flowio-flow-cytometry

# FlowIO — Flow Cytometry File Handler ## Overview FlowIO is a lightweight Python library for reading and writing Flow Cytometry Standard (FCS) files. It parses FCS metadata, extracts event data as NumPy arrays, and creates new FCS files. Supports FCS versions 2.0, 3.0, and 3.1. Minimal dependencies — ideal for data pipelines and preprocessing before advanced analysis. ## When to Use - Parsing FCS files to extract event data as NumPy arrays - Reading channel metadata (names, ranges, types) from FCS files - Converting flow cytometry data to pandas DataFrames or CSV - Creating new FCS files from NumPy arrays or processed data - Handling multi-dataset FCS files (separating combined datasets) - Batch processing directories of FCS files - Preprocessing flow cytometry data before downstream analysis - For **compensation, gating, and FlowJo workspace support**, use FlowKit instead - For **advanced cytometry visualization** (density plots, gating plots), use matplotlib or plotly ## Prerequisites ```bash pip install flowio numpy pandas ``` Requires Python 3.9+. No compiled dependencies — installs on any platform. ## Quick Start ```python from flowio import FlowData flow = FlowData("experiment.fcs") print(f"Events: {flow.event_count}, Channels: {flow.channel_count}") print(f"Channels: {flow.pnn_labels}") events = flow.as_array() # Shape: (n_events, n_channels) print(f"Data shape: {events.shape}") ``` ## Core API ### 1. Reading FCS Files The `FlowData` class is the primar...