CASIMIR v1.0.0

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LICENSE

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README.md

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+---
+license: apache-2.0
+library_name: casimir
+pipeline_tag: image-segmentation
+tags:
+- medical-imaging
+- mri
+- whole-body
+- segmentation
+- nnunet
+- pediatrics
+---
+
+# CASIMIR: An Open Pediatric Model for Whole-Body T1-Weighted MRI Anatomy Segmentation
+
+[![Code on GitHub](https://img.shields.io/badge/Code-GitHub-blue?style=for-the-badge)](https://github.com/fjhorvath/casimir)    [![License](https://img.shields.io/badge/License-Apache--2.0-blue?style=for-the-badge)](https://huggingface.co/fjhorvath/casimir/blob/main/LICENSE)
+
+CASIMIR (Child Anatomy Segmentation In MRI with Increased Robustness) is a 2D
+[nnU-Net v2](https://github.com/MIC-DKFZ/nnUNet) model that segments six visceral organs and
+seven skeletal structures in pediatric and young-adult whole-body T1-weighted MRI, paired
+structures labeled by side. This repository holds the weights. The inference code is on
+[GitHub](https://github.com/fjhorvath/casimir). The model and its evaluation are described
+in a manuscript that is not yet published, see Citation.
+
+<p align="center">
+  <img class="dark:hidden" src="assets/casimir-overview.png" width="560" alt="Four axial T1 slices with the CASIMIR overlay, mid thorax to lower leg, beside a whole-body rendering of CASIMIR output with each cutting plane marked, the lower legs from a second examination">
+  <img class="hidden dark:block mx-auto" src="assets/casimir-overview-dark.png" width="560" alt="Four axial T1 slices with the CASIMIR overlay, mid thorax to lower leg, beside a whole-body rendering of CASIMIR output with each cutting plane marked, the lower legs from a second examination">
+</p>
+
+## Inference
+
+```bash
+pip install git+https://github.com/fjhorvath/casimir.git@v1.0.0
+casimir -i <nifti file or directory> -o <output directory>
+```
+
+Add `--device cpu` if there is no NVIDIA GPU, or `--device mps` on Apple silicon.
+`casimir --help` lists all flags. The weights are downloaded from here on the first run.
+For offline use, set `CASIMIR_WEIGHTS_PATH` to a local copy.
+
+The input is NIfTI, `.nii` or `.nii.gz`. The tested volumes were converted from DICOM with
+dicom2nifti and reorientation disabled (`reorient_nifti=False`), which keeps the scanner's
+axis order. nnU-Net reads the voxel array as stored, so a volume saved in another axis
+order is untested.
+
+The output is one label map per input, on the input grid and under the input filename,
+with the voxel values listed below. One whole-body examination takes about 1.5 minutes on
+an RTX 4090 or on an Apple M2 Pro with `--device mps`, and about 4 minutes on the M2 Pro
+with `--device cpu`.
+
+## Files
+
+`dataset.json` and `plans.json` are the nnU-Net v2.5 dataset descriptor and plans.
+`fold_all/weights.pth` is the checkpoint, a single fold trained on all training cases, with
+no ensemble. `LICENSE` is the Apache License 2.0.
+
+## Structures
+
+The 13 structures give 20 labels, one per side for the paired ones:
+
+| | | | |
+|---|---|---|---|
+| 1 fibula left | 2 fibula right | 3 femur left | 4 femur right |
+| 5 tibia left | 6 tibia right | 7 spine | 8 liver |
+| 9 lung left | 10 lung right | 11 sacrum | 12 spleen |
+| 13 humerus left | 14 humerus right | 15 heart | 16 urinary bladder |
+| 17 pelvis left | 18 pelvis right | 19 kidney left | 20 kidney right |
+
+Background is `0`. The output is the raw argmax with no post-processing.
+
+## Intended use
+
+CASIMIR is a research tool, not a medical device. Do not use its output for clinical
+decisions.
+
+It was trained and evaluated on contrast-enhanced axial fat-suppressed T1-weighted
+gradient-echo whole-body MRI from a single 3-T PET/MR system, in patients aged 1 to 21
+years with lymphoma or post-transplant lymphoproliferative disorder. External validation is
+required to establish generalizability.
+
+## License
+
+These weights and the inference code are released under the Apache License 2.0, see
+`LICENSE`.
+
+## Citation
+
+Until the manuscript is published, cite the software:
+
+```bibtex
+@software{horvath2026casimir,
+  author  = {Horvath, Felix J. and Barrow, Michael J. and Singh, Shashi B. and Lokesha, Yashas U. and Okpokpo, Darlene and Sivanandam, Sharanya and Gatidis, Sergios and Daldrup-Link, Heike E.},
+  title   = {{CASIMIR}: An Open Pediatric Model for Whole-Body T1-Weighted {MRI} Anatomy Segmentation},
+  version = {1.0.0},
+  year    = {2026},
+  url     = {https://github.com/fjhorvath/casimir}
+}
+```
+
+CASIMIR is built on nnU-Net, please also cite
+[Isensee et al. (2021)](https://doi.org/10.1038/s41592-020-01008-z).
+
+## Funding
+
+This work was supported by a grant from the National Cancer Institute, grant number
+R01 CA269231. Felix J. Horvath was supported by a travel grant from the Rolf W. Günther
+Foundation for Radiological Sciences.

dataset.json

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+{
+    "labels": {
+        "background": 0,
+        "fibulaLeft": 1,
+        "fibulaRight": 2,
+        "femurLeft": 3,
+        "femurRight": 4,
+        "tibiaLeft": 5,
+        "tibiaRight": 6,
+        "spine": 7,
+        "liver": 8,
+        "lungLeft": 9,
+        "lungRight": 10,
+        "sacrum": 11,
+        "spleen": 12,
+        "humerusLeft": 13,
+        "humerusRight": 14,
+        "heart": 15,
+        "urinaryBladder": 16,
+        "pelvisLeft": 17,
+        "pelvisRight": 18,
+        "kidneyLeft": 19,
+        "kidneyRight": 20
+    },
+    "channel_names": {
+        "0": "MRI_MISC"
+    },
+    "file_ending": ".nii.gz",
+    "name": "CASIMIR",
+    "description": "CASIMIR: 20-structure anatomical segmentation for whole-body T1-weighted MR."
+}

fold_all/weights.pth

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plans.json

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