View tracked cells and their associated predictions

This page introduces the widget Single-cell features.

The demo files can be found here.

Installation

This widget requires additional dependencies.

If you already have the plugin installed, add these with:

pip install "./napari-iohub[clustering]"

When installing from scratch, there's also a shortcut that installs napari too:

pip install ".napari-iohub[all]"

Apple silicon

For macOS running on Apple Silicon (M-series SoC) machines, install higra via conda-forge before installing anything else in a clean environment (upstream issue):

conda create -n clustering -c conda-forge python=3.11 higra
conda activate clustering
pip install "./napari-iohub[all]"

Launch

From CLI

napari -w napari-iohub "Single-cell features"

From GUI

In napari GUI's menu bar, click Plugins -> napari iohub -> Single-cell features.

View tracking

Supply the paths for the images and the tracks by pasting the path or selecting via dialog.

tracks.mov

View features

When loading data, supply the path to the output of VisCy's embedding writer. After loading, use napari-clusters-plotter's plotter widget to plot UMAP:

plotter-clip.mov