AutoMICE

--- license: apache-2.0 language: en tags: - medical - computed-tomography - micro-ct - mouse - segmentation - multi-organ - monai - swin-unetr - pytorch library_name: monai pipeline_tag: image-segmentation --- # AutoMICE — Swin UNETR weights + Docker image (mouse micro-CT, 8-class) [](https://github.com/namijiang/AutoMICE) [](https://huggingface.co/spaces/namijiang98/AutoMICE) [](https://github.com/namijiang/AutoMICE/blob/main/LICENSE) [](https://doi.org/10.3390/bioengineering11121255) This repository hosts **both** the **pretrained checkpoint** *and* the **ready-to-run Docker image** for **AutoMICE** (*Automated Micro-CT Imaging Contouring Engine*): a Swin UNETR model for **fully automatic multi-organ segmentation** of **mouse micro-CT** volumes (7 organs + background). ## ⚡ One-line install (Docker) ```bash git clone https://github.com/namijiang/AutoMICE.git cd AutoMICE && ./scripts/install_from_hf.sh docker run --gpus all --rm \ -v /your/inputs:/data -v /your/outputs:/results \ automice:latest --data /data --results /results ``` `install_from_hf.sh` downloads `automice-image.tar.gz` from this repo and runs `docker load`, leaving you with `automice:latest`. No Docker Hub account is required. ## 📦 What is in this repo | File | Size | Description | |----------------------------|--------|--------------------------------------------------------------------------| | `model.pt` | ~150 MB| Swin UNETR checkpoint (training config **test4** in the original code). | | `automice-image.tar.gz` | ~3.7 GB| Pre-built Docker image (`automice:latest`) with `model.pt` baked in. | The Docker image is the **fastest path** for users who just want to run inference; the standalone `model.pt` is for users who prefer the Python CLI or want to load the weights into their own pipeline. ## 🧠 Associated publication > **Robust Automated Mouse Micro-CT Segmentation Using Swin UNEt TRansformers** > Lu Jiang, Di Xu, Qifan Xu, Arion Chatziioannou, Keisuke S. Iwamoto, Susanta Hui, Ke Sheng. > *Bioengineering* (MDPI), 2024. DOI: <https://doi.org/10.3390/bioengineering11121255>...

Source context: 0 downloads · 0 likes · Pipeline image-segmentation · Library monai · Repo namijiang98/AutoMICE