Install

Create a python 3.12 environment using your favorite package manager, e.g.

conda create -n merfish3d python=3.12

Activate the environment and install the GPU dependencies. This install method assumes an Nvidia GPU capable of running CUDA 12.8.

conda activate merfish3d

Next, clone the repository in your location of choice and enter the directory using

git clone https://github.com/QI2lab/merfish3d-analysis
cd merfish3d-analysis

and install using

pip install .

For interactive editing use

pip install -e .

Finally, install the merfish3d-analysis package using the command ``` setup-merfish3d ````

This will automatically setup the correct CUDA libraries and other packages in the conda environmnent. Note: Due to package incompatability, the install script currently creates a second conda/mamba environment called merfish3d-stitcher. In this environment, we install the minimal packages requried to read the datastore used by merfish3d-analysis and multiview-stitcher. The reason for this change is that one of the multiview-stitcher sub-dependencies (xarray-dataclass) now requires numpy>2.0, which is incompatible with the scientific computing packages used for merfish3d-analysis.

The merfish3d-stitcher environment is only used when individual tiles are registered into a global coordinate system. The code automatically invokes this second environment, but it is important to note that the current install strategy does create a new conda/mamba environment beyond what you as the user creates. As soon as the dependency issue is solved, we will remove this work around.

(Optional) Installing Baysor

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

Documentation

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/.