WARNING: alpha software. We are sharing this early in case it is useful to other groups. Please expect breaking changes. Examples of running the package are found in /Examples.
GPU accelerated post-processing for 2D / 3D iterative barcoded FISH data. This package currently Nvidia only and Linux only due to RAPIDS.AI package availabilty. Documentation is available at https://qi2lab.github.io/merfish3d-analysis/.
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 dependencies using the command
setup-merfish3d
This will automatically setup the correct CUDA libraries and other packages in the conda environmnent.
If you plan on re-segmenting cells using decoded RNA, please follow the Baysor installation instructions.
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/.