README.md

---
license: mit
task_categories:
- image-segmentation
language:
- en
tags:
- medical
pretty_name: IBDColEpi
size_categories:
- 1B<n<10B
---

# IBDColEpi: 140 HE and 111 CD3-stained colon biopsies of active and inactivate inflammatory bowel disease with epithelium annotated

To access and work with the data in Python, you can do so through the Python API with datasets. See this Jupyter Notebook on how to get started:
https://github.com/andreped/NoCodeSeg/blob/main/notebooks/IBDColEpi-load-dataset-example.ipynb

Note that it is also possible to download the data through the web interface at Hugging Face, but also through [this google drive](https://drive.google.com/drive/u/0/folders/1eUVs1DA1UYayUYjr8_aY3O5xDgV1uLvH)
and [this dataverseNO](https://dataverse.no/dataset.xhtml?persistentId=doi:10.18710/TLA01U) link.

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GENERAL INFORMATION
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1. Title of Dataset: 140 HE and 111 CD3-stained colon biopsies of active and inactivate inflammatory bowel disease with epithelium annotated: the IBDColEpi dataset
2. DOI: https://doi.org/10.18710/TLA01U
3. Contact Information
     Name: André Pedersen
     Institution: NTNU Norwegian University of Science and Technology
     Email: [email protected]
     ORCID: https://orcid.org/0000-0002-3637-953X

     
4. Contributors: See metadata field Contributor.
5. Kind of data: See metadata field Kind of Data.
6. Date of data collection/generation: See metadata field Date of Collection.
7. Geographic location: See metadata section Geographic Coverage.
8. Funding sources: See metadata section Grant Information.


9. Description of dataset: 
General description and ethics approvals: The dataset contains 140 HE and 111 CD3 stained, formalin fixed paraffin embedded (FFPE) biopsies of colonic mucosa. The biopsies were extracted from the NTNU/St. Olavs hospital, Trondheim University Hospital (Norway) biobank of patients with confirmed inflammatory bowel disease or healthy controls with gastrointestinal symptoms but no macroscopic- or microscopic disease. Inclusion and colonoscopies were performed at the Department of Gastroenterology and Hepatology at St. Olavs hospital, Trondheim University Hospital from 2007 to 2018. All patients gave written informed consent and ethical approvals were obtained from the Central Norway Regional Committee for Medical and Health Research Ethics (reference number 2013/212/REKMidt). Consent to publish the anonymized whole slide image (WSI) dataset was given by REKMidt in 2021. Each database ID number used in this study was changed to new anonymized IDs only containing the information “active” or “inactive” disease and whether the WSI has haematoxylin-eosin (HE) staining or CD3 immunostaining. The biopsies included in the biobank are sampled such that one biopsy from an unaffected/inactive area and one from an area affected/active area were included from each patient and given a separate ID number. Hence, two biopsies with different ID numbers can be from the same patient. "Active" is defined as the presence of intraepithelial granulocytes in one or more location in the biopsies. Still, the changes may be focal, hence majority of the epithelium may still lack intraepithelial granulocytes or other signs of active disease (crypt abscesses, granulation tissue, etc.).


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SHARING/ACCESS INFORMATION
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(See metadata record for dataset.)

1. Licenses/Restrictions: See Terms section.
2. Links to publications that cite or use the data: See metadata field Related Publication.
3. Links/relationships to related data sets: See metadata field Related Datasets.
4. Data sources: See metadata field Data Sources.
5. Recommended citation: See citation generated by repository.


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DATA & FILE OVERVIEW
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1. File List: 
00_README.txt
trained-models.zip
patch-dataset-CD3.zip
patch-dataset-HE.zip
qupath-project-annotations.zip
TIFF-annotations.zip
WSI_part_01.zip
WSI_part_02.zip
WSI_part_03.zip
WSI_part_04.zip
WSI_part_05.zip
WSI_part_06.zip
WSI_part_07.zip
WSI_part_08.zip
WSI_part_09.zip
WSI_part_10.zip

2. Relationship between files, if important: 
- trained-models.zip: the best performing trained models (for both HE and CD3) on the images from WSI_part_*.zip using the manual delineations from TIFF-annotations.zip.
- WSI_path_*.zip: the colon biopsies described in the metadata (1-10). For each ID, the active/inactive label Y is stored in the filename, with the format: "ID-X_Y.ndpi".
- TIFF-annotations.zip: the corresponding annotations to the WSIs. The filenames of the annotations are in the same structure as the corresponding WSIs, with the format: "ID-X_Y.tiff".
- patch-dataset-*.zip: the corresponding patch images and labels, split into train/validation/test sets, relevant for the evaluation of the design in the publication. Both for HE and CD3
- qupath-project-annotations.zip: the qupath project file, also containing the annotations of all WSIs, but can be directly read in QuPath (after renaming of WSI paths).