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FlowIO FCS Reader/Writer

Read, inspect, and write flow cytometry FCS 2.0/3.0/3.1 files correctly with FlowIO 1.4.0.

Data & AnalyticsIntermediate★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

  • Inspects HEADER, TEXT, ANALYSIS segments and PnN/PnS channel labels of FCS 2.0/3.0/3.1 files.
  • Extracts events as a (event_count, channel_count) NumPy array while making the preprocess=True vs preprocess=False distinction explicit.
  • Reads legacy multi-dataset files via read_multiple_data_sets() instead of hand-parsing $NEXTDATA offsets.
  • Writes FCS 3.1 list-mode single-precision files with create_fcs(), or copies/de-identifies with write_fcs(), always followed by a reopen-and-validate step.
  • Ships scripts/inspect_fcs.py for a metadata-first inventory report with size and memory limits.

Who it's for

  • Immunology and life-science researchers preprocessing cytometry data in Python.
  • Data engineers validating FCS structure before pandas or ML pipelines.
  • Core-lab staff diagnosing offset errors, vendor format defects, or corrupted acquisitions.

Example uses

  1. "Summarize channel labels and event counts for every FCS file in this folder" → metadata-only parsing or the bundled inspector.
  2. "Export my NumPy matrix as an FCS 3.1 file and verify the round trip" → create_fcs() plus reopen and np.testing.assert_allclose.
  3. "Produce a copy without subject/operator identifiers" → write_fcs(..., metadata={"src": "Deidentified export"}).

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/flowio/SKILL.md

What I want: (describe your task here)

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↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
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Install in Claude Code

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Install the skill I found on Claude Skill Mart.
Copy the skills/flowio folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/flowio/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/flowio ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and confirm Python 3.9–3.13 plus uv are available (uv --version).
  2. Clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Create the skills directory: mkdir -p ~/.claude/skills
  4. Copy the skill in: cp -r scientific-agent-skills/skills/flowio ~/.claude/skills/
  5. Install the pinned library: uv pip install "flowio==1.4.0" (or use uv run --no-project --with "flowio==1.4.0" per the examples).
  6. Restart Claude Code and ask something like "inspect the metadata of this FCS file" to trigger the skill.
  7. To run the inspector manually, set FLOWIO_SKILL_DIR=~/.claude/skills/flowio and run python "$FLOWIO_SKILL_DIR/scripts/inspect_fcs.py" sample.fcs.
View source on GitHub ↗License: MIT