TrackMate Spot Detection

Dear ImageJ community,

We are using TrackMate to generate lineages of stem cells in live zebrafish and are interested in how the intensity of a signal of interest changes over time, but also in the cell volume. Since most of our cells are not spherical and some are clustered close together, the LoG detector yields rather unsatisfying results. Is it possible to detect these cells based on their actual shape instead of assuming they are all spheres and measure the volume of such segmented cells?

Thank you for your help!

Hi @disputator1991

Unfortunately not that I know. There is no segmentation capabilities coupled to TrackMate, just detection.

@stelfrich did some work to extend TrackMate so that you can harness a proper segmentation in 2D, but I am not aware of anything 3D.

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