alterlab-flowio

# FlowIO: Flow Cytometry Standard File Handler ## Overview FlowIO is a lightweight Python library for reading and writing Flow Cytometry Standard (FCS) files. Parse FCS metadata, extract event data, and create new FCS files with minimal dependencies. Supports FCS versions 2.0, 3.0, and 3.1 — ideal for backend services, data pipelines, and basic cytometry file operations. ## When to Use This Skill Use this skill when: - FCS files require parsing or metadata extraction - Flow cytometry data needs conversion to NumPy arrays - Event data requires export to FCS format - Multi-dataset FCS files need separation - Channel information (scatter, fluorescence, time) must be extracted - Cytometry files need validation or inspection - Pre-processing is needed before advanced analysis **Related tool:** For advanced analysis (compensation, gating, FlowJo/GatingML support), recommend the **FlowKit** library as a companion to FlowIO. ## Installation ```bash uv pip install flowio ``` Requires Python 3.9 or later. ## Quick Start ```python from flowio import FlowData # Read FCS file and inspect flow = FlowData('experiment.fcs') print(f"FCS Version: {flow.version}") print(f"Events: {flow.event_count}") print(f"Channels: {flow.pnn_labels}") # Get event data as NumPy array, shape (events, channels) events = flow.as_array() ``` ```python import numpy as np from flowio import create_fcs # Write a new FCS file from a NumPy array. # Gotcha: create_fcs takes a WRITABLE BINARY FILE HANDLE ...