the exploration of folders is
4. ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE English only Download Algorithms BIG gt Download Algorithms gt MosaicJ Mosaic An ImageJ plugin for the creation of an image mosaic Philippe Th venaz Biomedical Imaging Group Swiss Federal Institute of Technology Lausanne Figure 1 Columnar epithelium t s of blind gut from rabbit This 3650x2068 mosaic has been assembled from seventeen 636x512 slices The version on display has been much reduced to save on bandwidth General Description The purpose of this plugin is to facilitate the assembly of a mosaic of overlapping individual images or tiles It provides a semi automated solution where the initial rough positioning of the tiles must be performed by the user and where the final delicate adjustments are performed by the plugin The Mosaic plugin requires that a second plugin named TurboReg is installed This ancillary plugin is available here I Download This distribution is dated July 6 2011 It includes the complete set of source files along with the precompiled classes e UNIX distribution 276 480 bytes e Macintosh distribution 148 461 bytes e PC distribution 128 868 bytes e This page in pdf format printer friendly 656 078 bytes II Related Work The Mosaic plugin requires that a second plugin named TurboReg is installed This ancillary plugin is available here This set of Java classes is based on the fo
5. des visual feedback on the fraction of work remaining to perform An error message is displayed when the rough mosaic created by the user is not simply connected B00 Select an Option There are 2 mosaics Cancel Abort Creation Create Largest Figure 5 Error message when the mosaic is not simply connected By choosing Cancel the user would abort the whole process of building a mosaic and would return to ImageJ By choosing Abort Creation the user would resume MosaicJ s interactive operations By choosing Create Largest the simply connected mosaic that contains the most tiles would be created while the other mosaics would be discarded In case of a tie in the number of tiles the simply connected piece that is chosen is arbitrary The Activate Deactivate Blending menu determines whether the bounds of the tiles do or do not fuse gradually with the inside of the other tiles in the final mosaic Before blending is deactivated like in Figure 3 the transition between tiles is smoothed out Once deactivated the menu switches to Activate Blending In this condition the tiles are uniformly averaged when creating the final mosaic The Activate Deactivate Rotation menu determines whether rotation is optimized for Before rotation is deactivated like in Figure 3 the tiles are translated and rotated Once deactivated the menu switches to Activate Rotation In this condition the final mosaic will consist of tiles t
6. has been selected Its purpose is to designate tiles over which the automatic refinement of the position will take place By default all tiles are unfrozen The menu Hide is active when at least one tile or group of tiles has been selected Its purpose is to deselect and to hide the currently selected objects from the upper part of the screen so that the remaining objects can be operated upon The spatial extent of the mosaic is not affected by the hiding of tiles The menu Show All is active when there is at least one hidden object Its purpose is to restore its visibility in the upper part of the screen The revealed objects remain unselected The menu Maximize Contrast is active when at least one tile or group of tiles has been selected Its purpose is to map to black the lowest grayvalue observed over the collection of selected tiles and to white the highest one The intermediate grayvalues are mapped linearly between these two extremes This contrast remapping is applied to the selected tiles It affects only their display but has no effect on the final mosaic The menu Set Contrast is active when at least one tile or group of tiles has been selected Its purpose is to map to black the user provided Min grayvalue and to white the user provided Max grayvalue These bounds are neither necessarily integers nor necessarily positive but Min must be less than Max they are set in the dialog shown in Figure 10 The intermediate gra
7. hat are only translated without being rotated The Activate Deactivate Log File menu determines if the operations applied to the tiles should be recorded in a file when the final mosaic is created Before the log file is activated like in Figure 3 no file is created Once logging is activated the menu switches to Deactivate Log File In this condition upon creation of the final mosaic the user is given the opportunity to save a text file that will contain the operations performed to create the mosaic These operations can be reapplied to recreate the same mosaic Another use emerges if the log file is edited before it is reapplied this allows one to process multichannel images for example by changing the source of the tiles The log file consists of lines Each line contains tab separated items The syntax is as follows The first line is a header that contains Gray or Color followed by the dimensions of the mosaic width and height Each of the next lines pertains to a single tile The first six floating point numbers give the source landmarks the next six floating point numbers give the target landmarks Two additional floating point numbers record the pre computed location of the bottom right corner of the tile The next number is the negative of the index of the slice in the stack from which the tile is originating The last item is the filename of the stack please note that such filenames should not contain tabs The menu Save Pre M
8. icJ can be used to discard any tile currently loaded and to empty a file based cache that MosaicJ is maintaining in the temporary folder of ImageJ These files are all prefixed by MosaicJ The user must confirm the operation before it takes place OC Reset Mosaic Cache Are you ready to reset Mosaic and its cache Deleting tmp Mosaic Figure 6 Request for confirmation before resetting MosaicJ and its cache The menu Abort is used to abort the whole process of building a mosaic after which the user is returned to ImageJ This can also be achieved by closing MosaicJ s window Edit Menu ImageJ File Object Scale Help Select All A Deselect D Stow a6 T Forget of X Nudge Right Nudge Up a6 T Nudge Left db Nudge Down 1 Figure 7 Edit menu The menu Select All is active when at least one tile has been placed It is not available when there are hidden tiles Its purpose is to select all the tiles and groups of tiles in the upper area of the screen The menu Deselect is active when at least one tile or group of tiles has been selected Its purpose is to deselect all selected tiles or groups of tiles The menu Stow is active when at least one tile or group of tiles has been selected Its purpose is to deselect all selected tiles or groups of tiles and to place them back in the lower area of the screen so that they are still available but do not participate in the construction of the final
9. is blue red when the tile is frozen In effect a group behaves like a tile that would have an arbitrary shape A dialog message is displayed when grouping a combination of frozen and unfrozen tiles 0O0O Select an Option Grouping a mixture of frozen and unfrozen tiles E Cancel Unfreeze All Freeze All Figure 9 Dialog to determine the course of action when grouping a mixture of frozen and unfrozen tiles The menu Ungroup is active when at least one group of tiles has been selected Its purpose is to break the group bonds one hierarchical level at a time After completion of the Ungroup command the individual group components are independent again and remain selected The menu Freeze is active when at least one tile or group of tiles has been selected Its purpose is to designate tiles over which no automatic refinement of the rough position will take place When the mosaic is been built the frozen tiles will maintain their current relative position If one single tile of the whole mosaic is frozen it will act as anchor and all the other tiles will align to it if no tile is frozen default condition the anchoring tile that is chosen is arbitrary if several tiles are frozen the closest unfrozen tiles will align to them The manual building of a mosaic is therefore achieved by freezing all tiles in which case no automatic refinement takes place The menu Unfreeze is active when at least one tile or group of tiles
10. llowing paper P Th venaz M Unser User Friendly Semiautomated Assembly of Accurate Image Mosaics in Microscopy Microscopy Research and Technique vol 70 no 2 pp 135 146 February 2007 Other relevant on line publications are available at http bigwww epfl ch publications Mosaic has been written as a plugin for ImageJ Please read the ImageJ documentation to learn how to install plugins III Technical Explanations After completion of the interactive stage the tiles are examined for mutual overlap Pairs of overlapping tiles are then aligned thanks to the registration engine TurboReg This alignment is organized by decreasing amount of overlap pairs of tiles are skipped if the two tiles have been registered already In the end an arbitrary tile is selected as anchor and all the other tiles are positioned by propagating the pairwise transformations The interactive stage is translational only Meanwhile the automatized refinement stage allows for subpixel translations and optional rotations A global mosaic is produced once the geometry of all tiles has been finalized Locations not covered by any tile are set to the background intensity or color defined by ImageJ according to the settings found under Edit Options Colors Locations where several tiles overlap are given a weighted contribution from each tile An optional blending mechanism reduces the visibility of tile edges when disengaged each
11. mosaic Upon being stowed all groups are dismantled and the tiles are individual again The menu Forget is active when at least one tile or group of tiles has been selected Its purpose is to deselect all selected tiles or groups of tiles and to remove them entirely from the mosaic They can then be accessed again only through Open File or Open Image Sequence The menus Nudge are active when at least one tile or group of tiles has been selected Their purpose is to offer a keyboard based way to displace the tiles by one pixel at a time The effective amount of displacement depends on the current magnification scale Object Menu Image File Edit Scale Help Send to Back a6 B Group G Ungroup dU Freeze F Unfreeze dF Hide 36H Show All TA Maximize Contrast 3L Set Contrast gL Reset Contrast AR Figure 8 Object menu The menu Send to Back is active when at least one tile or group of tiles has been selected and when the stacking order of all tiles is such that some selected tiles may obscure unselected ones Its purpose is to ensure that no unselected tile is obscured by the ones that are currently selected The menu Group is active when at least two tiles or groups of tiles have been selected Its purpose is to group tiles or groups of tiles together Once grouped the selection outline of an unfrozen set of tiles becomes green orange for frozen tiles while the selection outline of a single unfrozen tile
12. n works on its own to automatically refine this rough version The menu bar is holding five menus that are directly related to MosaicJ File Edit Object Scale and Help The operations that are not available through menus include the direct manipulation of tiles such as e Activating a tile This is performed by clicking a tile that lies in the lower area of the screen The tile will be placed in the center of the upper area where it can be operated upon It will be selected and previously selected tiles if any will be deselected e Moving a tile This is performed by dragging a tile or a set of selected tiles e Selecting a tile This is achieved by clicking a tile that lies in the upper area of the screen If the click is performed on a superposition of tiles only the topmost tile is selected conversely the last selected tile automatically becomes topmost In case a tile is inaccessible because it would be covered entirely by other tiles it is possible to temporarily hide the top tiles until the desired tile becomes accessible It is also possible to rearrange the tiles so that the topmost tile is sent to the back e Selecting several tiles This is achieved by shift clicking the tiles e Identifying a tile A tool tip identifies the name of the file associated with the tile and indicates its slice number in the stack This tool tip is displayed when the user hovers the cursor over a tile in the lower section of MosaicJ s window It does not
13. not hierarchical Types and sizes of images can be mixed freely An error message is displayed when an unrecognized file type is found O0O Select an Option Unable to open image samples non image file Figure 4 Error message when an unrecognized file is found By choosing Cancel the user would abort the whole process of building a mosaic and would return to ImageJ By choosing Stop Opening the images loaded so far if any would be retained but no more would be loaded By choosing Resume Opening the loading of images would be resumed until the folder content is exhausted or until the next unrecognized file is found By choosing Open All Valid the next unrecognized files are skipped silently The Activate Deactivate Smart Color Conversion menu determines how color images are desaturated Before smart color conversion is deactivated like in Figure 3 the intermediate images over which registration is performed are obtained from color images by attempting to maximize contrasts Once deactivated the menu switches to Activate Smart Color Conversion In this condition a standardized sum of the RGB color components is computed as Y 0 212671 R 0 71516 G 0 072169 B The menu Create Mosaic is active when at least one tile has been placed It is not available when there are hidden tiles Once Create Mosaic has been activated the second non interactive stage of building the mosaic can proceed A progress bar provi
14. osaic is active when a mosaic is ready to be produced It can be used to save the current configuration of tiles before the automatic refinement stage is applied Beware that no groupings are saved the overall reduction factor is also not saved The resulting text file is a set of line records each record being tab delimited A record contains the grayscale contrast and offset that is specific to the tile the weights being used to desaturate an RGB representation of the color image and the relative location of the tiles followed by a slice index by the frozen unfrozen state of the tile and by the name of the file from which the tile came Negative slice indices indicate that the tile belongs to the lower section The menu Load Pre Mosaic can be used to restore a configuration of tiles In the process any current tile is discarded The size of the tiles fits the actual reduction factor All resulting tiles are ungrouped The error message of Figure 4 pops up when a tile fails to load The menu Previous Pre Mosaic can be used to restore the configuration of tiles that was active the last time the operation Create Mosaic was called The usual limitations apply see Save Pre Mosaic and Load Pre Mosaic The menu Replay from Log can be used to recreate a mosaic from a log file see Activate Deactivate Log File It is accessible only when the upper section of the workspace contains no tiles The menu Reset Mosa
15. s to offer a centralized access to the switches that control the behavior of MosaicJ These switches are summarized in Figures 14 to 17 e00 Mosaic Status Display Export vV Smart Color Conversion Figure 14 Import status 00 Mosaic Status f Import Display Export Quick amp Dirty Rescaling Method Current Reduction Factor 1 4 25 0 There Are No Hidden Tiles Figure 15 Display status when there are no hidden files O0O Mosaic Status Import Display Export Quick amp Dirty Rescaling Method Current Reduction Factor 1 4 25 0 Some Tiles Are Hidden Reveal with Object Show All Done Figure 16 Display status when there are hidden files OO Mosaic Status Import Display Export M Seamless Blending of Tiles v Compensate for Rotation of Tiles _ Create a Log File Can Rebuild the Mosaic Done Figure 17 Export status Temporary files The present plugin MosaicJ is used as a front end to another plugin named TurboReg Several mechanisms are at work to exchange data between these plugins One of them involves temporary files which are written into the temporary directory that ImageJ defines The location of this directory can be examined by issuing the macro command print getDirectory temp The names of the written files are MosaicJPreMosaic MosaicJ where is an integer number sometimes followed by R G or B Warning
16. tile contributes equally The user may have positioned tiles in such a way that more than one simply connected mosaic is present The user receives a notification when this happens and is offered the opportunity to concentrate on the mosaic with the largest number of tiles Currently all ImageJ types are supported on input but the registration and the interaction always operate on grayscale images The color to grayscale conversion of Mosaic tends to maximize contrasts which makes it different from ImageJ s This behavior can be overridden if desired The output image is RGB color if at least one of the tiles that participate to the mosaic is in color else the output image is 32 bit grayscale IV User Manual Generalities 800 Mosaic Figure 2 Initial empty window here reduced for illustration purposes Once the plugin is fired an empty window covering the whole screen should appear This window contains two sections the upper and the lower one The upper section is the gridded area where the user can interactively arrange tiles the lower section contains tiles that have not yet been arranged This window cannot be resized but scroll bars appear when needed The mosaic is built in two stages First the user interactively loads discards arranges and otherwise manipulates tiles or thumbnails thereof This stage is visual mouse and menu driven and its goal is to provide a rough version of the final mosaic Second the plugi
17. yvalues are mapped linearly between these two extremes and out of bounds values are saturated This contrast remapping is applied to the selected tiles It affects only their display but has no effect on the final mosaic Range of Grays Min 0 0000 Max 255 0000 Cancel OK V Figure 10 Dialog to establish the range of displayed gray values The menu Reset Contrast is active when at least one tile or group of tiles has been selected Its purpose is to enforce the generic mapping where the value 0 0 corresponds to black and 255 0 to white The intermediate grayvalues are mapped linearly between these two extremes and out of bounds values are saturated This contrast remapping is applied to the selected tiles It affects only their display but has no effect on the final mosaic Scale Menu Image File Edit Object Help Minify Magnify a6 Activate Quick amp Dirty Scaling Figure 11 Scale menu The menu Minify is always active Its purpose is to reduce the size of the tiles by a linear factor two so that large tiles can be manipulated with more ease The current scale is displayed as the last item of the Scale menu The menu Magnify is active unless the tiles are displayed at full scale Its purpose is to magnify the size of the tiles by a linear factor two so that tiles can be manipulated with more precision The current scale is displayed as the last item of the Sca e menu The
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