| --- |
| title: CellMap |
| emoji: 🔬 |
| colorFrom: blue |
| colorTo: green |
| --- |
| |
| <img src="https://raw.githubusercontent.com/janelia-cellmap/cellmap-models/main/assets/CellMapLogo2.png" alt="CellMap logo" width="60%"> |
|
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| # CellMap - HHMI Janelia |
|
|
| The [CellMap](https://www.janelia.org/project-team/cellmap) project team at **HHMI Janelia Research Campus** develops machine learning models for segmentation of cellular structures in volume electron microscopy (vEM) data. |
|
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| ## Models |
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| We provide pre-trained deep learning models for 3D organelle segmentation, available in multiple formats: |
|
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| | Format | Extension | Use Case | |
| |---|---|---| |
| | PyTorch | `.pt` | Full model for Python workflows | |
| | TorchScript | `.ts` | Deployment without Python dependencies | |
| | ONNX | `.onnx` | Cross-framework inference | |
|
|
| ### Available Segmentation Targets |
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|
| - Mitochondria |
| - Endoplasmic Reticulum (ER) |
| - Nucleus |
| - Peroxisomes |
| - Plasma Membrane |
| - Vesicles |
| - And more... |
|
|
| ## Quick Start |
|
|
| ```bash |
| pip install cellmap-models |
| ``` |
|
|
| ```python |
| from cellmap_models.model_export.cellmap_model import CellmapModel |
| from huggingface_hub import snapshot_download |
| |
| # Download and load any model |
| path = snapshot_download(repo_id="cellmap/your-model-name") |
| model = CellmapModel(path) |
| |
| # Inference |
| output = model.ts_model(input_tensor) |
| |
| # Finetuning |
| trainable_model = model.train() |
| ``` |
|
|
| ## Resources |
|
|
| - [cellmap-models (GitHub)](https://github.com/janelia-cellmap/cellmap-models) - Model architectures, weights, and export tools |
| - [CellMap Project Page](https://www.janelia.org/project-team/cellmap) |
| - [OpenOrganelle](https://openorganelle.janelia.org/) - Browse our EM datasets |
|
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| ## Publications |
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| - Heinrich, L. et al. [Whole-cell organelle segmentation in volume electron microscopy](https://doi.org/10.1038/s41586-021-03977-3). *Nature* (2021) |
|
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| ## Contact |
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| For questions or collaborations, visit our [GitHub](https://github.com/janelia-cellmap) or reach out through the [Janelia CellMap](https://www.janelia.org/project-team/cellmap) project page. |
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