Allen Cell Discussion Forum

Using cellprofiler in place of diameterJ?

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!

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

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