ABDigitizer Version 1.0 User Manual
Contents
1. igitizer ABDigitizer Version 1 0 User Manual Manual Version 1 0 rev2 2012 Chinou Jouhou Shisutemu Inc All rights reserved For ABDigitizer 1 0 Table of Contents Bt e ge elle e EE e He ln EE 3 HOW NR Ee He EE 321 Stabe tne EEN 3 2 0pen Video EE 3 3 Calibration of Length A Oct E A A 3 4 Digitizing Settings Coordinates Detection 0occcoccoconcconnoncnnncancnnnnnnnnnan anos 3 5 Perform Digitizing Coordinates Detection eee eee ee tees eeeeaeeaee 11 3 6 Analysis Trajectory and Heat Map ee ence cece eeeeeeeeeeaeeaees 13 3 61 Trajectory it dba a RE ee Lae eaten ya Teena DEEN dE ee e EN ee dg 13 336 2 HeatMap PO POCO re i E E E E E TE 15 3 7 Creating Mask Image and Marker Image 18 3 7 1 Creating Mask Image ssssssnnnnnrssnnrrrrrnnrrnnnnrrnnnnnnrnnnnnnnnnn nunnana 18 3 7 2 Creating Marker Mage cuina ai di 20 3 8 Analysis from Position Coordinates eee eens eee este eeeeeeaeeeaeeaenaes 21 4 Other Operations iii A i es 22 4 1 Creating User Defined Color Bar ccccccccssecceeceeeeeseescesseessteeeseesaeeenes 22 4 2 Sereen SIZO EE 22 S Late UU EE 23 ABDigitizer 1 0 User Manual 1 Introduction ABDigitizer is a digitizing software which analyzes video images of animal behavior experiments recorded with video camera automatically retrieves position coordinates of multiple target animals and output them as time series data ABDigitizer has the following features e Extract multiple tar2. 186238532110092 0 250 21743119266055 922018348623853 147706422018349 186238532110092 0 300 21 8348623853211 931192660550459 147706422018349 186238532110092 0 350 21 8348623853211 940366972477064 148165137614679 186238532110092 0 400 21 8807339449541 954128440366972 148165137614679 186238532110092 0 450 21 9266055045872 963302752293578 148165137614679 184862385321101 0 500 21 9266055045872 972477064220184 148623853211009 186238532110092 0 550 21 9724770642202 981651376146789 14 8623853211009 186238532110092 0 600 220183486238532 990825688073395 148165137614679 186238532110092 0 650 220183486238532 10 148165137614679 186238532110092 0 700 220642201834862 100917431192661 148165137614679 186238532110092 0 750 220642201834862 102293577981651 147706422018349 186238532110092 0 800 221100917431193 103669724770642 148165137614679 184862385321101 0 850 221559633027523 104587155963303 147706422018349 186238532110092 0 900 221100917431193 105045871559633 147247706422018 186238532110092 0 950 221559633027523 106422018348624 147247706422018 186238532110092 0 1000 221559633027523 107339449541284 148165137614679 185321100917431 0 1050 222018348623853 108256880733945 147706422018349 185779816513761 0 1100 2220183486238653 109633027522936 147706422018349 186238532110092 0 1150 222018348623853 1110550458715596 1147247706422018 184403669724771 10 x Figure 10 Main Screen after Digitizing Finishe
3. button and finally push Marker Apply button Once the Marker Apply button is clicked this button changes to the Marker Remove button To erase the marker superimposed on the heat map click the Marker Remove button again In the bottom right area of the screen background color color bar and these value ranges used for the heat map are displayed The created heat map can be saved to file by clicking File Save Files Heat Map menu of the main screen Saved file format is Bitmap format bmp The color bar used for the heat map can be saved to file as image Click File Save Files Color Bar menu of the main screen Saved file format is Bitmap format bmp 17 23 ABDigitizer 1 0 User Manual 3 7 Creating Mask Image and Marker Image 3 7 1 Creating Mask Image Click Tools Make Mask Image menu of the main screen to draw mask image Draw Mask screen is displayed Draw Mask OI Displayed Frame Cancel Figure 16 Draw Mask Screen Input the frame number into the Displayed Frame box which is used for underlying basis of mask image The Draw Mask screen has five buttons of Arrow Fill Circle Square and Line e Arrow This button choices drawn shapes and moves them Click drawn shape move it with your mouse and click its new position again s Fill Click the position of the area you want to fill in with black Click again to erase the filled in area e Circle Square
4. Frame Frame Set Current Frame Target Target Color Remove Binarize Threshold 434 1099 Figure 8 Clicking the yellow target and adjusting the slide bar 9 23 ABDigitizer 1 0 User Manual Digitize Setting Backeround Frame Background D Frame Set Current Frame Analysis Range Start Frame Set Current Frame Frame Set Current Frame Binarize Threshold 356 1099 ok Cancel Figure 9 Three targets are registered yellow blue and pink 5 Complete the Settings Click the OK button 10 23 ABDigitizer 1 0 User Manual 3 5 Perform Digitizing Coordinates Detection Click the Digitization Execution menu of the main screen to perform digitizing of targets After digitizing finished showing tab changes from Video tab to Position Table tab in the main screen P ABDigitize File Digitization Analysis Tools Help Video Heat Map Trajectory Time ms TargetOX cm Target em Target cm Targetl km Target2Xlcm 21 605504587156 871559633027523 147706422018349 185779816513761 0 Dei 50 21 605504587156 885321100917431 14 7706422018349 18 5321100917431 0 100 21651376146789 894495412844037 147247706422018 186238532110092 0 150 21 697247706422 903669724770642 147247706422018 186238532110092 0 200 21 743119266055 912844036697248 147247706422018
5. Line Click the start point on the image move your mouse and click the end point again 18 23 ABDigitizer 1 0 User Manual e Erase the Drawn Shapes Click Arrow button and select shape you want to erase and push Delete button of your keyboard e Created mask image can be saved to file by File Save Files Mask menu m J Draw Mask Tools BE PA Displayed Frame Y Figure 17 Mask Drawing Sample Only fill in elimination area in actual 19 23 ABDigitizer 1 0 User Manual 3 7 2 Creating Marker Image Click Tools Draw Marker menu of the main screen to draw marker image The Draw Marker screen is displayed In this screen draw image you want to superimpose specially on the heat map such as the start position of the experiment animals Draw Marker Tools OI JM Displayed Frame Cancel Xi 18 Draw Marker Screen Input the frame number into the Displayed Frame box which is used for underlying basis of marker image The Draw Marker screen has six buttons of Arrow Fill Circle Square Line and Color e Arrow This button choices drawn shapes and moves them Click drawn shape move it with your mouse and click its new position again e Color This button below the Square button selects drawing color The default color is black Shape buttons such as square use the selected drawing color Fill button also uses the selected drawing color s Fill Clic
6. d Important Position coordinates shown in the Position Table tab assume the origin to be the bottom left corner of the frame image When the target position can t be detected position coordinates of the target in that frame will be displayed as 0 0 0 0 If you get many frames which can t detect targets adjust the slide bar described in the section 3 4 Digitizing Settings so that the white portion expands and perform digitizing again 11 23 ABDigitizer 1 0 User Manual Switching to the Video tab in the main screen you can review the detected target positions visually as video image Detected target positions are indicated as circle with the color of the specified target 4 ABDigitizer 1 0 54 File Digitization Analysis Tools Help Video Position Table Heat Map Trajectory 47 623 frame Figure 11 The Video tab of the Main Screen after Digitizing Detected position coordinates that is the contents of the Position Table tab can be saved to file by clicking File Save Files Position Table menu of the main screen Saved file format is the CSV format Detected position video that is the contents of the Video tab can be saved to file by clicking File Save Files AVI menu of the main screen Saved file format is the AVI format 12 23 ABDigitizer 1 0 User Manual 3 6 Analysis Trajectory and Heat Map 3 6 1 Trajectory Click Analysis Trajec
7. ecify frame number to calibrate Input the target frame number into the Displayed Frame box 2 Specify the known length on the calibration screen Click the start point of the known length on the screen then red line will be drawn Move your mouse to the end point of the known length and click again 3 Input the known length value into the Length box in the bottom of the screen Length unit can also be specified default unit is cm 4 To erase the drawn red line on the screen and redraw it click Reset button 5 If you succeeded to draw red line correctly then push OK button Calibration Displayed Frame a f LE ee Figure 5 Calibration with the Known Length 6 23 ABDigitizer 1 0 User Manual 3 4 Digitizing Settings Coordinates Detection After calibration of length you must configure digitizing settings Click Digitization Setting menu of the main screen The Digitizing Settings screen is displayed Y Digitize Setting Background Frame Background Y Frame Set Current Frame Analysis Range Start 0 Frame Set Current Frame 0 Frame Set Current Frame Set Delete Mask Target Target Color Binarize Threshold 0 1099 Figure 6 Digitizing Settings Screen Configure digitizing settings by the following procedures 1 Specify Background Frame Specify the background frame which contains no targets Background image is used for extrac
8. get position coordinates independently by color discrimination method e Output position coordinates not in pixels but in real length unit e Split experiment spaces to grids and create heat map of visit frequency of each target e Create trajectory chart of targets with time markers of constant time interval if you need e Output target position coordinates video with detected positions heat map and trajectory chart e You can create and save image mask which restricts experiment area e You can draw any shapes on the heat map freely 2 Requirements This software works with the following environment e CPU Intel Core 2 Duo 1 2 GHz or above e Memory 2 GB or above Processable video size is dependent on the memory capacity PC with large amount of memory is recommended e OS Microsoft Windows XP Windows Vista Windows 7 32 bit version 1 23 ABDigitizer 1 0 User Manual 3 How to use ABDigitizer Usage of ABDigitizer is described below 3 1 Start the Software Click Start All Programs ABDigitizer from Windows start menu Then ABDigitizer is started and the following screen called main screen is displayed gt ABDigitizer 1 0 E BR File Digitization Analysis Tools Help Video Position Table Heat Map Trajectory Figure 1 Main Screen immediately after started 2 23 ABDigitizer 1 0 User Manual 3 2 Open Video File Click File Open Files AVI
9. hart changes trajectories of the multiple targets The up and down button placed in the bottom right of the chart changes the size of the time markers in case you configured to draw them This trajectory chart can be saved to file by clicking File Save Files Trajectory menu of the main screen Saved file format can be selected from Enhanced Metafile format emf Bitmap format bmp or PNG format png 14 23 ABDigitizer 1 0 User Manual 3 6 2 Heat Map Click Analysis Heat Map menu of the main screen to split frame images to grids calculate visit frequency of each grid in concrete number of frames the target existed in the grid and create heat map chart The Heat Map Settings screen is displayed Heat Map Setting Grid Square shaped Grid Size pixel Color Bar Background Color MN Black Radiation v Auto Figure 14 Heat Map Settings Screen Setting items of this screen are described below e Grid Specify square grid size in pixels which split up the frame images Grid shape can only be square e Color Bar Specify color bar which is used for creating heat map The Background Color label is background color which defaults to blue Figure 14 Click the blue label and select background color you want Also select color bar from the drop down list User defined color bar can be loaded The range of the color bar can be set automatically by setting Auto checkbox on or input minimum and maxi
10. k the position of the area you want to fill in with the selected drawing color Click again to erase the filled in area 20 23 ABDigitizer 1 0 User Manual e Circle Square Line Click the start point on the image move your mouse and click the end point again e Erase the Drawn Shapes Click Arrow button and select shape you want to erase and push Delete button of your keyboard e Created marker image can be saved to file by File Save Files Marker menu Draw Marker Cancel Figure 19 Marker Drawing Sample 3 8 Analysis from Position Coordinates Click File Open Files Position Text menu of the main screen to load position coordinates to the Position Table tab which were digitized in the past Once you loaded position coordinates you can create trajectory chart and heat map 21 23 ABDigitizer 1 0 User Manual 4 Other Operations 4 1 Creating User Defined Color Bar Create horizontally long rectangle image with paint tool e g 256 pixels in width and 10 pixels in height Create the image so that the color changes from the left towards the right Create the height direction so that it becomes the same color In this software left side of the color bar is used as minimum value and right side of the color bar is used as maximum value Save the color bar image to file as the Bitmap format either 32 bit format or 24 bit format 4 2 Screen Size Moving your mouse to the bottom right cor
11. menu of the main screen to read input video file The Video File Selection screen is displayed Select video file and push Open button Readable video file format is the AVI format avi Open AVI file IES O data E mv1_0466 al 22224444 My Recent Documents File name ll My Network Files of type AVI files vil Cancel Figure 2 Video File Selection Screen 3 23 ABDigitizer 1 0 User Manual After reading video file video image is displayed in the Video tab of the main screen it ABDigitizer 1 0 f f JEJ File Digitization Analysis Tools Help Video Position Table Heat Map Traiectory 293 1099 frame Figure 3 Main Screen after video file was read You can play and stop the input video with the buttons placed in the bottom of Video tab Slide bar can be used to jump to any frame position of the input video Frame number is displayed on the right hand side of the slide bar 4 23 ABDigitizer 1 0 User Manual 3 3 Calibration of Length Next perform calibration of length to convert image length pixels to physical length real length Click Digitization Calibration menu of the main screen then the Calibration screen is displayed Y Calibration Displayed Frame Figure 4 Calibration Screen 5 23 ABDigitizer 1 0 User Manual Calibration of length can be performed by the following procedures 1 Sp
12. mum values manually by setting Auto checkbox off Click the OK button to see heat map in the Heat Map tab of the main screen 15 23 ABDigitizer 1 0 User Manual ABDigitizer 10 File Digitization Analysis Tools Help il x Video Position Table Heat Map Traiectary Target Gausian Filter oso Gaussian Apply TareetO b dan lauter a gei Les ke Marker Apply Figure 15 Heat Map Screen Heat Map tab of the main screen Usage of Heap Map tab of the main screen is described below s The Target drop down list placed in the bottom left of the screen will change the trajectories of multiple targets e The Gaussian Filter slide bar applies Gaussian filter to the heat map Adjust the slice bar and push Gaussian Apply button e Freely drawn pictures can be superimposed on the heat map as marker Push the Marker Apply button and select any marker images created by Tools Draw Marker menu of the main screen this procedure is described for detail in the subsequent section The Marker Apply button is enabled when marker image 16 23 ABDigitizer 1 0 User Manual was created by Tools Draw Marker menu or when marker image was read by File Open Files Marker menu Then Marker Apply button is enabled after the Gaussian Apply button was clicked If you don t want to apply Gaussian filter set Gaussian filter slide bar to the left most position push Gaussian Apply
13. ner of the main screen your mouse pointer shape will change to double arrow Drag the mouse pointer in that state and the size of the main screen will change 22 23 ABDigitizer 1 0 User Manual 5 Inquiry Please tell us inquiry about ABDigitizer below Chinou Jouhou Shisutemu Inc ABDigitizer Customer Support TEL 81 75 321 7300 FAX 81 75 321 7305 E mail abdigitizer chino js com Additional information might be published in our homepage ABDigitizer homepage URL http www abdigitizer com en 23 23
14. nu and can be saved by File Save Files Mask menu of the main screen How to create mask image is described later Now just click the Open button and select mask image This process is not necessary if you not need mask out measurement area X Digitize Setting Background Frame Background D Frame Set Current Frame Analysis Range Start Frame Set Current Frame Frame Set Current Frame Target Target Color Mask Binarize Threshold 0 099 Figure 7 Mask Image Setting Screen 4 Specify Targets Click the targets you want to auto detect Since this software detects and tracks targets based on the target color you must click the portion of the target specific color After clicking target the frame image is binarized 8 23 ABDigitizer 1 0 User Manual that is image is converted to black and white color Figure 8 Move and adjust the slide bar below the Set button to turn the target to white and others to black After adjusting the slide bar click the Set button The screen image will switch to normal and selected target will be displayed in the Binarize table Figure 9 Mask image will not be displayed To erase the registered target click the left most column of the target row in the Binarize table to highlight the row and click Remove button Digitize Setting Backeround Frame Background 0 Frame Set Current Frame Analysis Range Start Frame Set Current
15. ting target animals If image with no targets does not exists in the input video please refer to the following More Detail section and specify the head frame or any frame you want More Detail This software takes difference between all frames of the range between frame numbers of Start and End box and the background frame specified in this settings screen to extract targets with improved accuracy If this input video has no frame of background only image and if you specified frame between the frame numbers of Start and End box then this software can t extract targets of the specified background frame In this case specify the frame number out of the rage between Start and End 7 23 ABDigitizer 1 0 User Manual 2 Specify the Range of Analysis Input the start frame number into the Start box and the end frame number into the End box directly Alternatively move the slide bar in the bottom of the screen and click the Set Current Frame buttons below the Start and End box to input the current frame number automatically 3 Specify Mask Image Places other than the measurement area can be masked out If some image variation such as human shadow movement happens in the places out of the measurement area target detection accuracy might possibly be degraded To avoid such degradation places other than the measurement area should be masked out Mask image can be created by Tools Make Mask Image me
16. tory menu of the main screen to show the detected targets as trajectory chart The Trajectory Settings screen is displayed Trajectory Setting Range x Min D xMa 100 ams y Min 0 y Max 100 fom Auto Line Thickness 1 pixel Color Black D Time Marker I Use Time Marker Form Circle Color Black Marker Period 05 s Ok Cancel Figure 12 Trajectory Settings Screen Setting items are described below e Range Configure minimum and maximum value of each axis Setting Auto checkbox of each axis on drawing range of that axis will be set automatically e Line Configure drawing line width and color e Time Marker Draws time markers on the target trajectory with constant time interval Setting Use Time Marker checkbox on enables this drawing Configure time marker s shape color and time interval Click the OK button and you will see trajectory chart in the Trajectory tab of the main screen 13 23 ABDigitizer 1 0 User Manual ABDigitizer 10 File Digitization Analysis Tools Help Video Position Table Heat Map Trajectory 30 Target0 e Target0 Marker 2 s 24 18 E E 12 6 0 0 6 12 18 24 30 x cm Target Target0 e Figure 13 Trajectory Chart Screen Trajectory Tab of the Main Screen Usage of Trajectory tab of the main screen is described below The Target drop down list placed in the bottom left of the c
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