flowio

# FlowIO ## Purpose Use FlowIO as a lightweight, low-level reader and writer for Flow Cytometry Standard files. Examples in this skill target **FlowIO 1.4.0**, the current stable release verified on 2026-07-23. FlowIO is appropriate for: - Reading FCS 2.0, 3.0, and 3.1 files - Inspecting HEADER, TEXT, ANALYSIS, and channel metadata - Retrieving event data as a two-dimensional NumPy array - Reading legacy files that contain multiple datasets - Writing list-mode, single-precision FCS 3.1 files - Preparing data for pandas, machine-learning, or downstream cytometry tools FlowIO does **not** perform compensation, logicle/biexponential transforms, gating, clustering, or FlowJo workspace processing. Use FlowKit or another analysis package for those tasks. ## Install Create or activate a Python environment, then install the verified release: ```bash uv pip install "flowio==1.4.0" ``` Confirm the runtime version: ```bash uv run python -c "import flowio; print(flowio.__version__)" ``` FlowIO 1.4.0 supports Python 3.9 through 3.13 and depends on NumPy. ## Operating Workflow 1. **Clarify the operation.** Distinguish metadata inventory, event extraction, file repair, conversion, and downstream biological analysis. 2. **Inspect before loading events.** Use `only_text=True` for metadata-only work, especially with large or unfamiliar files. 3. **Choose event semantics explicitly.** Use `as_array(preprocess=True)` for gain/log/time scaling from FCS metadata, or `preproce...