zeztz-flow 0.1.0

Self-contained flow cytometry analysis helpers with a slim vendored Cytoflow runtime.

zeztz-flow

zeztz-flow is a 96-well plate flow-cytometry FCS analysis package. It bundles Xiaoyu's analysis helpers with a vendored Cytoflow runtime subset — no separate cytoflow installation needed.

Features: FCS import, metadata assignment, outlier removal, cell/doublet gating, histograms, density plots, well/row/column subsetting, and 96-well median export.

The vendored subset includes: FCS import, range/polygon/density gates, autofluorescence and linear bleedthrough correction, histogram/density views, and linear/log scales. The compiled logicle extension was removed — pure Python only.

Installation

mamba env create -f environment.yml
mamba activate zeztz-flow

Or in an existing Python >=3.9 environment: pip install -e .

Quick Start

import matplotlib.pyplot as plt
import zeztzflow as flow

expr = flow.zeztz_exp("path/to/fcs_directory")

cells = flow.auto_gate_FSC_SSC(expr.expr, keep=0.6)
single_cells = flow.auto_gate_FSC_A_H(cells, keep=0.7)

flow.density_plot(single_cells, xchannel="FSC 488/10-A",
                  ychannel="Alexa 647-A", xscale="log", yscale="log")
expr.median_96well(single_cells, channel="Alexa 647-A")

plt.show()

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.