Skip to content
Get packs

FlowIO FCS File Reader

Read, inspect, and write Flow Cytometry Standard (FCS) files with FlowIO, locally

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
7 files

What it does

Flow cytometry machines save measurements in a standard file format called FCS. This skill teaches the agent to open those files with the FlowIO Python library, list their metadata and channel names, pull out the measurement values as a table-like array, handle files that contain several datasets, and create new FCS 3.1 files. It is a low-level tool: it does not do compensation, gating, or transforms, and it points to FlowKit for those tasks.

Great for

  • Researchers or lab technicians who need to check what is inside a cytometry FCS file
  • Data scientists preparing flow cytometry measurements for pandas or machine-learning pipelines
  • Developers writing scripts that read or export FCS data

Skip it if

  • Gating, compensation, or biexponential display transforms, which the skill says FlowIO does not perform (use FlowKit instead)
  • Working with FlowJo workspaces, which the skill excludes
  • Files containing sensitive subject identifiers shared outside a controlled environment, because FCS metadata can include sample, subject, operator, and instrument IDs

Try asking

  • “Summarize the channels, event count, and acquisition date of sample.fcs without loading the events”
  • “Convert this FCS file into a pandas DataFrame with the channel labels as column names”
  • “Read every dataset in this legacy multi-dataset FCS file and report each event count”
  • “Write a filtered subset of events to a new FCS 3.1 file and verify it by reopening it”
Step-by-step guide: how to use FlowIO FCS File ReaderInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 7 original files, the MIT licence and an attribution note.

    flowio.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip flowio.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip flowio.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Start with metadata-only inspection (only_text=True) for large or unfamiliar files to avoid loading all events into memory.
  • State whether you want preprocessed (gain/log/time scaled) or raw decoded values, since the choice changes the numbers.
  • Ask the agent to reopen any newly written FCS file and check counts and labels before you rely on it.

What's inside

  • references/api_reference.md
  • references/fcs_semantics.md
  • references/sources.md
  • references/troubleshooting.md
  • references/workflows.md
  • scripts/inspect_fcs.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.