Possible to use Trackmate to track oval particles?

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I am trying to track oval particles (swimming cyprid larvae) using track mate, but I am having problems detecting the particles using the LoG detector. The plugin detects particles at the edges of the larvae but not the full larvae. I have tested may blob diameters and thresholds. Any advice of how to proceed?


Hi @Anna-Lisa_Wrange

Can you post a screenshot of your object here?



Hi, Here (above) are two images from the movies filming cyprids. The first one is a binary version (black and white after using adjust threshold) and the second one is the original film. The cyprids are roughly 500 um long. Thankful for any advice on how to proceed.


And here is a inverted image with the detected “circles” around larvae, i.e. does not detect the larvae itself…


This is because you are working with an image that has an inverted lookup-table (LUT), i.e. high intensities are displayed black, and zero intensity pixels are white (see the user guide).

You can set the Black background option in Process > Binary > Options… to work with a normal LUT by default when binarizing.

In general, I would recommend using the original image (possibly inverted) instead of a binary image, because that is where the (DoG and LoG) spot detectors work best:


To add to @imagejan, who found the reason why it did not work:

You can rather robustly detect such object by picked as diameter the longest axis of the object with the LoG detector. In my humble experience, it worked really great on bacteria (that were really well stained though).