This package contains the models used for segmention by the CellMap project team at HHMI Janelia.

We strongly recommend installing within a conda (or mamba) environment to install the package.

conda env create -y -n cellmap python=3.10 pytorch -c pytorch
conda activate cellmap
pip install cellmap-models

import cellmap_models

Different models are available in the cellmap-models module. For example, to use the models produced by the COSEM pilot project team, and published as part of Whole-cell organelle segmentation in volume electron microscopy:

import cellmap_models.cosem as cosem_models
print(cosem_models.models_list)

This will list the available models. To load a specific model, use the load_model function:

model = cosem_models.load_model('setup04/1820500')

More information on each set of models and how to use them is available in the README.md file in the corresponding subdirectory.