keejkrej/cellsam-onnx

license: other license_name: modified-apache-2.0 license_link: LICENSE pipeline_tag: image-segmentation tags:

• biology
• microscopy
• segmentation
• cell-segmentation
• onnx

CellSAM (ONNX)

This repository contains the ONNX export of the CellSAM model for cell segmentation.

⚠️ LICENSE WARNING: NON-COMMERCIAL / ACADEMIC USE ONLY ⚠️

This model is derived from the original CellSAM work and is subject to a Modified Apache License 2.0.

Grant of Copyright License: ... each Contributor hereby grants to You a non-commercial, academic perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license...

See the LICENSE file for full terms. Commercial use requires contacting the original authors (vanvalenlab@gmail.com).

Usage with cellsam-rs

This model is designed for high-performance inference using cellsam-rs.

# Install cellsam-rs (example)
cargo install cellsam-rs

# Run inference
cellsam-rs infer \
  --input image.tif \
  --model models/cellsam-onnx \
  --output mask.tif

Model Details

• Original Repository: vanvalenlab/cellSAM
• Architecture: SAM-based (Segment Anything Model) specialized for cell segmentation.
• Input: Phase contrast + Fluorescence images (2-channel).
• Format: ONNX (Opset 17).

Citation

If you use this model, please cite the original CellSAM paper:

@article{Israel2024,
  title={CellSAM: A Foundation Model for Cell Segmentation},
  author={Israel, Uri and others},
  journal={Nature Methods},
  year={2024}
}