Cell counting / Object tracking


I would like to use TrakEM2 (or a similar plugin) to count and analyze plaques/tangles in the brain. For example, I would like to create a trace surrounding the plaques & tangles of the image below.

Is there a plugin available to segment these and also provide location dependent information (i.e., the distance between one plaque and the nearest, the location of the plaque relative to the left/right corner, plaque size, etc). Is there are automatic detection tool available as well? Thank you!

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Hi, great question. I am working on a similar issue (automatically identifying cell/tissue types and separating them for measurements, counts, etc). Seeing as you have several color variations in your histology, I would play around with the trainable Weka.

You can train the Wekato identify structures based on color (see links above), so you could have the software automatically identify your plaques, nuclei and your grey matter in all of your images. Unfortunately, this is as far as I have gotten, training the computer with great accuracy. I am currently trying to learn how to analyze these images post processing. So its a start, but hopefully we can both learn from here.

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You might also want to give a try to TrackMate, it comes with some default blob detectors and it has a very friendly and powerful tracking interface.

Thank you both for your suggestions!!

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The Icy software also seems helpful for detection and analysis