trackmate-sc / trackmate-stardist Goto Github PK

Hi Jean-Vyes,

I wanted to create a Jython script to use the StarDistDetectorFactory to detect droplets and track them. I was trying to use the sample Jython script provided in this repo to analyze some images and quickly ran into errors.

I managed to make some changes and get it running. It still throws some errors which I have commented out in the code. But for the rest, it does the job of using the standard StarDist model to detect objects and track them.

I am attaching it here with a small sample image. I could also do a pull request if this looks okay.
stardist_trackmate.zip

Thanks and best,
Gayathri

At the moment, there is an issue with Tensorflow on Fiji which is stopping when an image is too large.

As discussed here, a workaround would be to increase the number of tiles which is not yet possible.

Thanks for looking into this :)

This component is not currently available from maven.scijava.org, because one of its dependencies, de.csbdresden:StarDist_, is not deployed there. We need to make de.csbdresden:StarDist_ available from https://maven.scijava.org/content/groups/public and then cut a release of TrackMate-StarDist.

Hello,

The documentation page returns 404:

https://imagej.net/plugins/trackmate/trackmate-stardist

There is no 3D for StarDist in Fiji. But at least we need to ensure compatibility with the new version.

Hallo,

currently I am working with your example script (First Image) for precise control of TrackMate-StarDist to analyze cell nuclei. I was wondering how to programmatically (Jython) export the csv-files one can generate during the workflow with the GUI (second image).

Thanks so much for your help!

Best,
Stefan