# Flow Cytometry Analysis

Complete flow cytometry analysis pipeline.

- Repository: https://github.com/synthetic-sciences/openscience (4321 stars)
- Category: Engineering
- License: MIT license
- Last updated: 2026-10-30
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add synthetic-sciences/openscience --skill flow-cytometry-analysis -g -a claude-code -y`
Codex: `npx skills add synthetic-sciences/openscience --skill flow-cytometry-analysis -g -a codex -y`
Cursor: `npx skills add synthetic-sciences/openscience --skill flow-cytometry-analysis -g -a cursor -y`
Gemini CLI: `npx skills add synthetic-sciences/openscience --skill flow-cytometry-analysis -g -a gemini-cli -y`

## Description

Complete flow cytometry analysis pipeline. FCS file handling, compensation, manual/automated gating, immunophenotyping, CFSE proliferation analysis, cell cycle analysis (Dean-Jett-Fox), and apoptosis assays. Extends flowio with analytical workflows. For raw FCS parsing only use flowio.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# Flow Cytometry Analysis: Complete Analysis Pipeline

## Overview

Flow Cytometry Analysis provides end-to-end computational workflows for analyzing flow cytometry data. Starting from FCS file parsing, through compensation matrix application, gating strategies (manual rectangular/polygon gates and automated Gaussian mixture model gating), to downstream analyses including immunophenotyping, CFSE proliferation tracking, cell cycle phase quantification (Dean-Jett-Fox model), and apoptosis assays (Annexin V/PI). This skill extends basic FCS file handling (flowio) with full analytical pipelines.

## When to Use This Skill

- Analyzing multi-color flow cytometry experiments
- Applying compensation matrices to correct spectral overlap
- Building sequential gating hierarchies (debris exclusion, singlet gating, live/dead, marker gating)
- Immunophenotyping with multi-marker panels (CD3, CD4, CD8, etc.)
- Quantifying cell proliferation from CFSE/CellTrace dilution
- Determining cell cycle phase distribution from DNA content histograms
- Analyzing apoptosis from Annexin V / propidium iodide staining
- Creating density plots, histograms, and overlay visualizations
- Automated gating for high-throughput cytometry experiments

**Related Skills:** For raw FCS file parsing and creation use `flowio`. For single-cell RNA-seq analysis use `scanpy`.

## Installation

```bash
uv pip install flowio fcsparser scipy numpy pandas matplotlib scikit-learn
```

## Quick Start

```python
from flowio import FlowData
import numpy as np

# Read FCS file
fcs = FlowData('sample.fcs')
events = fcs.as_array()
channels = fcs.pnn_labels

print(f"Events: {events.shape[0]}, Channels: {len(channels)}")
print(f"Channels: {channels}")

The rest: https://github.com/synthetic-sciences/openscience/blob/HEAD/backend/cli/skills/biology/flow-cytometry-analysis/SKILL.md