Install

Python environment creation

Because merfish3d-analysis relies on a number of GPU-only functions, we strongly recommend that you create a specific python environment to ensure proper functioning.

Here are instructions using Mamba, a very fast implementation of conda.

Create a python 3.10 environment using your favorite package manager, e.g. mamba create -n merfish3d python=3.10

Installing merfish3d-analysis

Activate the environment and install the GPU dependencies. This install method assumes an Nvidia GPU capable of running CUDA >= 12.0.

mamba activate merfish3d
mamba install -c conda-forge -c nvidia -c pytorch -c rapidsai cupy cucim=24.08 pylibraft=24.08 raft-dask=24.08 cudadecon "cuda-version>=12.0,<=12.5" cudnn cutensor nccl onnx onnxruntime pytorch torchvision 'pytorch=*=*cuda*'

Finally, clone the repository using git clone https://github.com/QI2lab/merfish3d-analysis and install using pip install .. For interactive editing use pip install -e ..

To build the documentation, install using pip install .[docs]. Then execute mkdocs build --clean and mkdocs serve. The documentation is available in your web browser at http://127.0.0.1:8000/.

Installing Baysor

Please follow the Baysor documentation to install for Linux. Keep track of the installation directory for use with merfish3d-analysis.