[](https://github.com/janelia-cellmap)
<img src="https://raw.githubusercontent.com/janelia-cellmap/cellmap-models/main/assets/CellMapLogo2.png" alt="CellMap logo" width="85%">
# cellmap-models
[](https://github.com/janelia-cellmap/cellmap-models/actions/workflows/tests.yaml)
[](https://github.com/janelia-cellmap/cellmap-models/actions/workflows/black.yaml)
[](https://github.com/janelia-cellmap/cellmap-models/actions/workflows/mypy.yaml)
[](https://codecov.io/gh/janelia-cellmap/cellmap-models)
This package contains the models used for segmention by the CellMap project team at HHMI Janelia.
## Installation
We strongly recommend installing within a [conda](https://docs.anaconda.com/free/miniconda/#quick-command-line-install) (or [mamba](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html#automatic-install)) environment to install the package.
```bash
conda env create -y -n cellmap python=3.10 pytorch -c pytorch
conda activate cellmap
pip install cellmap-models
```
## Usage
```python
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](https://doi.org/10.1038/s41586-021-03977-3):
```python
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:
```python
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.
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