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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 Miniforge as it is a minimal version of Anaconda Distribution and includes mamba, which is faster than conda.

First, create a new conda environment. To do this, you can look for Miniforge Prompt which we will use for running the commands below:

mamba 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 for installing 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" "tifffile==2025.1.10"

Info

Using uv ensures the installs are fast!

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

mamba 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"