| --- |
| license: cc-by-nc-4.0 |
| pretty_name: OrganMNIST3D Subset (Bladder and Femur-Right) |
| task_categories: |
| - image-classification |
| tags: |
| - biomedical-imaging |
| - 3d |
| - NIfTI file format (.nii.gz) |
| - medmnist+ |
| - autoencodix |
| --- |
| |
|
|
| # Info |
| Subset of the MedMNIST+ OrganMNIST3D dataset containing only the organ classes bladder and femur-right, prepared for use with the [AUTOENCODIX ](https://github.com/jan-forest/autoencodix_package) Imagix3D tutorial. The complete MedMNIST dataset collections can be found [here](https://medmnist.com/). |
|
|
| OrganMNIST3D is a three-dimensional biomedical image classification dataset derived from abdominal CT scans. The MedMNIST+ version provides the volumes at a spatial resolution of 64 × 64 × 64 voxels. |
|
|
| For this tutorial dataset, only samples belonging to the bladder and right-femur classes were retained. The volumes were converted from its original .npz file format to compressed NIfTI files (.nii.gz). |
|
|
|
|
| # Contents |
| - 345 images (174 bladder, 171 femur-right) with a spatial size of 64 × 64 × 64 voxels. |
|
|
| - organmnist3d_images.zip: compressed archive containing the individual volumes in NIfTI format (.nii.gz). |
| |
| - organmnist3d_mappings.csv: comma-separated annotation file containing the sample identifiers, paths to the corresponding NIfTI files, and organ-class labels. |
|
|
|
|
| # Loading |
| The files can be downloaded from Hugging Face using huggingface_hub: |
| |
| ```python |
| from huggingface_hub import hf_hub_download |
| import zipfile |
|
|
| mapping_path = hf_hub_download( |
| repo_id="autoencodix/OrganMNIST3D-subsample", |
| repo_type="dataset", |
| filename="organmnist3d_mappings.csv", |
| ) |
|
|
| zip_path = hf_hub_download( |
| repo_id="autoencodix/OrganMNIST3D-subsample", |
| repo_type="dataset", |
| filename="organmnist3d_images.zip", |
| ) |
|
|
| with zipfile.ZipFile(zip_path) as zf: |
| zf.extractall("data/images/") |
| ``` |
| |
| |
| # License |
| Original dataset licensed under [Creative Commons Attribution 4.0 International (CC BY 4.0)](https://creativecommons.org/licenses/by/4.0/), see: https://medmnist.com/. |
| The [Apache-2.0](https://www.apache.org/licenses/LICENSE-2.0) license associated with the MedMNIST project applies to the MedMNIST software code, see: https://github.com/MedMNIST/MedMNIST/. |
| |
