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Part 1: Document Description
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Citation |
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Title: |
140 HE and 111 CD3-stained colon biopsies of active and inactivate inflammatory bowel disease with epithelium annotated: the IBDColEpi dataset |
Identification Number: |
doi:10.18710/TLA01U |
Distributor: |
DataverseNO |
Date of Distribution: |
2021-12-09 |
Version: |
2 |
Bibliographic Citation: |
Pettersen, Henrik Sahlin; Belevich, Ilya; Røyset, Elin Synnøve; Smistad, Erik; Jokitalo, Eija; Reinertsen, Ingerid; Bakke, Ingunn; Pedersen, André, 2021, "140 HE and 111 CD3-stained colon biopsies of active and inactivate inflammatory bowel disease with epithelium annotated: the IBDColEpi dataset", https://doi.org/10.18710/TLA01U, DataverseNO, V2 |
Citation |
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Title: |
140 HE and 111 CD3-stained colon biopsies of active and inactivate inflammatory bowel disease with epithelium annotated: the IBDColEpi dataset |
Identification Number: |
doi:10.18710/TLA01U |
Authoring Entity: |
Pettersen, Henrik Sahlin (Department of Pathology, St. Olavs hospital, Trondheim University Hospital; Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology; Clinic of Laboratory Medicine, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway*) |
Belevich, Ilya (Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland*) |
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Røyset, Elin Synnøve (Department of Pathology, St. Olavs hospital, Trondheim University Hospital; Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology; Clinic of Laboratory Medicine, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway*) |
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Smistad, Erik (Department of Health Research, SINTEF; Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway*) |
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Jokitalo, Eija (Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland*) |
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Reinertsen, Ingerid (Department of Health Research, SINTEF; Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway*) |
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Bakke, Ingunn (Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology; Clinic of Laboratory Medicine, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway*) |
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Pedersen, André (Department of Health Research, SINTEF; Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, Trondheim, Norway*) |
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Other identifications and acknowledgements: |
Røyset, Elin Synnøve |
Other identifications and acknowledgements: |
Bakke, Ingunn |
Other identifications and acknowledgements: |
Pettersen, Henrik Sahlin |
Other identifications and acknowledgements: |
Pedersen, André |
Other identifications and acknowledgements: |
St Olavs hospital, Trondheim University Hospital |
Other identifications and acknowledgements: |
NTNU – Norwegian University of Science and Technology |
Producer: |
NTNU – Norwegian University of Science and Technology |
Software used in Production: |
QuPath |
Software used in Production: |
MIB |
Software used in Production: |
FastPathology |
Grant Number: |
1331998 |
Grant Number: |
1331998 |
Grant Number: |
1331998 |
Grant Number: |
1331998 |
Grant Number: |
1331998 |
Distributor: |
DataverseNO |
Distributor: |
NTNU – Norwegian University of Science and Technology |
Access Authority: |
Pedersen, André |
Depositor: |
Pedersen, André |
Date of Deposit: |
2021-11-15 |
Holdings Information: |
https://doi.org/10.18710/TLA01U |
Study Scope |
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Keywords: |
Computer and Information Science, Medicine, Health and Life Sciences, Digital Pathology, Deep Learning, Segmentation, Annotations, Colon biopsies, Inflammatory Bowel Disease, Crohn's disease, Ulcerative colitis |
Abstract: |
<p><b>ALTERNATIVE DOWNLOAD ON GOOGLE DRIVE! </b> To access the data, click "Read Full Description" [+] and then click <a href="https://drive.google.com/drive/folders/1eUVs1DA1UYayUYjr8_aY3O5xDgV1uLvH?usp=sharing">here</a> </p> <p><b>General description and ethics approvals:</b> 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.).</p> <p><b>Annotation procedures:</b> While annotating epithelium, we strived to draw lines as close to the basement membrane as possible where visible. All annotations were finally refined by the following QuPath scripts to ensure consistency throughout the datasets: - Minimum fragment size min 75 um^2 - Minimum hole size min 100 um^2 - remove white background with intensity greater than 220 average all channels with sigma 2.5 - expand and shrink all annotations 1.0 mm.</p> <p><b>Laboratory methods:</b> FFPE sections of 4 µm were cut, mounted on slides and either stained with hematoxylin (Mayer’s) and Eosin (Y) (HE) or subjected to standard pre-treatment with quenching of endogenous peroxidase and boiling in Tris EDTA pH9 for antigen retrieval before immunohistochemistry. Primary antibody for the T lymphocyte marker was mouse anti-human CD3 (M7254, clone F7.2.38, Dako Agilent, CA, USA), diluted 1:50 in antibody diluent Tris buffer with 0.025% Tween-20 and 1% BSA and incubated overnight at 4 °C. Immunoreactions were visualized with the secondary antibody rabbit/mouse EnVisionHRP/DAB+ kit (K5007, Dako Agilent) and counterstaining with haematoxylin. Omission of the primary antibody was used as negative control and sections from human peripheral lymph node as positive control.</p> |
Kind of Data: |
Annotated histopathological whole slide images |
Kind of Data: |
Annotated histopathological image patches |
Kind of Data: |
Pretrained segmentation models |
Methodology and Processing |
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Sources Statement |
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Data Access |
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Other Study Description Materials |
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Related Publications |
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Citation |
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Title: |
Pettersen, Henrik Sahlin, Ilya Belevich, Elin Synnøve Røyset, Erik Smistad, Eija Jokitalo, Ingerid Reinertsen, Ingunn Bakke and André Pedersen. (2021). “Code-free development and deployment of deep segmentation models for digital pathology”. arXiv:2111.08430 [q-bio.QM] |
Identification Number: |
2111.08430 |
Bibliographic Citation: |
Pettersen, Henrik Sahlin, Ilya Belevich, Elin Synnøve Røyset, Erik Smistad, Eija Jokitalo, Ingerid Reinertsen, Ingunn Bakke and André Pedersen. (2021). “Code-free development and deployment of deep segmentation models for digital pathology”. arXiv:2111.08430 [q-bio.QM] |
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