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.

Nematostella vectensis moving its tentacles, phase contrast time lapse — Phase contrast

Nematostella vectensis under a DAPI filter set, fluorescence time lapse — Fluorescence, DAPI filter set

Recording Plugin

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

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

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

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

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

Install¶

Neither plugin is published on PyPI — both install from source.

Recording PluginAnalysis Plugin

git clone https://github.com/s1alknau/Nematostella-time-series.git
cd Nematostella-time-series
pip install -e .

git clone https://github.com/s1alknau/napari-hdf5-activity.git
cd napari-hdf5-activity
pip install -e ".[zarr]"

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

Recording with the HIK GigE camera needs more than pip

The recording plugin takes its frames from the napari layer that ImSwitch publishes, so ImSwitch, the Hik Robotics MVS SDK, a Qt binding with the GUI packages (qtpy, napari, pyqtgraph, qdarkstyle — ImSwitch's own install brings none of them) and the camera setup JSON have to be in place first — all inside one conda environment (imswitch21, Python 3.12), and installed before ImSwitch is started. See Software Setup for the full walkthrough, or Get started for the short version.

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