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Installation

This section will guide you through the installation of napari-lattice using conda. The commands can be copied by clicking the copy button at the right side of the respective code blocks below.

We recommend the installation of Miniconda as is a minimal version of Anaconda Distribution.

Tip

If you can install mamba in your environment, the conda installation commands will be much faster. Once configured correctly, just replace conda with mamba in the commands below.

First, create a new conda environment:

conda create -n napari-lattice -c conda-forge "python==3.10" uv pycudadecon "numpy<2"

Info

We include pycudadecon to enable GPU accelerated deconvolution.

Activate that environment:

conda activate napari-lattice

Then use uv to quickly install the napari-lattice suite using the following 2 commands:

uv pip install lls-core napari-lattice

uv pip install --upgrade aicsimageio "napari==0.5.5" "numpy<2"

CLI only

If you do not need to use napari, then you can install just the command line interface only, which has all the features

conda create -n napari-lattice -c conda-forge "python==3.10" uv pycudadecon "numpy<2"

uv pip install lls-core

Development Installation

To install the development version of lls-core, create the napari-lattice environment as above, but instead of installing from pip in the last step:

git clone https://github.com/BioimageAnalysisCoreWEHI/napari_lattice.git
cd napari_lattice
uv pip install -e core -e plugin
uv pip install napari --upgrade "numpy<2"