| | --- |
| | 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%"> |
| |
|
| | # 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. |
| |
|
| | ## Models |
| |
|
| | We provide pre-trained deep learning models for 3D organelle segmentation, available in multiple formats: |
| |
|
| | | 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 |
| |
|
| | - 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 |
| |
|
| | ## Publications |
| |
|
| | - Heinrich, L. et al. [Whole-cell organelle segmentation in volume electron microscopy](https://doi.org/10.1038/s41586-021-03977-3). *Nature* (2021) |
| |
|
| | ## Contact |
| |
|
| | 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. |
| |
|
