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whitews / FlowUtils

FlowUtils is a Python package containing various utility functions related to flow cytometry analysis, primarily focused on compensation and transformation tasks commonly used within the flow community.
https://flowutils.readthedocs.io
BSD 3-Clause "New" or "Revised" License
13 stars 8 forks source link

Feature Suggestion Compensation #12

Open valentinwust opened 1 month ago

valentinwust commented 1 month ago

Hello,

panelbuilder has some nice unmixing options that go beyond OLS. I haven't tried too much of it, but especially removing specific spectra from the data (e.g. an autofluorescence from single stain cells) seems interesting. I'll probably reproduce a lot of what they do in Python anyway, would you be interested in me adding that functionality to the package? Their special unmixing would add a torch dependency, but that could be treated as an optional dependency. (I could technically also implement it in pure numpy, but GPU support is pretty useful if the data get large.)

Greetings Valentin

whitews commented 1 month ago

Hi @valentinwust

Thanks for reaching out and apologies for the delayed response, I was out last week. I would be interested in this, though Torch is a pretty heavy dependency. How about we add this to the flowkit-extras package, which I by the issue you submitted there that you also found.

FlowKit-extras started as somewhat of a catch-all package for experimental ideas or things that don't fit nicely in the main packages (FlowIO, FlowUtils, and FlowKit). It's a playground where I don't worry about new dependencies so much. It would be nice to utilize the FlowKit Sample class for inputting the data to such a function. How does that sound?

Thanks again, Scott