Using cellprofiler in place of diameterJ?

Software & Code Miscellaneous
1

Does anyone know if using something like the analyse skeleton option on the cellprofiler pipeline can provide the same results as diameterJ on imageJ? I am quantifying vascular networks in 3D and to get density, branching etc I can get using cellprofiler, it would be nice to get all data sets from the same pipeline.

Thanks!

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i agree with you that if would be great to have all steps in a single workflow. to do this, i have used our segmenter to do some skeleton analysis on our data, e.g, tight junction. the tool i used together with segmenter is a python packa
ge called skan. https://jni.github.io/skan/index.html

hope that could be useful for you. @amycaitriona

1 Like
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let me know if there is any other question we ca help.