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flowio

Parse FCS files and extract event data as NumPy arrays.

33.0k|3.2k|Updated Oct 19, 2025
Search Tags:#csv#numpy#data-extraction#data-processing#flowio#fcs#flow-cytometry
One-click install
npx skills add https://github.com/K-Dense-AI/scientific-agent-skills --skill flowio-k-dense-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: flowio
Source: https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/scientific-skills/flowio
Command: npx skills add https://github.com/K-Dense-AI/scientific-agent-skills --skill flowio-k-dense-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

FlowIO enables users to read Flow Cytometry Standard (FCS) files, extract event data as NumPy arrays, and access rich metadata, simplifying integration into data pipelines and analytics workflows.

Core Features & Use Cases

  • Read FCS files (versions 2.0, 3.0, 3.1) and expose channel information (PnN, PnS) and data type.
  • Extract event data as preprocessed NumPy arrays or raw data for downstream analytics, visualization, or CSV export.
  • Create or modify FCS files from arrays and metadata, including support for multi-dataset files and metadata extraction.

Quick Start

Read an FCS file and obtain a preprocessed data array with channel labels.

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 into NumPy arrays?▼

You can parse FCS flow cytometry files into NumPy arrays by reading the file to extract event data and metadata, then calling the as_array method with the preprocess parameter set to True for analysis-ready data or False for raw data.

What FCS file versions are supported for flow cytometry data extraction?▼

Supported FCS file versions for flow cytometry data extraction include 2.0, 3.0, and 3.1. The parser extracts event data and exposes channel information such as PnN and PnS labels for these versions.

Can I extract metadata and channel labels from an FCS file?▼

Yes, you can extract metadata and channel labels from an FCS file. The parsed FlowData object exposes text metadata alongside pnn_labels and pns_labels, providing access to comprehensive channel information.

How do I export flow cytometry event data to CSV?▼

To export flow cytometry event data to CSV, you first parse the FCS file and extract the event data as a NumPy array or DataFrame. This structured data can then be written to CSV format for downstream analysis.

Does FlowIO support creating or modifying FCS files from arrays?▼

Yes, FlowIO supports creating or modifying FCS files from arrays and metadata. This includes handling multi-dataset files and allowing you to write event data back into the Flow Cytometry Standard format.

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