flowio

SUMMARY

What it does

This skill provides guidance for using the FlowIO Python library to read, inspect, and write Flow Cytometry Standard (FCS) files. It covers reading FCS 2.0, 3.0, and 3.1 files, inspecting metadata and channels, extracting event data as NumPy arrays, handling multi-dataset files, exporting tables, and creating FCS 3.1 files. The skill includes detailed instructions, code examples, and references for common workflows. It explicitly does not perform compensation, transforms, gating, or FlowJo workspace processing, directing users to FlowKit for those tasks. The skill requires Python 3.9-3.13, uv, and FlowIO 1.4.0, and operates locally without network access or credentials.