| Name | amid JSON |
| Version |
0.12.5
JSON |
| download |
| home_page | https://github.com/neuro-ml/amid |
| Summary | A curated list of medical imaging datasets with unified interfaces |
| upload_time | 2023-08-04 09:54:25 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.6 |
| license | |
| keywords |
medical imaging
dataset
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
|
[](https://neuro-ml.github.io/amid/)
[](https://neuro-ml.github.io/amid/latest/CONTRIBUTING/)
[](https://pypi.org/project/amid/)
Awesome Medical Imaging Datasets (AMID) - a curated list of medical imaging datasets with unified interfaces
# Getting started
Just import a dataset and start using it!
Note that for some datasets you must manually download the raw files first.
```python
from amid.verse import VerSe
ds = VerSe()
# get the available ids
print(len(ds.ids))
i = ds.ids[0]
# use the available methods:
# load the image and vertebrae masks
x, y = ds.image(i), ds.masks(i)
print(ds.split(i), ds.patient(i))
# or get a namedTuple-like object:
entry = ds(i)
x, y = entry.image, entry.masks
print(entry.split, entry.patient)
```
# Available datasets
| Name | Entries | Body region | Modality |
|:-----------------------------------------------------------------------------------------------------------------------------------|----------:|:------------------------------------|:--------------------------------------------------|
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.amos.dataset.AMOS">AMOS</a> | 360 | Abdomen | CT, MRI |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.bimcv.BIMCVCovid19">BIMCVCovid19</a> | 16335 | Chest | CT |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.brats2021.BraTS2021">BraTS2021</a> | 5880 | Head | MRI T1, MRI T1Gd, MRI T2, MRI T2-FLAIR |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.cc359.dataset.CC359">CC359</a> | 359 | Head | MRI T1 |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.cl_detection.CLDetection2023">CLDetection2023</a> | 400 | Head | X-ray |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.crlm.CRLM">CRLM</a> | 197 | Abdomen | CT, SEG |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.ct_ich.CT_ICH">CT_ICH</a> | 75 | Head | CT |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.crossmoda.CrossMoDA">CrossMoDA</a> | 484 | Head | MRI T1c, MRI T2hr |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.deeplesion.DeepLesion">DeepLesion</a> | 20094 | Abdomen, Thorax | CT |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.egd.EGD">EGD</a> | 3096 | Head | FLAIR, MRI T1, MRI T1GD, MRI T2 |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.flare2022.FLARE2022">FLARE2022</a> | 2100 | Abdomen | CT |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.lidc.dataset.LIDC">LIDC</a> | 1018 | Chest | CT |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.lits.dataset.LiTS">LiTS</a> | 201 | Abdominal | CT |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.liver_medseg.LiverMedseg">LiverMedseg</a> | 50 | Chest, Abdomen | CT |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.midrc.MIDRC">MIDRC</a> | 155 | Thorax | CT |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.mood.MOOD">MOOD</a> | 1358 | Head, Abdominal | MRI, CT |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.medseg9.Medseg9">Medseg9</a> | 9 | Chest | CT |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.cancer_500.dataset.MoscowCancer500">MoscowCancer500</a> | 979 | Thorax | CT |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.covid_1110.MoscowCovid1110">MoscowCovid1110</a> | 1110 | Thorax | CT |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.nlst.NLST">NLST</a> | 13624 | Thorax | CT |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.nsclc.NSCLC">NSCLC</a> | 422 | Thorax | CT |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.rsna_bc.dataset.RSNABreastCancer">RSNABreastCancer</a> | 54710 | Thorax | MG |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.stanford_coca.StanfordCoCa">StanfordCoCa</a> | 971 | Coronary, Chest | CT |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.totalsegmentator.dataset.Totalsegmentator">Totalsegmentator</a> | 1204 | Head, Thorax, Abdomen, Pelvis, Legs | CT |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.upenn_gbm.upenn_gbm.UPENN_GBM">UPENN_GBM</a> | 671 | Head | FLAIR, MRI T1, MRI T1GD, MRI T2, DSC MRI, DTI MRI |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.vs_seg.dataset.VSSEG">VSSEG</a> | 484 | Head | MRI T1c, MRI T2 |
| <a href="https://neuro-ml.github.io/amid/latest/datasets-api/#amid.verse.VerSe">VerSe</a> | 374 | Thorax, Abdomen | CT |
Check out [our docs](https://neuro-ml.github.io/amid/) for a more detailed list of available datasets and their fields.
# Install
Just get it from PyPi:
```shell
pip install amid
```
Or if you want to use version control features:
```shell
git clone https://github.com/neuro-ml/amid.git
cd amid && pip install -e .
```
# Contribute
Check our [contribution guide](https://neuro-ml.github.io/amid/latest/CONTRIBUTING/) if you want to add a new dataset to
AMID.
Raw data
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|\n|:-----------------------------------------------------------------------------------------------------------------------------------|----------:|:------------------------------------|:--------------------------------------------------|\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.amos.dataset.AMOS\">AMOS</a> | 360 | Abdomen | CT, MRI |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.bimcv.BIMCVCovid19\">BIMCVCovid19</a> | 16335 | Chest | CT |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.brats2021.BraTS2021\">BraTS2021</a> | 5880 | Head | MRI T1, MRI T1Gd, MRI T2, MRI T2-FLAIR |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.cc359.dataset.CC359\">CC359</a> | 359 | Head | MRI T1 |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.cl_detection.CLDetection2023\">CLDetection2023</a> | 400 | Head | X-ray |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.crlm.CRLM\">CRLM</a> | 197 | Abdomen | CT, SEG |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.ct_ich.CT_ICH\">CT_ICH</a> | 75 | Head | CT |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.crossmoda.CrossMoDA\">CrossMoDA</a> | 484 | Head | MRI T1c, MRI T2hr |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.deeplesion.DeepLesion\">DeepLesion</a> | 20094 | Abdomen, Thorax | CT |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.egd.EGD\">EGD</a> | 3096 | Head | FLAIR, MRI T1, MRI T1GD, MRI T2 |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.flare2022.FLARE2022\">FLARE2022</a> | 2100 | Abdomen | CT |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.lidc.dataset.LIDC\">LIDC</a> | 1018 | Chest | CT |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.lits.dataset.LiTS\">LiTS</a> | 201 | Abdominal | CT |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.liver_medseg.LiverMedseg\">LiverMedseg</a> | 50 | Chest, Abdomen | CT |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.midrc.MIDRC\">MIDRC</a> | 155 | Thorax | CT |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.mood.MOOD\">MOOD</a> | 1358 | Head, Abdominal | MRI, CT |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.medseg9.Medseg9\">Medseg9</a> | 9 | Chest | CT |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.cancer_500.dataset.MoscowCancer500\">MoscowCancer500</a> | 979 | Thorax | CT |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.covid_1110.MoscowCovid1110\">MoscowCovid1110</a> | 1110 | Thorax | CT |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.nlst.NLST\">NLST</a> | 13624 | Thorax | CT |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.nsclc.NSCLC\">NSCLC</a> | 422 | Thorax | CT |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.rsna_bc.dataset.RSNABreastCancer\">RSNABreastCancer</a> | 54710 | Thorax | MG |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.stanford_coca.StanfordCoCa\">StanfordCoCa</a> | 971 | Coronary, Chest | CT |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.totalsegmentator.dataset.Totalsegmentator\">Totalsegmentator</a> | 1204 | Head, Thorax, Abdomen, Pelvis, Legs | CT |\n| <a href=\"https://neuro-ml.github.io/amid/latest/datasets-api/#amid.upenn_gbm.upenn_gbm.UPENN_GBM\">UPENN_GBM</a> | 671 | Head | FLAIR, MRI T1, MRI T1GD, MRI T2, DSC MRI, DTI MRI |\n| <a 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