[](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.
Raw data
{
"_id": null,
"home_page": "",
"name": "cellmap-models",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.7",
"maintainer_email": "",
"keywords": "machine learning,deep learning,cell segmentation,cellpose,cellmap",
"author": "",
"author_email": "Jeff Rhoades <rhoadesj@hhmi.org>",
"download_url": "https://files.pythonhosted.org/packages/32/01/33ee36fcccd113607f844aeb74f597294f1c767780a495dfca2c911b2c54/cellmap-models-0.0.2.tar.gz",
"platform": null,
"description": "[](https://github.com/janelia-cellmap)\n\n\n<img src=\"https://raw.githubusercontent.com/janelia-cellmap/cellmap-models/main/assets/CellMapLogo2.png\" alt=\"CellMap logo\" width=\"85%\">\n\n# cellmap-models\n\n\n\n\n\n[](https://github.com/janelia-cellmap/cellmap-models/actions/workflows/tests.yaml)\n[](https://github.com/janelia-cellmap/cellmap-models/actions/workflows/black.yaml)\n[](https://github.com/janelia-cellmap/cellmap-models/actions/workflows/mypy.yaml)\n[](https://codecov.io/gh/janelia-cellmap/cellmap-models)\n\nThis package contains the models used for segmention by the CellMap project team at HHMI Janelia.\n\n## Installation\n\nWe 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.\n\n```bash\nconda env create -y -n cellmap python=3.10 pytorch -c pytorch\nconda activate cellmap\npip install cellmap-models\n```\n\n## Usage\n\n```python\nimport cellmap_models\n```\n\nDifferent 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):\n\n```python\nimport cellmap_models.cosem as cosem_models\nprint(cosem_models.models_list)\n```\nThis will list the available models. To load a specific model, use the `load_model` function:\n```python\nmodel = cosem_models.load_model('setup04/1820500')\n```\n\nMore information on each set of models and how to use them is available in the `README.md` file in the corresponding subdirectory.\n",
"bugtrack_url": null,
"license": "BSD 3-Clause License",
"summary": "Repository of model architectures and network weights used for CellMap segmentations.",
"version": "0.0.2",
"project_urls": {
"homepage": "https://janelia-cellmap.github.io/cellmap-models",
"repository": "https://github.com/janelia-cellmap/cellmap-models"
},
"split_keywords": [
"machine learning",
"deep learning",
"cell segmentation",
"cellpose",
"cellmap"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "8a9be277b1c3a1b9ee78e83e6683a7997e0c17972b6f36667135d6214713205c",
"md5": "5ade87c0c61ea395ebbf7a00236bb0d6",
"sha256": "a0c553ba0e3486f186db4f2db7b895b9828def8fbf67cb6cb9951aadb8c09450"
},
"downloads": -1,
"filename": "cellmap_models-0.0.2-py3-none-any.whl",
"has_sig": false,
"md5_digest": "5ade87c0c61ea395ebbf7a00236bb0d6",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.7",
"size": 19230,
"upload_time": "2024-03-18T18:24:09",
"upload_time_iso_8601": "2024-03-18T18:24:09.925672Z",
"url": "https://files.pythonhosted.org/packages/8a/9b/e277b1c3a1b9ee78e83e6683a7997e0c17972b6f36667135d6214713205c/cellmap_models-0.0.2-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "320133ee36fcccd113607f844aeb74f597294f1c767780a495dfca2c911b2c54",
"md5": "9c56a66d48ad373bb46637ff50a2d002",
"sha256": "762f9de16291cd5566d10526b730047363c8dedb4a9917ecc6787de20c69d9e9"
},
"downloads": -1,
"filename": "cellmap-models-0.0.2.tar.gz",
"has_sig": false,
"md5_digest": "9c56a66d48ad373bb46637ff50a2d002",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.7",
"size": 14826,
"upload_time": "2024-03-18T18:24:11",
"upload_time_iso_8601": "2024-03-18T18:24:11.096754Z",
"url": "https://files.pythonhosted.org/packages/32/01/33ee36fcccd113607f844aeb74f597294f1c767780a495dfca2c911b2c54/cellmap-models-0.0.2.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-03-18 18:24:11",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "janelia-cellmap",
"github_project": "cellmap-models",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "cellmap-models"
}
JSON
