Using CellProfiler 2 plugin in CellProfiler 3 (CellStar)

cellprofiler
plugin

#1

To help identify yeast from transmitted-light images, I’d like to try the CellStar algorithm.

However, after downloading the plugins from here to my CellProfiler plugins directory, I still don’t see the new modules. I think the plugin directory is specified correctly because I do see the module from a different plugin that I have in the same directory.

Is this because the original plugin was written for CP 2, and if so, are there guidelines for updating plugins to be compatible with CP 3?

@fafafft, do you have any advice for using CellStar in CellProfiler 3?

Thanks!


#2

Hi @tswayne!

Great to hear that you are interesting in giving CellStar a try!

The plugin has been written for CellProfiler 2 so I’m not sure that it can work for CP 3 - however maybe it is the same as to be CP 2.3 - time passes so fast : )

Anyway I will take a look at it this weekend and let you know how much work is necessary to make it work.


#3

Thanks so much, @fafafft!


#4

Ok, so it works with CellProfiler 3.0.0 and after a small change it also works with CP 3.1.8.

Please use this version: https://github.com/Fafa87/CellProfiler-plugins/tree/sstoma-yit-seg. Use cellstar folder and identifyyeastcells.py from repo instead of the ones from the zip that you downloaded:

Let me know if have any problems, I will be glad to help.


#5

Thank you! I will try it out soon!