whitews / FlowKit

A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces
https://flowkit.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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FACSDiscover S8 Cellview uses 32 bit encoding -> problem with transforms that assume 18 bit encoding by default #232

Open samdepaauw opened 4 hours ago

samdepaauw commented 4 hours ago

Is your feature request related to a problem? Please describe. The logicle transformation parameters are hardcoded for 18 bit fcs data. Data collected from new generation flow cytometers such as the BD cellview encodes data in 32 bit. The hardcoded parameters are incompatible with my data. When transforming my data, the transformation yields the same value for all my datapoints. How can the parameters be adjusted in such a way that they allow for 32 bit encoded index data?

Describe the solution you'd like Parameter estimation so that 32 bit index data can be transformed.

Describe alternatives you've considered Using the max value of float32 as a max value and increasing the channel range by two fold. This did not yield to a successful transformation.

Additional context I can provide an example plate sort index data.csv file.

whitews commented 2 hours ago

Hi Sam,

Thanks for submitting this issue. I can look into it and would be interested in getting your input file. It would be helpful to have the output file from the transformation results you are getting as well (in case I cannot replicate the same values). I think you should be able to attach files to this issue. If not, we can figure out a different way to provide them.

Thanks again, Scott