Please use the online documentation website going forward: https://bahanonu.github.io/ciatah/

Tracking

Code for ImageJ and Matlab based image tracking.

ImageJ based tracking

Functions needed (have entire miniscope_analysis loaded anyways):

• mm_tracking.ijm is the tracking function for use in ImageJ, place in plugins folder.
• removeIncorrectObjs.m is a function to clean-up the ImageJ output.
• createTrackingOverlayVideo is a way to check the output from the tracking by overlaying mouse tracker onto the video.

Instructions for ImageJ and Matlab

Example screen after running mm_tracking within ImageJ, click to expand.

Once ImageJ is finished, within Matlab run the following code (cleans up the ImageJ tracking by removing small objects and adding NaNs for missing frames along with making a movie to check output). Modify to point toward paths specific for your data.

% CSV file from imageJ and AVI movie path used in ImageJ
moviePath = 'PATH_TO_AVI_USED_IN_IMAEJ';
csvPath = 'PATH_TO_CSV_OUTPUT_BY_IMAGEJ';
% clean up tracking
[trackingTableFilteredCell] = removeIncorrectObjs(csvPath,'inputMovie',{moviePath});
% make tracking video
% frames to use as example check
nFrames=1500:2500;
inputMovie = loadMovieList(moviePath,'frameList',nFrames);
[inputTrackingVideo] = createTrackingOverlayVideo(inputMovie,movmean(trackingTableFilteredCell.XM(nFrames),5),movmean(trackingTableFilteredCell.YM(nFrames),5));
playMovie(inputTrackingVideo);

Example output from 2017_09_11_p540_m381_openfield01_091112017

Matlab based tracking

• Refer to https://github.com/schnitzer-lab/miniscope_analysis/issues/21 for additional details about testing this function.