Self-contained flow cytometry analysis helpers with a slim vendored Cytoflow runtime.
Project description
zeztz-flow
zeztz-flow is an marimo-compatible flow-cytometry FCS analysis package.
Derived from cytoflow, this package is designed to become a minimal platform, allowing users to perform vibe analysis with their own AI agents.
Features:
- FCS import with automatic well-plate metadata
- Cleanup gating: scatter, doublet removal, polygon, custom thresholds
- Density plots, faceted histograms, ridgeline plots
- Subset by row, column, or well
- Median-fluorescence export
- Self-contained — vendored Cytoflow runtime, no extra installs
- Pure Python — no compiled extensions
- Designed for AI-assisted analysis
Installation
pip install zeztz-flow
For local development: mamba env create -f environment.yml
Quick Start
Open a marimo notebook, import zeztzflow, and
describe your analysis to your AI agent. The agent reads AGENTS.md
and PROJECT_GUIDE.md to generate the right code — from loading FCS
files to gating, plotting, and exporting results.
Documentation
- PROJECT_GUIDE.md — API reference, workflows, testing, publishing
- AGENTS.md — guide for AI coding agents
- llms.txt — machine-readable project map
Testing
MPLCONFIGDIR=/tmp/mplconfig python test/package_smoke_test.py
License
GPL-compatible. See LICENSE.txt and THIRD_PARTY_NOTICES.md.
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