User Manual
Contents
1. 1 L 1 L L 1 L 1 L L Parameters 50 MicronPixel 0 08 MinSpLen Micron 041 Min STD MexsTD 75 Low Thr L Upp Thr i LnkRad a Link Dir 1 MinSpLent Pixel MaxSpLen Pixel 50 MinDenLen Pixel 1504 F r View Image Stack First Last 2004 L sido S Sioe Enter a slide number or use the slider Slide Number 250 4 g 300 4 r 350 4 F 4004 z 4504 F m Features Dendrite Len Total Spine Num Spine Label Spine Status 500 4 in i i T m Spine Area Spine Length 50 100 150 200 250 300 350 400 450 500 Sp Neck Wid Spine Peri Neuroni Application 9 84S v1 2 42 Current imagesdir N A Auto Processed N A Manual Edited N A Spine Class Sp Head Wid The above Graphic User Interface GUI is divided into 8 parts and each part is explained in the following sections 1 Algorithm Selection CADMOS Curvilinear based Automatic Detection and Measure of Spines MADMOS Morphology based Automatic Detection and Measure of Spines The user can select any one of them for single processing or batch processing The MADMOS is selected by default To learn more details about the algorithms please refer to our published paper 1 2 2 Parameters Two parameters Micron Pixel Min Sp Len are required for MADMOS while four parameters Micron Pixel Min Sp Len MaxSTD Lnk Rad are for CADMOS Details For both CADMOS and MADMOS Micron Pixel ratio2. 094284 0 259281 0 306423 0 0 659988 4 5 6 fCloz1bN1 42 53536 2 13 14 0 29 0 04702 0 305628 0 329138 0 0 681786 7 8 9 fcore slice 53 16512 E 5 22 0 39 0 169284 0 094047 0 413805 0 0 733564 10 11 12 fdorsal slic 80 79944 17 23 17 0 58 0 210397 0 284655 0 210397 of orza 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 2 37 38 39 40 41 42 43 44 45 46 47 48 M 4 gt gt I Sheeti Z Sheet2 Sheet3 NeuronIQ1 I lt Ti Ready NUM This file listing for each image dendritic backbone length spine count in each class total spine count spine density by class spine count in spine class N dendritic backbone length total spine density total spine count dendritic backbone length 2 4 Close Directory Press the Close Directory button in the Toolbar Note During the batch processing if some images can t be processed by NeuronlIQ the file names will be stored in Error txt Reference 1 J Cheng X Zhou E Miller R M Witt J Zhu B L Sabatini and S T Wong A novel computational approach for automatic dendrite spines detection in two photon laser scanning microscopy J of Neurosci Methods 165 122 134 2007 2 Y Zhang X Zhou R M Witt B L Sabatini D Adjeroh and S T Wong Dendritic spine detection using curvilinear structure detector and LDA classifier Neuroimag 36 346 360 2007
3. 16 Min STD 1 Max STD 4 LowThr 1 Upp Thr 4 Link Rad 4 Link Dir o7 MinSpLen Pixel 2 MaxSpLen Pixe 50 Default View Image Stack First r Last Slide m D Slide Enter a slide number or use the slider Slide Number O View Raw View Project a Select Mode 7 View Spine Boundary Erase Spine O Add Spine 7 View Spine Label Split Spine View Dendrite Boundary Erase Den Boundary Z View Dendrite Backbone Add Den Boundary O Erase Den Backbone Add Den Backbone Save Manual Changes Discard Manual Changes J r Features Dendrite Len 122 4363 Total Spine Num 59 Spine Label N A Spine Status NIA Spine Area NIA Spine Length NA Sp Neck Wid NIA Spine Peri NIA 50 100 150 200 250 300 350 400 450 500 adebtesi bei Adac tusi As Neuroni Application Sts 7 1311 Current image dir img001 tif Auto Processed Yes Manual Edited Yes This figure shows the result of CADMOS in combined mode under View Project 1 5 Manual Change Including Erase Spine Add Spine Split Spine Erase Den Boundary Add Den Boundary Erase Den Backbone Add Den Backbone Enter manual editing mode by clicking the button Click the selected manual editing button again if you want to quit manual editing mode 1 6 Save Result Press the save result button in the Toolbar an excel file with the statistical in
4. 5 7052 1 30216 1 641462762 3 18 Cloz1bN1D1 Ism tif 16 16 1 926655 2 3872 6 07488 0 9656 1 282497563 3 19 Cloz1bN1D1 Ism tif 17 17 2 183575 1 8112 9 5592 0 73936 1 052235715 3 20 Cloz1bN1D1 Ism tif 18 18 1 681904 3 4688 9 53168 1 31592 2 001599361 3 21 Cloz1bN1D1 Ism tif 19 19 1 76 2 272 10 56072 1 46216 1 04 3 22 Cloz1bN1D1 Ism tif 20 20 1 111396 0 64 4 48584 0 75312 1 111395519 2 23 Cloz1bN1D1 Ism tif 21 21 1 697056 2 5984 11 0076 1 4456 2 828427125 3 24 Cloz1bN1D1 lsm tif 22 22 1 36 3 296 8 1936 1 69936 2 64 3 25 Cloz1bN1D1 Ism tif 23 23 0 452548 0 704 5 12864 0 9628 0 4 1 26 Cloz1bN1D1 lsm tif 24 24 0 288444 0 1216 1 2056 0 60968 0 24 1 27 Cloz1bN1D1 Ism tif 25 25 1 202664 2 2336 8 65704 1 77936 2 405327421 2 28 Cloz1bN1D1 Ism tif 26 26 0 609262 0 5504 3 6168 0 51312 1 218523697 2 29 Cloz1bN1D1 Ism tif 27 27 0 48 0 4864 3 00432 0 83312 0 96 1 30 Cloz1bN1D1 Ism tif 28 28 0 737564 0 6336 2 94088 0 54624 0 98954535 2 31 32 33 fCloz1bN1D1 1sm tif 1 1 1 442221 1 152 4 3368 0 48 1 043072385 3 34 fCloz1bN1D1 Ism tif 2 2 2 406657 0 9408 5 73832 0 24 0 6835203 3 35 fCloz1bN1D1 Ism tif 3 3 1 302306 0 1792 1 51184 a 0 407921561 3 36 fCloz1bN1D1 Ism tif 4 4 0 252982 0 16 2 05808 0 16 0 505964426 1 37 fCloz1bN1D1 Ism tif 5 5 1 609969 0 6976 4 30648 0 16 0 60926184 3 38 fCloz1bN1D1 Ism tif 6 6 0 976524 0 2496 2 05808 0 0 4 2 39 fCloz1bN1D1 lsm tif 7 7 1 07629 0 5568 3 52024 0 57936 0 85041 1665 2 40 fCloz1bN1D1 Ism tif 8 8 0 91214 0
5. been manually edited Save Close Single Save Current Directory cs a Pan Resylts Image Load an Image 4 sgl W si N BiN TE p Batch Close Exit a Ey bot Export Image Process Out Directory e Load an Image display process etc e Load Directory e Save Result file e Batch Export load single 3D neuron image stack or a single 2D image to load directory of neuron images to be batch processed save the statistical information of the current image in excel save the statistical information of the images in current folder in two excel file One is a single summary Excel file listing for each image the other is an Excel file with compiled spine data from all images Close Image Stack Close Directory Exit Single Processing Batch Processing Save Current Image save the current displayed figure as a bitmap image close the current image close the directory quit NeuronIQ processing single 3D neuron image processing all the 3D neuron images in current directory Zoom in Zoom out Pan How to use NeuronIQ to process images 1 Single Processing 1 1 Load image 1 2 Select algorithm amp Set parameter NeuroniQ BE File Analysis Mode Tools Help wea Gem gt P aakl Algorithm O caDmMos MADMOS Parameters MicroniPixel 0 08 MinSpLentMicrony 016 Min STD Max STD Low Thr Upp Thr Lk Rad Link Dir MinSpLen Pixel _ MaxSpLent Pixel View Image Stack First m
6. 2944 2 18776 0 16 0 582408791 2 41 fCloz1bN1D1 Ism tif 9 9 1 24964 1 152 5 15896 0 8828 1 249639948 2 42 fCloz1bN1D1 Ism tif 10 10 1 264911 2 0352 5 76864 1 15592 1 553319027 3 43 fCloz1bN1D1 Ism tif 11 11 1 68 0 6976 4 14928 0 16 0 64 3 44 fCloz1bN1D1 Ism tif 12 12 0 976524 0 224 1 6884 0 0 512249939 2 45 fCloz1bN1D1 lsm tif 13 13 0 576888 0 1344 1 47872 0 08 0 288444102 2 46 fCloz1bN1D1 Ism tif 14 14 1 770875 0 1088 1 2856 0 0 178885433 3 47 fCloz1bN1D1 1sm tif 15 15 1 53675 1 5168 5 37144 1 49528 1 424359505 3 48 fCloz1bN1D1 lsm tif 16 16 1 936595 2 0288 5 7852 0 94904 182428068 3 na 4 gt oI Sheeti Sheet2 Sheet3 NeuronIQ1 K a Ready Sum 118 NUM This file would report for each spine spine length spine head width spine neck width spine head area spine head perimeter and spine classes Excel file 2 Summary for all the images in current folder E Microsoft Excel NeuronlQ_BatchSummary_MADMOS xls i69 gie Edit view Insert Format Tools Data Window Help Adobe PDF Le laa a aa A aia al aahh L12 M Fe 0717826757215149 A B D E G i e e K M oM N 0 P Q R 5 T 1_ File Name Dendrite Li Spines Nu Spines Nu Spines Nu Spines Nu Total Spine Spine Den Spine Den Spine Den Spine Den Total Spine Density 2 3 Cloz1bN1C 42 42504 4 11 13 0 28 0
7. Last Slide L Ei Slide Enter a slide number or use the slider Slide Number O View Raw View Project Select Mode View Spine Boundary Erase Spine 5 Add Spine View Spine Label O Split Spine View Dendrite Boundary Erase Den Boundary View Dendrite Backbone Add Den Boundary Erase Den Backbone Add Den Backbone Hint Left click at one boundary point of the aimed spine move mouse around the spine then right double click to add it Features Dendrite Len 95 5558 Total Spine Num 74 Spine Label NIA Spine Status NIA Spine Area NIA Spine Length NA Sp Neck Vid NIA Spine Peri NIA 50 100 150 200 250 300 350 400 450 500 BEA Oe Ea ansta Les Neuroni Application krene Stus k vi3 41 Current image dir img001 tit Auto Processed Yes Manual Edited NA 1 Algorithm Selection CADMOS or MADMOS 2 Setting Parameter If CADMOS is selected 10 parameters in Region 2 can be adjusted e Micron Pixel MinSpLen Micron Min STD Max STD MaxSTD gt MinSTD MaxSTD should not be too high We advised that MaxSTD is set under the view project model and MaxSTD lt 10 Low Thr Upp Thr Lnk Rad Lnk Dir e MinSpLen Pixel e MaxSpLen Pixel If MADMOS is selected 2 parameters in Region 2 can be adjusted e Micron Pixel e MinSpLen 1 3 Single processing By press single processing button in Toolbar or Menu Analysis Single Processing 1 4 Vie
8. NeuronIQ version 1 5 Manual Installation NeuronIQ is running under Matlab environment for both Windows and Linux Before the installation the following should have been installed on the local machine 1 Matlab version 7 0 or up http www mathworks com products matlab e if you use matlab in Windows download the NeuronIQ Windows version e if you use matlab in Linux download the NeuronIQ Linux version 2 Matlab toolbox e image processing toolbox e bioinformatics toolbox 3 javax package which is included in the freely available Java 2 Platform http java sun com products archive Then download correspond NeuronIQ package and unpacked into one folder on the local machine Change the current Matlab directory to the folder containing the unpacked files To run the software type NeuronIQ in the command window of Matlab Team Members Project Leader Dr Stephen TC Wong Dr Zhong Xue Graphic User Interface Dr Jie Cheng Dr Yong Zhang CADMOS Dr Yong Zhang MADMOS Dr Jie Cheng Software Improvement amp Optimization Kun Chen Qing Li Software Testing Dr Fei Cao Ying Zhu Dr Peng Shi Vinothini Kamalesan Contact Dr Jie Cheng The Methodist Hospital Research Institute Radiology Department 6565 Fannin Street B5 022 Houston Texas 77030 Office 713 441 8676 Email Address jcheng tmhs org Users Manual Data Requirement NeuronIQ is designed to be used with datasets obtained by con
9. add part of the dendrite backbone left click once to change the mouse cursor to cross shape then left click at a desired location as one backbone point move mouse slowly then right click at a desired location as the other backbone point to connect them If the Left_Ctrl key is pressed the program will automatically connect the nearest detected dendrite backbone points User will need to confirm the adding after the selection e Save Manual Changes To save the manual editing results in a separate mat file e Discard Manual Changes To discard all manual editings Feature e Dendrite Len total dendrite length in the image stack micron e Total Spine Num e Spine Label e Spine Status e Spine Area e Spine Length e Sp Neck Wid detached spines e Spine Peri e Spine Class e Spine Head Wid Image Status e Current image dir directory e Auto Processed e Manual Edited otherwise N A Toolbar number of currently marked spines label number of a certain spine if the spine is removed as Deleted area of a certain spine micron length of a certain spine micron width of the neck of a certain spine micron O for perimeter of a certain spine micron class of spine based on the spine length the maximum width perpendicular to the length the name of the loaded image the name of the loaded Yes if the loaded image has been processed otherwise N A Yes if the loaded image has
10. between micron amp pixel default value is 0 084 Min Sp Len Micron the minimal length of a spine to be counted default value is 0 1 micron MinSpLen Pixel the minimal length of a spine to be counted equal to MinSpLen Micron Micron Pixel This parameter can also be adjusted after the processing For CADMOS Only MinSTD minimum standard deviation Default value is 1 MaxSTD maximum standard deviation Based on the width of the dendrite MaxSTD gt MinSTD and it is suggested that MaxSTD lt 10 Default value is 7 5 Low Thr vesselness response threshold to select the linking ending point default value is 1 Upp Thr vesselness response threshold to select the linking starting point default value is 4 Lnk Rad Linking radius It is better to set 2 lt LnkRad lt 5 Default value is 4 Lnk Dir Linking Direction Default value is 0 7 MaxSpLen Pixel the threshold of the length to distinguish spine and dendrite Default value is 50 pixels 3 View Image Stack Slider draw to the slice index which you want to observe Slide Number input the slice index which you want to observe Raw view the original image slide by slide Project view the MIP maximal intensity projection image Adjust image contrast the image contrast will be adjusted when the user drags rectangle in the view panel It works when none of the manual editing functions is selected This adjustment is only for visual purpose 4 View Mode View Sp
11. focal or multi photon fluorescence microscopy The program supports files in TIFF Tagged Image File Format with suffix tif or tiff or JPEG jpg or jpeg format both in 3D volume data or 2D single slice Currently the program only accepts greyscale images of 8 or 16 bit depth For other types of images it should be converted to the TIFF or JPEG format before using the software Menu 1 File Load an Image load a single image to process Load Directory load all images in a directory to process Save Result Export the processing results of an image into an Excel file Batch Export Export the batch processing results into an Excel file Save Current Image Save the displayed image in bmp format Close Current Image Close currently displayed image Close Directory Close currently opened directory Exit Exit NeuronIQ 2 Analysis CADMOS Curviline based spine detection and measurement MADMOS Morphology based spine detection and measurement Single Processing Automatic process for a single image Batch Processing amp Save Results Automatic process for a collection of images 3 Tools Filtering Median filter for denoising Interpolation Interpolation of images with low resolution 4 Help NeuronIQ Help load NeuronIQ Manual Online Resources Contact Contact information What s New Latest changes of NeuronIQ new functions bug corrections etc About NeuronIQ Version and authorization information Graphic User Interface
12. formation will be saved 1 7 Close Image Stack 2 Batch Processing 2 1 Load Directory 2 2 Algorithm Selection amp Parameter Same with Single Processing 2 3 Batch Processing amp batch export Two excel file will be generated Excel file 1 Statistical information of spines for all the images in current folder C ms fl 1_ File Name Spine Idx Label NumLength Area Peri NeckWid HeadWidth Spine Class 2 3 Cloz1bN1D1 Ism tif i 14 1 21062 1 2864 4 30648 0 56 1 28996124 2 4 Cloz1bN1D1 Ism tif 2 2 2 397332 1 2608 5 67488 0 16 0 536656315 3 5 Cloz1bN1D1 Ism tif 3 3 1 517893 0 7552 4 14368 0 0 6835203 3 6 Cloz1bN1D1 Ism tif 4 4 0 576888 0 4928 3 00432 0 48 0 576888204 2 7_ Cloz1bN1D1 Ism tif 5 5 1 975854 1 1328 5 7852 0 78624 0 6835203 3 8 Cloz1bN1D1 Ism tif 6 6 1 067333 0 7104 3 71056 0 0 91214034 2 9 Cloz1bN1D1 lsm tif 7 7 1 114271 2 0096 6 73704 1 3656 1 1892855 2 10 Cloz1bN1D1 Ism tif 8 8 1 131371 0 7808 3 72992 0 57936 0 724430811 2 11 Cloz1bN1D1 lsm tif 9 9 1 153776 0 6016 3 10368 0 46624 1 153776408 2 12 Cloz1bN1D1 Ism tif 10 10 0 905097 0 96 4 08304 0 8828 1 35764502 2 13 Cloz1bN1D1 lsm tif 11 11 0 339411 0 2304 1 75184 0 43312 0 339411255 1 14 Cloz1bN1D1 lsm tif 12 12 1 369379 2 1824 5 75208 1 05936 1 776288265 3 15 Cloz1bN1D1 Isrn tif 13 13 1 647301 1 9456 5 73832 0 48 2 004794254 3 16 Cloz1bN1D1 lsm tif 14 14 1 933287 0 7872 4 91896 0 24 0 609261848 3 17 Cloz1bN1D1 Ism tif 15 15 1 641463 1 824
13. ine Boundary view the boundaries of detected spines Blue means valid yellow means deleted while cyan means this spine is clicked cyan won t show in manual editing model View Spine Label view spine label information on image View Dendrite Boundary view the boundaries of detected dendrite Draw with color red View Dendrite Backbone view the backbone of the dendrites Draw with color magenta All the above modes can be viewed individually or in a combination mode superimposed on either original image View Raw or projected image View Project If the image has been processed by both two algorithms different results can be viewed by selecting CADMOS or MADMOS Manual Edit e Erase spine To erase un erase a spine left click on that spine to erase un erase all the spines attached to a dendrite piece left click on the dendrite piece e Add spine To add a spine left click once to change the mouse cursor to cross shape then left click at a desired location as one spine neck point move mouse around the spine and then right click or double click to finish the boundary drawing If the Left_Ctrl key is pressed the nearest detected spine boundary point will be searched as the current point User will need to confirm the adding e Split spine To split a spine left click once to change the mouse cursor to cross shape then left click at a desired location on one spine boundary point then right click on an
14. other boundary point of the same spine to draw a line to split the spine User will need to confirm the split after the selection e Erase Dendrite Boundary To erase part of dendrite boundary left click once to change the mouse cursor to cross shape then left click a dendrite boundary point note this point does not need to be exactly the boundary point but must be close enough to a boundary point the program is able to automatically find the nearest boundary point around the clicked point move mouse to select a segment then right click or double click to erase it User need to confirm after the selection e Add Dendrite Boundary To add a segment of dendrite boundary left click once to change the mouse cursor to cross shape then left click at a desired location and move mouse slowly note too fast mouse moving may result in some boundary points missing then right click the desired ending location to connect them If the Left_Ctrl key is pressed the program will automatically connect the nearest detected dendrite boundary points User will need to confirm the adding after the selection e Erase Dendrite Backbone To erase part of dendrite backbone left click once to change the mouse cursor to cross shape then left click at a location close to the dendrite backbone move mouse to select the segment then right click or double click to select it User will need to confirm the erasion after the selection e Add Dendrite Backbone To
15. w Result 1 If this image has been processed both by CADMOS and MADMOS different result can be viewed by changing in the Algorithm CADMOS or MADMOS 2 The Feature block show the statistical information of the clicked spine with the cyan color File Analysis Mode Tools Help Ian Gem gt ei aa 50 100 150 200 r Image Status Neuroni Application x 7 Current image dir img001 tif Algorithm capmos Q MADMOS m Parameters MicronPixet 0 08 MinSpLen Micron 0 24 MinSTD Max STD Low Thr Upp Thr Lnk Rad Link Dir MinSpLen Pixel MaxSpLen Pixel View Image Stack Last First Slide See Slide Enter a slide number or use the slider Slide Number O View Raw View Project Select Mode 7 View Spine Boundary Erase Spine Add Spine O Spit Spine v View Spine Label 7 View Dendrite Boundary Erase Den Boundary View Dendrite Backbone Add Den Boundary O Erase Den Backbone O Add Den Backbone Features Dendrite Len 95 5558 Total Spine Num 74 Spine Label 36 Spine Status Valid Spine Area 1 4528 Spine Length 2 2528 Sp Neck Wid 0 Spine Peri 71067 Spine Class 3 Sp Head Wid 1 5284 This figure shows the result of MADMOS in combined mode under View Project File Analysis Mode Tools Help Sepia gadan gt s PrP Aaah r Algorithm CADMOS O MADMOS pr Parameters MicronPixel 0 08 MinSpLen Micron 0
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