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flowio

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Parse Flow Cytometry Standard (FCS) files v2.0–3.1 and extract events/metadata for preprocessing workflows (e.g., when you need NumPy arrays, channel info, or CSV/DataFrame export from cytometry files).

scientific-skills/Data Analysis/flowio/SKILL.md

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Sep 17, 2026
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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

## When to Use

- You need to read FCS v2.0/3.0/3.1 files and extract event matrices for downstream preprocessing.
- You want to inspect or validate FCS metadata (TEXT segment) without loading event data (memory-efficient parsing).
- You need channel definitions (PnN/PnS), ranges (PnR), and automatic identification of scatter/fluorescence/time channels.
- You need to handle problematic FCS files with offset inconsistencies or multi-dataset content.
- You want to export cytometry events to CSV/Pandas DataFrame or write new/modified FCS files.

## Key Features

- **FCS parsing (v2.0–3.1):** Reads HEADER/TEXT/DATA and optional ANALYSIS segments.
- **Event extraction to NumPy:** Returns event data as `ndarray` with shape `(events, channels)`.
- **Optional preprocessing:** Applies standard FCS transformations (gain/log/time scaling) when enabled.
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