Motion Analysis High School teacher

I am a high school science teacher. My students complete science projects. We often video the motion of organisms such as Planaria and Crabs. We would like to track their movement for example to see how far they move and how long they are moving. We think that Fiji may be able to help but we are not sure how to apply it to our videos.
Any help that we could have would be greatly appreciated.

You may want to start with something like this:
There should be a few YouTube tutorials to get started.

The presentation of Dave Mason gives a really nice and easy overview of image analysis in general.

However, one chapter is dedicated to tracking with TrackMate (as already recommended by @Research_Associate) in a very condensed and clear way, see (starts at slide 96):


Thanks for the direction rk

Thanks Bio7 really appreciate

Thanks for the props @Bio7, much appreciated. FYI, as I don’t know how long my account at Liverpool will be active, I copied the hosted slides to this URL instead (same content):

Also, although not hosted, the source is available @ Bitbucket:

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In case anyone stumbles on this and is interested in a similar sort of outreach activity, I’ve just posted a write up on my blog about how we went about solving this problem.

I’ll offer a couple of hints to TrackMate users but there’s way more detail in the post.

  1. Downsample your original data as much as possible whilst keeping precision. I used one of my favourite tools, FFMPEG to extract at 2 fps from the original movie (which is 25 fps) and scale them to 50%. Less data mean smaller files and faster processing!

  2. Trackmate only detects bright blobs on dark backgrounds so you need to invert the image before tracking

    (note that you can re-invert after feature detection to run “Capture Overlay”)

  3. Make your background as consistant as possible. The inclusion of a grid (above) is a really smart idea, but the gap on the right of the dish, makes tracking harder. Keep a consistant background if at all possible!

Overall though, it worked really well and I thank @Richard_Kurtz for getting in touch!