Nyxus Napari
Nyxus Napari is a Napari plugin for running feature calculations on image-segmentation image pairs, using the Nyxus application to compute features. Nyxus is a feature-rich, highly optimized, Python/C++ application capable of analyzing images of arbitrary size and assembling complex regions of interest (ROIs) split across multiple image tiles and files.
For more information on Nyxus, see https://github.com/PolusAI/nyxus.
Installation
To install Napari, it is recommended to first create a separate Conda environment.
conda create -y -n napari-env -c conda-forge python=3.9
conda activate napari-env
After creating the Conda environment, install Napari using pip
python -m pip install "napari[all]"
python -m pip install "napari[all]" --upgrade
or using conda
conda install -c conda-forge napari
conda update napari
Next, Nyxus must be installed. Note that the version of Nyxus must be greater than or equal to 0.50 to run the Napari plugin.
pip install nyxus
or build from source using the instructions at https://github.com/PolusAI/nyxus#building-from-source using the conda build for the python API.
After installing Napari and Nyxus, the Nyxus Napari plugin can be installed by cloning this repo and then building the plugin from the source. An example of this process is provided below.
git clone https://github.com/PolusAI/napari-nyxus.git
cd napari_nyxus
pip install -e .
Napari can then be ran by running
napari
Use
After installing the plugin, start Napari by running the command napari from the command line. Once the Napari GUI is loaded, the Nyxus plugin can be loaded from the Plugins menu in the toolbar by going to Plugins -> nyxus-napari.
A widget will appear in the Napari viewer to run Nyxus.