Does this skill handle gating and compensation?

FlowIO is primarily focused on reading and writing FCS files. For advanced analysis like gating and compensation, it is best used as a companion to the FlowKit library.

Can I convert FCS files to CSV or Excel format?

Yes, this skill provides workflows to extract FCS event data into NumPy arrays or Pandas DataFrames, which can then be exported to CSV or other common data formats.

Can I create new FCS files from my own data?

Yes, FlowIO can generate standards-compliant FCS 3.1 files using NumPy arrays and custom metadata keywords.

Which FCS versions are supported by this skill?

FlowIO supports reading and parsing of FCS versions 2.0, 3.0, and 3.1.

How does it handle files with multiple datasets?

The skill includes specialized functions to detect and read multi-dataset FCS files, allowing you to access each dataset independently via its offset.

Flow Cytometry Data Processor

Name: Flow Cytometry Data Processor
Author: K-Dense-AI

byK-Dense-AI

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2,188

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Data Science & ML

Parses and manipulates Flow Cytometry Standard (FCS) files, converting biological data into NumPy arrays and CSV formats for scientific analysis.

FlowIO is a specialized skill designed for handling Flow Cytometry Standard (FCS) files across versions 2.0 to 3.1. It enables researchers and developers to extract event data as NumPy arrays, access rich instrument metadata, and create new FCS files with minimal dependencies. This tool is essential for building scientific data pipelines, validating cytometry files, and performing pre-processing workflows before advanced analysis. By automating the extraction of scatter, fluorescence, and time-series data, it bridges the gap between raw biological instrument data and modern Python-based analysis libraries.

Key Features

01Accesses comprehensive TEXT and ANALYSIS metadata segments

022,188 GitHub stars

03Handles multi-dataset FCS files and complex offset discrepancies

04Full support for FCS versions 2.0, 3.0, and 3.1

05Creates and exports standards-compliant FCS files from custom datasets

06Extracts event data directly into NumPy arrays or Pandas DataFrames

Use Cases

01Converting proprietary instrument data to open formats like CSV or Parquet

02Preprocessing raw flow cytometry data for machine learning models

03Automated metadata extraction and quality control for high-throughput biological experiments

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add k-dense-ai/claude-scientific-skills flowio

For use in Claude.ai and ChatGPT

Download Skill