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CellProfiler / CellProfiler-plugins

Community-contributed and experimental CellProfiler modules.
http://plugins.cellprofiler.org/
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Implementing a DeepProfiler Plugin #171

Open jenna-tomkinson opened 1 year ago

jenna-tomkinson commented 1 year ago

Is your feature request related to a problem? Please describe.

This feature request isn't one that solves a problem, it is adding to the functionality of CellProfiler as a whole. It will allow a user to extract features from single cells using a different method as compared to what is already established.

Describe the solution you'd like

I am hoping to work on a DeepProfiler plugin for CellProfiler, where you can have deep learning features extracted from single cells along with the features from the already established CellProfiler measurement modules.

@bethac07 Is there any advice that you (or others) can provide on this? If you think it is possible or do you have a best place to start?

Thank you!

bethac07 commented 1 year ago

I think it is possible, and I think we definitely want it to be done! I think @jccaicedo and @Arkkienkeli were planning to do it (or if they weren't, I was!), though, so I would definitely not want to duplicate efforts here.

There is a template for making Measurement class modules in CellProfiler (which this would be), but I would say this is probably not a good candidate for anyone's first CellProfiler plugin, I expect it may be fiddly.

bethac07 commented 1 year ago

Looking back at our notes, @rsenft1 had also expressed interest in taking a crack at it.

jenna-tomkinson commented 1 year ago

Thank you for the reply Beth!

I totally understand this being a big first endeavor for myself, so I would love to be involved in this as much as I can with everyone. I can't wait to see where this goes soon!

ErinWeisbart commented 1 year ago

@jenna-tomkinson FYI, we are actively working on this now. We are discussing this in #183. @fefossa is spearheading it with help from @callum-jpg. If you still have interest and bandwidth in being involved, let us know.

jenna-tomkinson commented 1 year ago

@ErinWeisbart @fefossa @callum-jpg

This is awesome! I still have interest and love to participate, but mainly in the form of PR reviews/testing with the plugin/adding comments in the discussion. I have much to learn from this about the technical aspects of creating CellProfiler plugins.

Let me know how best to be able to participate and be involved!