FlowKit

When to use

Use FlowKit to apply or build cytometry gating strategies, analyze batches of FCS samples, or reproduce supported FlowJo workspace analyses. It supports GatingML 2.0 and a subset of FlowJo 10 features. Import success alone does not establish agreement with FlowJo.

The examples and bundled helper target FlowKit 1.3.2 on Python 3.13. Upstream supports additional Python versions; those were not exercised here. The helper and examples were tested on synthetic FCS data, including a public FlowJo 10.7.1 synthetic workspace fixture. They are not biological validation.

Install

Use a separate environment; FlowKit 1.3.2 requires NumPy >2 and pandas <3: