Flowio

If you're working with flow cytometry data, this handles the file parsing grunt work. It reads FCS files (versions 2.0 through 3.1), extracts event data as NumPy arrays, and writes modified data back out. The library stays lightweight by focusing on file I/O rather than analysis like gating or compensation, so it slots into pipelines where you need clean data extraction before passing to analysis tools. It handles common FCS quirks with flags for offset discrepancies and has conveniences like automatic channel type detection (scatter vs fluorescence vs time). Useful for preprocessing workflows, converting cytometry data to CSV or DataFrames, or building backend services that need to validate and parse FCS files without pulling in heavy analysis dependencies.

skills.sh installs: 209
GitHub stars: 33.2K
last updated: Aug 21, 2026

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Install

$ npx -y skills add davila7/claude-code-templates --skill flowio --agent claude-code

Installs into .claude/skills of the current project.

Files

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. The library supports FCS versions 2.0, 3.0, and 3.1, making it ideal for backend services, data pipelines, and basic cytometry file operations.

When to Use This Skill

This skill should be used when:

FCS files requiring parsing or metadata extraction
Flow cytometry data needing conversion to NumPy arrays
Event data requiring export to FCS format
Multi-dataset FCS files needing separation
Channel information extraction (scatter, fluorescence, time)
Cytometry file validation or inspection
Pre-processing workflows before advanced analysis

Related Tools: For advanced flow cytometry analysis including compensation, gating, and FlowJo/GatingML support, recommend FlowKit library as a companion to FlowIO.