---
id: flowio
version: "1.4.0"
license: BSD 3-Clause License Copyright (c) 2019, Scott White All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following… (full text in the JSON record)
license_treatment: permissive
maintenance: aging
---

# FlowIO — FlowIO is a Python library for reading / writing Flow Cytometry Standard (FCS) files

License: permissive · Maintenance: aging · Downloads: 120.1K/mo

## What it is and what it does

FlowIO is a lightweight Python library for reading and writing Flow Cytometry Standard (FCS) files. It focuses on minimal dependencies and straightforward parsing, making it suitable for scenarios like web server backends or simple metadata extraction from flow cytometry datasets. The library depends only on numpy and targets Python 3.9 through 3.13.

For users needing only FCS file I/O and basic data access, FlowIO provides a direct, low-overhead solution. The package is marked Production/Stable and has been maintained since 2018, though recent activity has slowed. For more advanced cytometry analysis—compensation, transformation, gating, or FlowJo workspace import—the related FlowKit library is recommended instead.

Use it for:

- Parse FCS metadata and parameters from flow cytometry experiments in a web service backend.
- Extract raw flow cytometry data from FCS files for downstream processing in data pipelines.
- Write standardized FCS files from processed cytometry data to share with other analysis tools.
- Batch convert or validate FCS file format compliance across a dataset collection.
- Integrate FCS file reading into lightweight command-line tools without heavy dependencies.

## Worth the install?

AI-flagged interpretation of the facts above — verify before relying.

FlowIO reads and writes Flow Cytometry Standard (FCS) files, the standard format for flow cytometry data, with minimal dependencies suitable for parsing and metadata extraction.

Yes, if you need straightforward FCS file I/O with minimal overhead. The BSD 3-Clause license is permissive, and the package is stable and production-ready. However, the 462-day gap since the last release and aging maintenance status mean you should verify that the package still meets your needs and that any bugs or compatibility issues with newer Python versions have been addressed. For advanced cytometry analysis, use FlowKit instead.

## Install

pip install flowio
uv add flowio
poetry add flowio

## Installing FlowIO

Before you install: High install friction due to numpy as a compiled dependency. The package is in aging maintenance status—last release was 462 days ago—though the repository remains active with a recent commit on 2025-11-05 and no archived status.

License in practice: BSD 3-Clause License permits commercial and private use with minimal restrictions; you must retain copyright notices and disclaimers in source and binary distributions.

Quickstart:

pip install flowio
import flowio
fcs = flowio.FlowData('sample.fcs')
print(fcs.text)

Requires numpy; Python 3.9 or later.

Verify before relying:

- Whether the 462-day gap since the last release (2025-05-09) reflects planned stability or reduced active development.
- Performance characteristics when handling large FCS datasets or batch processing scenarios.

## Package facts

- License: BSD 3-Clause License Copyright (c) 2019, Scott White All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following… (full text in the JSON record) (permissive)
- Python support: unspecified
- Install friction: high
- Maintenance: aging
- Downloads: 120.1K/month (top 15,000 on PyPI)
- Known vulnerabilities: none known

## Tags

FCS file reader, flow cytometry data parsing, FCS format library, cytometry file I/O, flow cytometry standard, FCS file writer, cytometry data extraction, bioinformatics, file-format, cytometry

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