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Mice Profiler Video Label Maker

by Fabrice de Chaumont

Mice Profiler Video Label Maker processes tracking data to label a sequence thanks to a repertoire.

Publication Id
ICY-T1R9E8
See technical details
View complete changelog
Tags: tracking - mice

Documentation

Tutorial about this software:

 

Note:


-  A new checkbox, 'freeze setting' allows one to avoid the update of the parameters (threshold, speed, fps...) of selected animals. This is useful if a problem like different fps or different cage size is used for different animals. Still this should be exceptionnaly used, videos format and camera setup should be always the same for the whole set of animals.

 - You can now add your own events:

  1. Create an XML file using the same name as the one use to store the tracking. ( if your video is myvideo.avi, you should find an XML file in your folder called myvideo.avi.xml . To add your labels, just create a new file called myvideo.avi.extra.xml )
  2. Here is an example file:

- Or you can choose to import avisoft files. They should have the name myvideo.avi.avisoft.txt

This text file is seperated by tabs, and should contain at least the following columns: line number, label name, duration, interval (not used) and starttime. Those labels will appear in blue.


Here is an example of avisoft output:

1    tt    0,0366    -1    7,4513
2    to    0,0546    0,0904    7,5417
3    j12    0,0153    0,1041    7,6458

Heatmaps:

Generation:

          « Detection/Tracking »

          « Video Label Maker »

          Upload the xml file for the different videos

          Click on the « Create location heat map » button for each video.

          If several files were uploaded, you can put the heatmaps together (on the same image) by using the « stitch heatmap files » command in « File »: You should select the heat map files that you want to compile and press the « Load heat map files » button. This will create a tif file « heatmap stitched »

 

Display and settings:

          You should then open the « heat map stitched.tif » file with Icy (drag and drop the file on the black background of Icy.

          A window with the picture on black background will open.

          Play with cursors in the « look up table » section of the « Sequence » tab: you should move the cursor while pressing shift to improve the contrast for all channels together.  Make sure to always keep the same contrast settings (take note of the pixel number, displayed on the red cursor) for all the images within a dataset.

          Save your image with new settings by clicking on « Take a screenshot of current view with original sequence dimensions » in png to avoid compression.

          If you had different setup for your cages, you should then work on your picture to align the images and center them.