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Cell motility assessment is a branch of experimental biology or medical science. One example could be an assessment of treatment effects on sperm motility of an animal. The standard procedure involves taking film clips of sperm (or any other moving objects) through a microscope and measuring average linear velocity of particles on these film clips. The program used for measuring these linear velocities is important, and there are not too many choices to my knowledge. However, my knowledge might be limited.

I have previously used CellTrak for measuring sperm swimming speeds. The program works well, but lacks a batch processing function. As the assessment bases on a considerable number of replicates, I end up with 1000-2000 film clips to be analyzed and clicking my way through CellTrak is a tedious and irritating process. Also CellTrak licence costs a lot of money for such a poorly written program.

Therefore, my question is: Is someone aware of a similar program to CellTrak, which includes batch processing option, or even better, which works through command line and can be looped? Are there open source options or extensions to widely used open source programs (ImageJ, Bioconductor, etc.)? Please give a short tutorial/personal experience to the usage of the suggested program (if any).

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    $\begingroup$ I wonder if you could adapt Digital Particle Image Velocimetry for your purposes. holomap.com/dpiv.htm $\endgroup$ – kmm Mar 27 '13 at 13:39
  • $\begingroup$ I don't know of a specific program but the MATLAB file exchange is likely to have scripts for that purpose. It may also help to migrate this to StackOverflow $\endgroup$ – Drosophila Mar 27 '13 at 14:02
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ImageJ has several tracking plugins, a good one being TrackMate. Most of it's functions can be scripted in various languages and the Fiji distribution can also run in headless mode. It's open source and won't cost you any mony for a much lager feture set.

I personally have used ImageJ in headless mode scripted with its own macro language because it is relatively easy to learn. TrackMate also should output average speeds for the tracks, if I remember correctly. Otherwise you would have to write a script to measure those from the tracking data. You can use the IJ macro language, Python, Java or one of the other supported languages.

In combination with a bash script wrapper for its headless mode I even use it in Makefiles to convert my tiff stacks to avi and put scale bars and time stamps on everything.

Hope this helps.

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