LabTrack 2.3 manual
Contents
1. Push the button to install the current selection and to leave Retrieve mode In Retrieve mode delete an entry by selecting its index at the top of the window press enter and press the trash icon You will be prompted for a confirmation that you want to delete the selected entries upon exiting Retrieve mode 17 of 18 B I O R AS LabTrack User Manual page 18 Rapid Analysis Systems for Biology and Life Sciences Tips i e Make sure that the 716 Search radius pixels control is set to a large enough value s i 3 If you do not care about large objects being tracked set the gs50 Max size pixels control to a large value s l z Make sure the 710 50 _ Min velocity pixelict _ control is not set too high izel lQuarter e If you have few and large objects consider decreasing the resolution Size 7 Quarter_ this reduces noise both from the original video signal and from small particles etc It also results in less complex objects that might have a tendency to fragment especially if the edge detector Edge detection is turned on 4 e If your objects are moving very slowly increase the Every mit frame s value so that they begin to move at least 1 pixel per frame Troubleshooting Please check Frequently Asked Questions on www bioras com lf you cannot find an answer to your questions on the FAQ page please do not hesitate to contact us info bioras com 18 of 182. depending on the range of object velocities and the resolution of the video sequences Lab Track works in grey scale Color video is automatically converted Objects are isolated from the background using a grey scale threshold value Optional image analysis functions enhance contrast and remove uneven lighting The tracking procedure consists of 1 2 3 4 5 6 T Starting LabTrack Selecting a digital video file Choosing the background threshold value Setting the tracking parameter controls Initiating the tracking procedure Viewing the result Saving tracks and related information for further processing oe od oer od 4 4 360x288 1 1 8 bit image 168 88 237 720x576 1 2 8 bit image 0 392 264 a Palette Rainbow Stop Palette Binary Stol 2 Od OG do 4 4 720x576 1 2 93 bit image 0 306 238 720x576 2 1 8 bit image 0 396 103 C Palette Binary Stop d Palette S Binary Stop j The sequence above shows a An imported movie bacteria moving along a gradient The movie is displayed with a Rainbow color palette b A Threshold has been applied and the Edge Detector turned on which brings out faint particles and removes uneven lighting effects The color palette is switched to binary to highligt light particles against a black background c the result of tracking the bacteria tracks are always displayed with a binar
3. LabTrack version 2 3 Bioras 2007 All rights reserved Play and processing Tracking Export E Track export alz Averaging frames 0 0400 Time step 1 00 Pixel size Tracks Pk I Save tracks ee 360x298 17 1 68 bit image 0 354 260 Falette SlRainbow Sto The Track export functions Track export Averaging selects the frame velocity average 2 Averaging frames Time step indicates the actual length of time 0 0400 Time step between frames taking skipped frames into 11 00 Pixel size account if only every n th frame is registered as Tacs specified in the Play tab Movie control A F F Pixel size Size of a pixel in units of length for 0 xani yx Bl Save racks calibration of LabTrack using an image of a ruler or another object with known size Tracks The track array object Choose file to write Click on the Save track button to save the track data in tab separated text Save in Video clips J elr Be BEL format M Save tracks fe A file dialog window will appear nea Name the document and save E he file can opened in spreadsheet ae programs etc 2 E UM Eomia File name E Places Save as type fan Files v Cancel 7 12 of 18 B I O R AS LabTrack User Manual page 13 Rapid Analysis Systems for Biology and Life Sciences Frame velocity average ay er a2 Averaging frames Select the frame velocity av
4. on a panel The panel is logged for the first time by first activating its window click somewhere on it with the mouse and then selecting the menu option Operate gt Data logging gt Log If the menu option Operate gt Data logging gt Change log file binding is faded then you will be asked to create a new log file and the program will subsequently log the panel in that file If the menu option Operate gt Data logging gt Change log file binding is not faded it means that a file name is associated with the panel for logging If a log file of that name does not exist the program will create a new one and log the panel there If a log file does exist the program will append a log entry for the panel after the entries that already exist When logging multiple times you can choose to log several entries in the same log file or you can create a new log file each containing one entry for each entry An advantage with the first approach is that utility programs can more easily access the entries for automatic processing of the data The facility Operate gt Data logging gt Change log file binding allows you to either switch the destination for logging to an already existing log file or to specify the name of a new log file for subsequent logging The facility Operate gt Data logging gt Clear log file binding allows you to make sure that no logging can occur to an existing log file before a specific file is s
5. which to stop tracking The minimum number of tracks that a track must be in order to be kept The radius in pixels from the current track heads within which searches are conducted for track continuation The minimum area of particles in pixels which are tracked The maximum area of particles in pixes which are tracked The minimum average velocity in pixels frame which tracks must be in order to be kept The number of frames between compaction operations were terminated tracks are kept or disregarded Interval of erasion of not to kept tracks After these settings have been considered tracking can be activated by pushing the Track button Track The button can be released any time which finishes the tracking session and saves the tracks accumulated so far into the Tracks object Otherwise tracking will be terminated at the frame specified in the End frame control Track display LabTrack 2 1 LabTrack LabTrack version 2 3 Bioras 2007 All rights reserved Tracking settings eel le a Start frame snos End frame ao Min length frames aa Search radius pixels a4 Min size pels 50 Maz size piels 10 50 _ Min velocity pixel soe Compaction interval Tracks E84 Particles 118 1 O8 Frame Track display ais Tail length I ate 360x298 17 1 68 bit image 355 103 Falette Rainbow Sto 10 of 18 B I O R AS LabTrack User Manual page 11 Rapid Analysi
6. 9 Optimizing tracking PELfOPMANCE ccccceecccseeeeceeeeceeeeeseeeesaeeeeseucessueeeseeeessasesseeeesseeesseeesaaees 9 TE AG FI ccnp cust anaes atic EEE E EEE ttc E E E EN 9 Track SOWING eea E canola E E E 10 Trackdio pid V ressas A A ne een ree een ene Cree ners 10 Indicators SHOWN While trACKiNG ccccecccsecceeeceeeceecceeeceeeceeeseeseeeseeeseeeseeeseeeseeeseeeteeeseeeteeees 11 EDO 4 cle Fenton ent Merten tere eer er mere Sere ee rer en errr eter er Serre errr tr errr eer er errr errr tt Te 12 The Track export TUNCUONS sincuancsrauwiniinauanesiaawansione aE RE E Nidaa 12 Frame velocity avera Chenin auncent sum auieaiteinoainanoratteun E Een eRe Een iind 13 Calibration of time between frames and pixel SIZEC cccccceeeeceeeeeceeeeceeeeeseeeesseeeeeeeesaeeesaes 13 Ar aV ODEO oa eee ee eee nee ee eer eee eee eee ee ne ee eee 14 EX DORE WG a E E 14 saving retrieving and deleting Gata ccccccccsececcsecsceecesceescceecescesecceeseccesesceeeescesesceecesseessceaes 16 TiO Suepisastacptsdudsaptlagindp E tae baauathGeacubitebaauetsacaaubatetanusticdadatanciadestsacanndanetanuishciauntadatanuiiae 18 TOUS S OO TING opran E E E E E EE E E E teaasaceaties 18 20f18 B I O R AS LabTrack User Manual page 3 Rapid Analysis Systems for Biology and Life Sciences General description LabTrack is a program for tracking moving objects between successive video frames LabTrack can track hundreds of objects simultaneously
7. B O R AS LabTrack User Manual page 1 Rapid Analysis Systems for Biology and Life Sciences LabTrack User Manual Version 2 3 March 2010 B l O R AS LabTrack User Manual page 2 Rapid Analysis Systems for Biology and Life Sciences LabTrack Particle tracking in digital video sequences Indhold Ganer deSeiip iON anen rete er tere ernie erie tenet ene ern E eer ee ern Ae eee eee eer 3 PTS TUNIC E E A doaeccumnaus ace Gens T N E E E E E 4 AAM LADT AICR eae E E E eee eee 4 Orena Delara E A E A EE EE ESS 4 Start and Stop LaD TACK ssis EE nse en eer EEES 5 Reinitialize to CETAUIt 2 0 ccc cceccceececeeeceeeeceeeese cece eeseeeeseeeseeeseuesseeseueesaeessueeseesseeeseueesaeesaueeseeeeaes 5 Play and Processing tab for opening viewing and cropping QUICKTIME MOVIES c seceeeeee ees 5 MIO WI contol Opern MOVIE visa a eiersdecanenotnansaneesansastensansGasceeivenscuueetomnataienannece sense eneuaceedeeestenede 6 MOVIS DIY Cl a viccunirastent S a ReeentyietN 6 lageto sgeids e cca E N E T E E T T E E 7 NSO SO eenen A a leatartomtoartanneaaletatontonntan 7 Me CS DOMANO cranent cetsueutnetonend sotououd uetenend E botewoud metenen Rane maou nee eRe 8 FTI UL arnan 8 Tools for VIEWING and Cropping cccceeccceecceeeeceeeceeeseeeceueeseeeceucesaeesseeeseeeeseeeseeeeseueeseeesseesseeees 8 LOOM MNAn OU e E E E E EE EAE E E E E EE 9 10 0 0 ge MEINA i EE REEE ee EOS 9 POOD IEE ene ee eer ee nen E E eo O ee ee ee ee eee
8. Edge J Small Eyer all frame s detection Movie player Tracking setup Play i Frame 2 Forward 0 00 Delays Full frame Falette aR alnbow On line help All controls have tip strios associated with them These are pop up text strips that appear when the cursor is moved over them Right clicking on a control also offers a Description and tip dialog that describes the function of the control Ctl h opens a help window which shows the documentation of the control under the cursor 4of 18 B I O R AS LabTrack User Manual page 5 Rapid Analysis Systems for Biology and Life Sciences Start and stop LabTrack LabTrack starts in run mode To stop LabTrack click the SSE button lower right side of frame This allows you to log the panel if required To re start LabTrack click on the arrow at the upper left of the window or choose the Operate gt Run command from the menus Reinitialize to default Settings can be reinitialized to default by right clicking the value and choose Reinitialize to default ut Dieta Copy Data Paste Wate FReinttialize to Default Value Description and Tip In order to reinitialize all values to default Stop LabTrack open the coder a Operate menu and choose Reinitialize to default o _ _ The menu will only appear when LabTrack is stopped Print at Completion Log at Completion Data Logging Reiniti
9. alize All to Default Connect to Remote Panel Play and Processing tab for opening viewing and cropping QuickTime movies LabTrack 2 1 L a bT ra C k LabTrack version 2 3 2 Bioras 2007 All nghts reserved Play and processing Tracking Export Movie control Image frame processing Open movie L Invert Size SHar Threshold A 220 Frames 108 Edge J Small yan aT jamel detection Movie player Tracking setup Tla alt Frame 2 Forward i 0 00 Delays Full frame 360x288 17 1 68 bit image 168 88 237 Palette Rainbow Sto 5 of 18 B I O R AS LabTrack User Manual page 6 Rapid Analysis Systems for Biology and Life Sciences Movie control Open movie Movie contral Open movie _ Size SHa H Frames i 0g E frame s Open movie Opens a digital movie file Size Movie frame size resolution Choose between Full Half Quarter etc Frames The number of frames in the movie Every n frame s Specify to use every n th frame from the movie sequence This can speed up tracking for objects moving slowly relative to the video frame rate Every Push the Open movie E button and select a QuickTime movie file a browser window will appear Open Ei ES Look in E Videos e pi tur Preview D My Great Movie iMovieProject O My Great Movie iMovieProject DSCN2960 MOV ay avi G aS awi File name Epit ovobacter awi Files of
10. calibrated and averaged acceleration vector Microsoft Excel Ovobacter txt Bax Eaj File Edit View Insert Format Tools Data Window Help Acrobat Daje larbhraavy r 2 at Ml 4 10 2 Track Angle Ax 153 1250 90 0 90 625 625 0 312 0 0 04 0 06 0 12 0 16 0 2 0 04 0 06 0 12 28 5 0 16 ld 4 H Ovobacter Ready Example of data imported into a spreadsheet 1 1 1 1 1 d 1 1 2 2 2 2 2 3 3 3 3 3 A 4A 4A 4 4 5 5 5 14 of 18 B I O R AS LabTrack User Manual page 15 Rapid Analysis Systems for Biology and Life Sciences 15 0f 18 B I O R AS LabTrack User Manual page 16 Rapid Analysis Systems for Biology and Life Sciences Saving retrieving and deleting data The Menu bar appears when the program is stopped Lower right Stop button File Edit SVitrica Project Windows Help Run Stop Print at Completion Log at Completion Data Logging A Log suspend when Called Retrieve Purge Data klake Current Yalues Default Reinitialize All To Default Change Log File Binding Clear Log File Binding Change to Run Kode EM The data logging menu Data is saved and retrieved through a procedure called data logging This means that a snapshot of the panel including all objects containing data is saved in a log file This feature can be used both for saving different configurations for a panel as well as for saving data that resides
11. erage with this control At each video frame the velocity of a particle is calculated as the length of the vector over the specified number of frames for averaging projected forward in time divided by the time that the given number of frames represents NOTE The total length of tracks are truncated at the end by the number of frames that are used to average the velocity Averaging provides a smoothing effect on all derived parameters from the track data Calibration of time between frames and pixel size Parameters can be calibrated with the 0 0400__ Time step ang 1 00___ Pixel size settings Time step Indicates the length of time between frames or multiples thereof taking skipped frames into account if only every n th frame is registered as specified in the Play tab Movie control Pixel size The size of a pixel in units of length The system can be calibrated using an image of a ruler or another object with known size see example below NOTE The coordinate system has its origin at the top left of the video frame fal LabTrack 2 1 j 7 E L a bT ra G k LabTrack wersion 2 3 Bioras 2007 Play and processing Tracking Export All rights reserved Track export Je Averaging frames 0400 Time step 7 i 00 Pixel size Tracks Rectangle tool Comments aaa Sq uare d rawn p with the Rectangle tool 400x203 1 1 8 bit image 19 1 0 gt 298 88 _ Square size in pixels length x height The size i
12. nd Turn edge detection by convolution on or off and adjust edge detection level Small Medium Large Edge detection enhances object definition and counteracts uneven lighting Adjust until objects are clearly defined and background noise is removed Invert The Image processing procedure works by selecting a range or grey scales the entire range is O 255 starting from the brightest 255 The lower range from 0 to the selection is considered background and the selection to 255 is considered potential objects If you have dark objects against a bright background depress the Invert button to invert the image If the Threshold OFFI button is off the background is automatically taken to be grey level 0 and everything else will be considered as potential objects If you need to set a threshold to more precisely isolate objects of interest against the background then while playing the movie depress the button and adjust the threshold level until you see the objects you want to track Edge lf there are problems with contrast or uneven lighting depress the detection button and re adjust the threshold until you see the objects appearing against the background The Edge Detection sensitivity control offers three levels which are actually related to the size of a convolution kernel for performing edge enhancement Small 3x3 pixels Medium 5x5 pixels Large 9x9 pixels Lower setting result in higher sensitivity of the analysis L
13. on 360x288 pixels Size 1 1 8 bit image Cursors coordinate within the frame 88 237 Palette Change grey scale palette to false color spectrum to highlight objects The color palette will ony affect the video display but NOT the video analysis Gray 360286 Binary Gradient Palette Temperature Set to Rainbow or Binary when using sensitive edge detection Tools for viewing and cropping Magnifier tool Pointer tool Hand tool for moving the image The rectangle tool for selecting a rectangular part of the video 8 of 18 B I O R AS LabTrack User Manual page 9 Rapid Analysis Systems for Biology and Life Sciences Zoom in and out The display window can be enlarged using the magnifier tool IP tool from the Tools Palette holding down the shift key shrinks the display window Cropping the image The image can be cropped using the rectangle tool and dragging Full frame Pushing the Full frame button can be restored the full frame size Color palettes a The Palette menu Palette giRainbow _ can attach color palettes to grey scale values The most useful are the Rainbow grey scale 0 is blue and Binary attaches a random color to each grey scale value grey scale 0 is black Optimizing tracking performance While the Play button is depressed the threshold and image processing controls can be used to optimize tracking performance The button must be released in order
14. ower settings also result in more noise sensitivity A larger setting can be beneficial to limit fractionation of larger particles Video display The video display frame is visible in all tabs 5 LabTrack 2 1 LabTrack a worsen Bioras 2007 All right d Play and processing Tracking Export rights reserve m Movie control Image frame processing Open movie Invert Size galt Threshold A220 Frames eo Edge Sem Video display Every i framefs detection f ra m e Movie player Tracking setup Py j a Frame 2 Foward 0 00 Delay s Full frame jij 360x283 1 1 3 bit image 168 88 237 f Mette Rainbow 7 of 18 B l O R AS LabTrack User Manual page 8 Rapid Analysis Systems for Biology and Life Sciences oer ol Oe vo 360x288 1 1 8 bit image 168 88 237 720x576 1 2 8 bit image 0 392 264 Palette iRainbow Stop Palette Binary Sto Left A movie displayed with a Rainbow palette Right A threshold has been applied in this case 80 and the Edge Detector turned on in this case Medium which brings out faint particles and removes uneven lighting effects The color palette has been changed to Binary to highligt light particles against a dark background The color palette does not affect the analysis only the display Image information Image information is displayed below the video display 360x258 1 1 85 bit image 168 88 237 Movie Resoluti
15. pecified before subsequent logging Example If you have a panel that you would like to log in a new log file you can do one of two things 1 Choose Operate gt Data logging gt Clear log file binding if a file is currently associated otherwise this option will be faded followed by Operate gt Data logging gt Log You will then be prompted for a file name and your panel will be logged there 16 of 18 B I O R AS LabTrack User Manual page 17 Rapid Analysis Systems for Biology and Life Sciences 2 Choose Operate gt Data logging gt Change log file binding You will be prompted for a new or existing file Choose Operate gt Data logging gt Log and your panel will be logged in the file you specified _ ay A comment can be written in the comment box before logging for documentation purposes The data for a panel that resides in a log file can be retrieved by selecting the panel in question followed by choosing Operate gt Data logging gt Retrieve If Retrieve is faded it means that no log file is currently associated with the panel You can specify an existing file with the command Operate gt Data logging gt Change log file binding In Retrieve mode you can view the entries each representing a snap shot of the panel at the time of logging including data You can either type in the index of a particular entry or you can sequentially move through them with the small arrow controls
16. s Systems for Biology and Life Sciences Track display Animate j p 1 z Tail length E Label Animate tracks Tail length control in Draw all tracks with until button is frames to use for unique colors released track animation Indicators shown while tracking The Tracks indicator shows the number of tracks already terminated Tracks 682___ The Particles indicator shows the number of objects that are considered for tracking within each video frame Particles 113 l he Frame indicator shows what frame the tracking algorithm is working on Frame 57 You may wish to view tracks in at least two situations 1 You have just finished a tracking session and want to see the results 2 You have retrieved a previously logged tracking session see below and wish to see those results In both cases tracks can be displayed in a window by pushing the Label button Labell Each track is given a unique color Tracks can also be animated by pushing the Animate button Animate The tracks will be plotted with time in units of video frames and with a certain tail length specified in the Tail length control 15 Tail length 11 of 18 B I O R AS LabTrack User Manual page 12 Rapid Analysis Systems for Biology and Life Sciences Export tab Inthe Export tab stored tracks can be exported Export of tracks is very easy simply push the Save tracks button and name the export file LabTrack 2 1 La bT rac K
17. s be shown by right clicking on the sqare Take a video sequence of a ruler or object with known size Use the Rectangle tool to draw a square In this example the square was 5 cm long Read the length of the square in pixels by right clicking on the square length 297 pixels Calculation of pixel size Square length mm square length pixels 50mm 297pixels 0 168 mm pixel e Enter the pixel size in the Export tab Lab Track Play and processing Tracking Export Track export 13 of 18 B I O R AS LabTrack User Manual page 14 Rapid Analysis Systems for Biology and Life Sciences Array object Tracks Tracks are stored in an array object consisting of and x and y coordinate j 1 3 x an46 e for each video frame The first index of the array is the track index and the second is the frame number both starting from 0 Export file The exported file contains 11 columns 1 Track number The number of the track 2 Time Calibrated time 3 X Calibrated X coordinate origin is top left 4 Y Calibrated Y coordinate origin is top left 5 Vx Calculated and averaged velocity in x direction left to right 6 Vy Calibrated and averaged velocity in y direction top to bottom 7 V Length of the calibrated and averaged velocity vector 8 Angle Angle of the velocity vector 9 Ax Calibrated and averaged acceleration in the x direction 10 Ay Calibrated and averaged acceleration in the y direction 11 A Length of the
18. to continue with the tracking procedure Tracking Tracking works optimally for objects moving 2 or 3 pixels in the image per frame If they are moving much slower than that it can be an advantage to track every second frame or some other multiple of frames This can be specified in the Play and processing tab Movie control change aj the number in the frame control Every J frame s A number of parameters can be set for optimizing the tracking procedure These are listed and described below LabTrack 2 1 L a bT ra C K LabTrack version 2 3 2 Bioras 2007 All rights reserved Tracking settings Track a all Start frame alt jg End frame ap Min length frames tTracks D jE search radius pixels ee Particles il 16 doo Min i IPE Frame FT a50 Max size pixels ue 10 50 Min velocity piel ct alt gg Compaction interval Track display Animate 35 Taillength E Label 360x288 1 1 8 bitimage 0 5 167 Palette Rainbow Sto 9of 18 BIORAS Rapid Analysis Systems for Biology and Life Sciences Tracking settings Tracking settings Track Tracks fr Particles 116 i af Start frame JEN ain frame Bo Min length Mame af En che pixels Mo Min ace Pixels ao Mar size DEES EE Min venc aie sioe Compaction interyal Frame LabTrack User Manual page 10 The frame number to start tracking from The frame number at
19. type Movies Cancel preate I Show Preview The number of frames in the movie file will appear in the Frames indicator Frames F197 x Select the resolution that you want to work with in the size popup menu Size alha View the movie by pushing the Play button ay Movies will play back at different rates depending on the compression algorithm used Type ina start frame number at any time in the Frame control Jo F Frame Sooo Delay control Inter frame delay 710 00 _ Detay s Movie player Movie player Play the movie until the button is released Crop frames with the rectangle tool Play J 31 Framet 2 Frame 2 Current frame number Forward 0 00 Delay s Direction forward or backward through video frames Delay Delay for playback display Full frame jj Full frame Restore to full frame after cropping 6 of 18 B I O R AS LabTrack User Manual page 7 Rapid Analysis Systems for Biology and Life Sciences Image processing The image processing settings determine the quality of the tracking analysis Image frame processing Turn grey scale inversion on or off LabTrack tracks light objects against a dark background Use only if the digital video is of dark objects against a light background Threshold 7 Set the grey scale threshold from white 255 down to the Edge given value The objects to be tracked should be clearly detection distinguishable from the backgrou
20. y palette d Close up of tracks 3 of 18 B I O R AS LabTrack User Manual page 4 Rapid Analysis Systems for Biology and Life Sciences Installing LabTrack The setup exe program is a Windows Installer which installs the program and other components If you have a previous version of LabTrack installed the installer will uninstall the previous version run the setup exe program again to install the new version LabTrack requires QuickTime to be installed It can be downloaded free from www apple com QuickTime enables LabTrack to interpret virtually all digital video formats LabTrack can interpret all formats that the QuickTime Player can display and you can test if QuickTime is installed properly by opening video in the QuickTime Player The first time LabTrack is run you will be asked to enter a license key The license key can be acquired from info bioras com Two different keys are available e Time limited trial key activates LabTrack with its full functionality for a time period of 1 month e Permanent license key upon purchase of license The trial license can be upgraded to a permanent license Starting LabTrack LabTrack opens with the Play and Processing tab and without a video loaded LabTrack 2 1 La bT rac k LabTrack version 2 3 2 Bioras 2007 All nights reserved Play and processing Tracking Export Movie control Image frame processing Open movie Invert Size Halt Threshold Azz H Frames T
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