Napari plugin automating structured illumination microscopy (SIM) reconstruction and diagnostics from the mcSIM package
Create a python environment using favorite package manager (conda, mamba, etc...) with Python >= 3.9. For example, with conda
conda create -n napari-mcsim python=3.9
conda activate napari-mcsim
Once you have activated that environment, the best way to use this python package is to install it with pip
git clone https://github.com/QI2lab/napari-mcsim.git
cd napari-mcsim
pip install .
If you would like to edit the code, then install using the -e option,
git clone https://github.com/QI2lab/napari-mcsim.git
cd napari-mcsim
pip install -e .
For more information on GPU support through CUDA, please see the installation instructions in the mcSIM repo.
Activate the conda environment (if you not already) and start napari
conda activate napari-mcsim
napari
The napari-mcsim plugin is now available in the "plugins" menu. A detailed video walkthrough is in the works.