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flowio

Parse FCS files into NumPy arrays and metadata for cytometry workflows.

48|6|Updated Mar 9, 2026
Search Tags:#metadata#csv#numpy#data-extraction#flowio#fcs#flow-cytometry
One-click install
npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill flowio-qinyan-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: flowio
Source: https://github.com/qinyan-ai/qinyan-academic-skills/tree/main/skills/05-%E7%94%9F%E7%89%A9%E4%BF%A1%E6%81%AF%E4%B8%8E%E5%9F%BA%E5%9B%A0%E7%BB%84%E5%AD%A6/flowio
Command: npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill flowio-qinyan-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Parse Flow Cytometry Standard (FCS) files to efficiently extract events as NumPy arrays, read metadata and channel information, and convert results to CSV or DataFrame for downstream analysis.

Core Features & Use Cases

  • Read and write FCS files (versions 2.0, 3.0, 3.1) with minimal dependencies.
  • Access event data as preprocessed NumPy arrays and raw data, plus channel metadata like PnN, PnS, and PnR.
  • Convert data to CSV or Pandas DataFrames for analysis pipelines; handle multi-dataset files and partial reads.
  • Use in back-end cytometry workflows, data curation, and preprocessing tasks.

Quick Start

Install FlowIO and load an FCS file to obtain a NumPy array of events and metadata.

Frequently Asked Questions about flowio

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I parse FCS flow cytometry files and extract event data in Python?▼

You can parse FCS flow cytometry files to extract event data as NumPy arrays and read metadata using FlowIO. It supports FCS versions 2.0, 3.0, and 3.1, enabling conversion to CSV or DataFrames for downstream analysis.

Can I convert FCS file data to a CSV or Pandas DataFrame for analysis?▼

Yes, you can convert FCS file data to CSV or Pandas DataFrames for analysis pipelines. The Skill extracts events as NumPy arrays and channel metadata like PnN, PnS, and PnR, facilitating seamless cytometry data curation.

Does FlowIO support reading multi-dataset FCS files and different FCS versions?▼

FlowIO supports reading multi-dataset FCS files and handles FCS versions 2.0, 3.0, and 3.1. It provides robust error handling for common offset and dataset issues, allowing partial reads and multi-dataset management.

What is the best way to access raw flow cytometry data and channel metadata programmatically?▼

The best way to access raw flow cytometry data is by using FlowIO to retrieve preprocessed NumPy arrays and raw event data. It also extracts channel metadata including PnN, PnS, and PnR values for comprehensive cytometry workflows.

How do I handle offset or dataset errors when extracting events from FCS files?▼

To handle offset or dataset errors when extracting events from FCS files, FlowIO provides robust error handling for common dataset issues. This ensures reliable data extraction even with partial reads or multi-dataset FCS file structures.

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