PyMicroglia Wiki

This wiki is the long-form PyMicroglia reference. It explains how to inspect, run, review, and reproduce microglial bioluminescence time-lapse analyses.

Start Here

Page	Purpose
Installation	Install the core package or the optional analysis features.
First analysis	Check the environment, inspect a pipeline, and start a recorded run.
Check a run	Find outputs, read the run record, and recover the equivalent script.
Action index	Find one of the 26 runnable operations.
Single-cell dLuc pipeline	Run the complete segmentation, tracing, controls, and rhythm workflow.
Artefact store	Understand what is kept, rebuilt, or reused.
Recording and Batch	Read results without opening the source pixels.
Troubleshooting	Diagnose installation, action, store, and Fiji problems.

Choose the Right Entry Point

Need	Use
A complete analysis of one recording	A pipeline.
One processing, measurement, figure, or video step	A named action.
Results that already exist on disk	Recording or Batch from the results interface.
A quick health check	pymicroglia doctor.

Main Reference

Page	Purpose
Analysis flow	The order from raw pixels to a reviewable result.
API reference	Public Python objects and functions grouped by task.
Using actions	Describe, validate, run, and record an action.
Pipelines	End-to-end workflows and their scientific boundaries.
Results	Stored outputs, lazy access, and provenance.
Workflows	Task-based guides.
Glossary	Short definitions of package terms.
Developer docs	Maintainer guidance and documentation upkeep.