Metadata-Version: 2.1
Name: cellmap-models
Version: 0.0.5
Summary: Repository of model architectures and network weights used for CellMap segmentations.
Author-email: Jeff Rhoades <rhoadesj@hhmi.org>
License: BSD 3-Clause License
Project-URL: homepage, https://janelia-cellmap.github.io/cellmap-models
Project-URL: repository, https://github.com/janelia-cellmap/cellmap-models
Keywords: machine learning,deep learning,cell segmentation,cellpose,cellmap
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: torch
Requires-Dist: torchvision
Requires-Dist: numpy
Requires-Dist: tqdm
Requires-Dist: cellpose
Requires-Dist: ml-collections
Provides-Extra: dev
Requires-Dist: pytest; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Requires-Dist: pytest-mock; extra == "dev"
Requires-Dist: black; extra == "dev"
Requires-Dist: mypy; extra == "dev"
Requires-Dist: pdoc; extra == "dev"
Requires-Dist: pre-commit; extra == "dev"
Provides-Extra: pretrained
Requires-Dist: cellpose[gui]; extra == "pretrained"
Provides-Extra: all
Requires-Dist: cellmap-models[dev,pretrained]; extra == "all"

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# cellmap-models

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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.
