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Sign T

An easy-to-use GUI to perform contour tracking.

Uses movies from any common video file format to perform contour tracking, either RGB or grey levels (e.g. IR).

- Globally based on thresholding and simple mask operations as morphological opening/closing, that allow to deal with common problems such as cables hanging between the and the subject. Parameters can be adjusted manually while checking the result on the tracking performance, by replaying the movie or manually navigating through the frames

- Allows to choose a specific channel in an RGB movie (useful to deal with certain reflections)

- Allows to process a background picture offline, either from automatically or manually selected frames (helpful when the animals remain a long time in the same spot)

- Allows to prepare tracking for several files, and then launch batch to process them together


Output: a single .mat file with the parameters used for the analysis, and for each frame:

- XY coordinates for the contour

- XY coordinates for the center of gravity

- A value for the motion of the animal: % of pixel changes from the previous frame (between the corresponding masks)


The current version has not been tested for compatibility and dependencies; in particular, it might not run under MATLAB versions older than R2018a.


Future implementations/changes:

- Expand the manual and explain the different functionalities

- Take into account potential differences in screen resolutions/sizes

- Use parallel processing for a single movie to increase speed

- Auto-detect if parallel computing toolbox is available and adapt batch-processing accordingly; same for MATLAB releases.

- Calibration (pixels <-> cm) to have absolute values

- Process speed as well (either absolute if calibration or pixel-based)

- Add "online" processing (display tracking while also saving the results)

- Add progress bar and/or infos in the command window

- Auto-resize plots to accomodate different ratios

- Adjust some parameters to get a smooth browsing (some movies have ridiculous FPS and resolution that are too heavy to handle like this)

- Add the possibility to compute a "moving" background

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