| ---
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| license: cc-by-4.0
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| tags:
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| - medical-imaging
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| - anatomy
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| - ultrasound
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| - computed-tomography
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| - image-classification
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| task_categories:
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| - image-classification
|
| ---
|
|
|
| # OrganScan training corpus — recipe and provenance
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|
|
| This repository publishes the **recipe**, not the pixels.
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|
|
| Medical imaging corpora carry licences that differ source by source, and several forbid
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| redistribution outright. More importantly, frames rendered from DICOM can carry burned-in patient
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| identifiers even after tag-level de-identification. Rather than ship images that are easy to misuse,
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| this repo contains everything needed to rebuild the corpus from the pinned upstream releases.
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|
|
| ## What is here
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|
|
| | File | Purpose |
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| |---|---|
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| | `sources.json` | Every source with its pinned revision, checksum, licence, access status, and training decision |
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| | `anatomy-tiers.json` | The three-level taxonomy, the organ -> region parent map, and which classes are actually trained |
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| | `anatomy-mappings.json` | Explicit decision for every upstream class and DICOM tag value; no default branch |
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| | `canonical-frame-row.schema.json` | The row schema every source is normalised to |
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| | `preprocessor.json` | Exact pixel handling, so a rebuild is byte-comparable |
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| | `build-manifest.json` | Counts by split, source, modality, organ — and **patients**, not just frames |
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|
|
| ## Corpus shape
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|
|
| | Split | Frames | Patients |
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| |---|---:|---:|
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| | train | 82,354 | see `build-manifest.json` |
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| | validation | 10,280 | see `build-manifest.json` |
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| | test | 15,395 | see `build-manifest.json` |
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|
|
| | Modality | Frames |
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| |---|---:|
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| | CT | 83,318 |
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| | MR | 1,880 |
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| | US | 14,907 |
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| | XR | 7,924 |
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|
|
| ## Why patient counts are printed next to frame counts
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|
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| 300 consecutive frames from one cine loop carry roughly the information of one sample. MedMNIST
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| OrganAMNIST is 58,830 images from **201** CT scans — 293 images per patient. Training on the raw
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| count inflates every metric and teaches the model scanner identity. `sampling_policy` in
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| `sources.json` caps frames per patient before anything is written, and the builder enforces it.
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|
|
| ## Redistribution status by source
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|
|
| | Source | Licence | Access | Redistributed here |
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| |---|---|---|---|
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| | `medmnist-plus-organamnist-224` | CC-BY-4.0 | open | recipe only |
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| | `medmnist-plus-organcmnist-224` | CC-BY-4.0 | open | recipe only |
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| | `medmnist-plus-organsmnist-224` | CC-BY-4.0 | open | recipe only |
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| | `medmnist-plus-breastmnist-224` | CC-BY-4.0 | open | recipe only |
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| | `medmnist-plus-chestmnist-224` | CC-BY-4.0 | open | recipe only |
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| | `msu-abdominal-ultrasound` | CC-BY-4.0 | open_manual_browser_download | recipe only |
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| | `fetal-planes-db` | CC-BY-4.0 | open | recipe only |
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| | `totalsegmentator-ct-sample` | CC-BY-4.0 | open | recipe only |
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| | `totalsegmentator-ct-v300` | CC-BY-4.0 | open | recipe only |
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| | `amos22` | CC-BY-4.0 | open | recipe only |
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| | `medical-segmentation-decathlon` | CC-BY-SA-4.0 | open_but_unresolved_host | recipe only |
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| | `rocov2` | CC-BY-NC-4.0 | open | **no** — licence forbids |
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| | `radimagenet` | undefined | registration_and_agreement_required | **no** — licence forbids |
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| | `camus` | undefined | registration_required | **no** — licence forbids |
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| | `echonet-dynamic` | Stanford EchoNet-Dynamic Dataset Research Use Agreement | signed_research_use_agreement | **no** — licence forbids |
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| | `echonet-lvh` | Stanford EchoNet-LVH Dataset Research Use Agreement | signed_research_use_agreement | **no** — licence forbids |
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| | `busi-original` | undefined | mirror_only | **no** — licence forbids |
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| | `tn3k` | undefined | third_party_drive | **no** — licence forbids |
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| | `ddti` | undefined | source_site_unavailable | **no** — licence forbids |
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| | `mmotu` | undefined | third_party_drive | **no** — licence forbids |
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| | `pocus-covid19-ultrasound` | mixed per-file (CC-BY-4.0, CC-BY-NC-4.0, all-rights-reserved) | open | **no** — licence forbids |
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| | `biomedclip` | MIT tag, but the model card restricts use | open | **no** — licence forbids |
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| | `usfm` | CC-BY-NC-4.0 | third_party_drive | **no** — licence forbids |
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|
|
| ## Rebuild it
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|
|
| ```bash
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| git clone https://github.com/palarnab/organscan && cd organscan
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| python downloaded-training-data/download.py # pinned revisions, checksum-verified
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| python scripts/build_frame_dataset.py
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| python scripts/validate_frame_dataset.py # leakage, mask coherence, coverage
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| ```
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|
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| The build fails rather than silently dropping data when an unmapped upstream class appears, and
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| validation fails on patient leakage across splits, identical frames in two splits, or a weak label
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| found in an evaluation split.
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|
|
| ## Attribution
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|
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| Every source below requires credit, and every one of them was modified — sliced from volumes or cine
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| loops, windowed, resized to 224×224, capped per patient, and relabelled into the OrganScan taxonomy.
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| Full per-source detail, including the exact modifications, is in `sources.json` under each entry's
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| `attribution` block.
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|
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| | Source | Creators | Licence | Frames used |
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| |---|---|---|---:|
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| | [TotalSegmentator CT dataset v3.0.0](https://zenodo.org/records/22688904) | Jakob Wasserthal et al. | [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) | 61,902 |
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| | [AMOS22: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation](https://zenodo.org/records/7262581) | Yuanfeng Ji et al. | [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) | 11,480 |
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| | [FETAL_PLANES_DB: Common maternal-fetal ultrasound images](https://zenodo.org/records/3904280) | Xavier P. Burgos-Artizzu et al. | [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) | 10,748 |
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| | [MedMNIST v2 (ChestMNIST, 224px)](https://zenodo.org/records/10519652) | Jiancheng Yang et al. | [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) | 7,924 |
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| | [MedMNIST v2 (OrganSMNIST, 224px)](https://zenodo.org/records/10519652) | Jiancheng Yang et al. | [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) | 4,000 |
|
| | [MedMNIST v2 (OrganAMNIST, 224px)](https://zenodo.org/records/10519652) | Jiancheng Yang et al. | [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) | 3,914 |
|
| | [MedMNIST v2 (OrganCMNIST, 224px)](https://zenodo.org/records/10519652) | Jiancheng Yang et al. | [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) | 3,902 |
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| | [Abdominal Ultrasound Image Dataset for Organ Classification and Disease Detection](https://scholarsjunction.msstate.edu/research-data/5/) | Sifat Zina Karim | [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) | 3,380 |
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| | [MedMNIST v2 (BreastMNIST, 224px)](https://zenodo.org/records/10519652) | Jiancheng Yang et al. | [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) | 779 |
|
|
|
| ```
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| OrganScan is trained on the following datasets, all of which were modified
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| (sliced to 2D, windowed, resized to 224px, and relabelled):
|
|
|
| - TotalSegmentator CT dataset v3.0.0
|
| Jakob Wasserthal, Hanns-Christian Breit, Manfred T. Meyer, Maurice Pradella, Daniel Hinck, Alexander W. Sauter, Tobias Heye, Daniel T. Boll, Joshy Cyriac, Shan Yang, Michael Bach, Martin Segeroth - CC-BY-4.0
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| https://zenodo.org/records/22688904
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| - AMOS22: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation
|
| Yuanfeng Ji, Haotian Bai, Chongjian Ge, Jie Yang, Ye Zhu, Ruimao Zhang, Zhen Li, Lingyan Zhang, Wanling Ma, Xiang Wan, Ping Luo - CC-BY-4.0
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| https://zenodo.org/records/7262581
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| - FETAL_PLANES_DB: Common maternal-fetal ultrasound images
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| Xavier P. Burgos-Artizzu, David Coronado-Gutierrez, Brenda Valenzuela-Alcaraz, Elisenda Bonet-Carne, Elisenda Eixarch, Fatima Crispi, Eduard Gratacós - CC-BY-4.0
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| https://zenodo.org/records/3904280
|
| - MedMNIST v2 (ChestMNIST, 224px)
|
| Jiancheng Yang, Rui Shi, Donglai Wei, Zequan Liu, Lin Zhao, Bilian Ke, Hanspeter Pfister, Bingbing Ni - CC-BY-4.0
|
| https://zenodo.org/records/10519652
|
| - MedMNIST v2 (OrganSMNIST, 224px)
|
| Jiancheng Yang, Rui Shi, Donglai Wei, Zequan Liu, Lin Zhao, Bilian Ke, Hanspeter Pfister, Bingbing Ni - CC-BY-4.0
|
| https://zenodo.org/records/10519652
|
| - MedMNIST v2 (OrganAMNIST, 224px)
|
| Jiancheng Yang, Rui Shi, Donglai Wei, Zequan Liu, Lin Zhao, Bilian Ke, Hanspeter Pfister, Bingbing Ni - CC-BY-4.0
|
| https://zenodo.org/records/10519652
|
| - MedMNIST v2 (OrganCMNIST, 224px)
|
| Jiancheng Yang, Rui Shi, Donglai Wei, Zequan Liu, Lin Zhao, Bilian Ke, Hanspeter Pfister, Bingbing Ni - CC-BY-4.0
|
| https://zenodo.org/records/10519652
|
| - Abdominal Ultrasound Image Dataset for Organ Classification and Disease Detection
|
| Sifat Zina Karim - CC-BY-4.0
|
| https://scholarsjunction.msstate.edu/research-data/5/
|
| - MedMNIST v2 (BreastMNIST, 224px)
|
| Jiancheng Yang, Rui Shi, Donglai Wei, Zequan Liu, Lin Zhao, Bilian Ke, Hanspeter Pfister, Bingbing Ni - CC-BY-4.0
|
| https://zenodo.org/records/10519652
|
| ```
|
|
|
| ## Author
|
|
|
| Arnab Pal — [LinkedIn](https://www.linkedin.com/in/pal-arnab) · [GitHub](https://github.com/palarnab)
|
|
|
| <!-- patients by source: {"amos22": 360, "fetal-planes-db": 1792, "medmnist-plus-breastmnist-224": 3, "medmnist-plus-chestmnist-224": 3, "medmnist-plus-organamnist-224": 3, "medmnist-plus-organcmnist-224": 3, "medmnist-plus-organsmnist-224": 3, "msu-abdominal-ultrasound": 3380, "totalsegmentator-ct-v300": 1936} -->
|
| |
