---
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.