Read Flow Cytometry Standard (fcs) files

scverse / squidpy

Spatial Single Cell Analysis in Python

https://squidpy.readthedocs.io/en/stable/

BSD 3-Clause "New" or "Revised" License

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Closed LLehner closed 1 year ago

LLehner commented 1 year ago

Reading files in fcs format is not yet supported by squidpy. However, e.g. the output of CODEX experiments is fcs formatted.

There is demand for this functionality as seen here.

[x] Add functionality to read fcs files (or csv files in fcs format), in particular files processed by CODEX/PhenoCycler

LLehner commented 1 year ago

This is currently being worked on. Soon to be finished.

LLehner commented 1 year ago

This can now be done with the reader codex() in spatialdata-io.

Note: This reader is specifically for CODEX/PhenoCycler formatted .fcs files.