Metadata-Version: 2.1
Name: amid
Version: 0.9.1
Summary: A curated list of medical imaging datasets with unified interfaces
Home-page: https://github.com/neuro-ml/amid
License: UNKNOWN
Download-URL: https://github.com/neuro-ml/amid/archive/v0.9.1.tar.gz
Keywords: medical imaging,dataset
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3 :: Only
Requires-Python: >=3.6
Description-Content-Type: text/markdown
License-File: LICENSE

[![docs](https://img.shields.io/badge/-docs-success)](https://neuro-ml.github.io/amid/)
[![contribute](https://img.shields.io/badge/-contribute-success)](https://neuro-ml.github.io/amid/latest/CONTRIBUTING/)
[![pypi](https://img.shields.io/pypi/v/amid?logo=pypi&label=PyPi)](https://pypi.org/project/amid/)
![License](https://img.shields.io/github/license/neuro-ml/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>                                     |       600 | 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.cc359.dataset.CC359">CC359</a>                                  |       359 | Head                                | MRI T1                          |
| <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.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.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.


