Nematostella Toolkit

An open-source napari toolkit for studying circadian rhythms and sleep-like behavior in Nematostella vectensis — from synchronized image capture to automated activity analysis.

•   Recording Plugin

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  Synchronized timelapse capture with dual-LED illumination (IR + White) and ESP32-based hardware synchronization for drift-free, long-term recordings.

  Overview · Hardware · Flash firmware

•   Analysis Plugin

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  Quantify activity and movement from HDF5, Zarr, and AVI recordings, then run circadian rhythm and sleep-like state analysis — all inside napari.

  Overview · User Guide · Circadian analysis

How the toolkit fits together

•   Record

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  Build the imager, flash the ESP32, and capture synchronized light/dark time series with the Recording Plugin.

•   Analyze

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  Detect ROIs and quantify movement over the recording with the Analysis Plugin.

•   Interpret

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  Derive circadian rhythms and sleep-like states — see Circadian Analysis and Extended Analysis.

Install

Recording PluginAnalysis Plugin

pip install nematostella-time-series

pip install napari-hdf5-activity

Both plugins appear under napari's Plugins menu after installation.

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Built from the recording and analysis repositories with MkDocs + Material.