Analysis Plugin — Overview¶

napari-hdf5-activity is a napari plugin for analyzing activity and movement behavior from HDF5, Zarr, and AVI timelapse recordings — the companion to the Recording Plugin.

Key features¶

ROI detection

Automatic region-of-interest detection and per-animal movement quantification across the recording.
Circadian analysis

Activity over light/dark cycles, rhythm detection, and sleep-like state classification.
Multiple formats

Reads HDF5, Zarr, and AVI — analyze live recordings or archived data.
Fast

Multiprocessing pipeline tuned for large multi-ROI, multi-day datasets.

How it works¶

The analysis plugin is organized as a modular pipeline. Data sources (HDF5/Zarr image stacks and their telemetry) feed a core set of modules — ROI detection, activity extraction and the circadian analysis engine (Chi² periodogram, FFT, cosinor, coherence). A Plot/Export module renders activity traces and periodograms and writes CSV and figure exports.

Software architecture of the napari-hdf5-activity analysis plugin

Get started¶

Install
```
pip install napari-hdf5-activity
```
Follow the User Guide — a walkthrough of the GUI tabs.
Analyze rhythms — see Circadian Analysis and the in-depth Extended Analysis reference.

Documentation¶

User Guide — step-by-step walkthrough of the GUI tabs.
Circadian Analysis — activity over light/dark cycles.
Entrainment Protocol — experimental LD/DD design for entrainment studies (part of the Circadian Protocol page).
Extended Analysis — in-depth analysis reference.
Performance Optimizations — multiprocessing & tuning.
AVI Integration — working with AVI recordings.

Note

These pages are pulled automatically from the napari-hdf5-activity repository when the site is built.