CytoNuke Dataset: Towards reliable whole-cell segmentation in bright-field histological images
Creators
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Raufeisen, Johannes
(Data collector)1, 2
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Xie, Kunpeng
(Data collector)1, 2
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Hörst, Fabian
(Other)3, 4
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Braunschweig, Till
(Data collector)5, 6
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Li, Jianning
(Other)3, 4
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Kleesiek, Jens
(Other)3, 4, 7
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Röhrig, Rainer
(Other)2
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Egger, Jan
(Other)3, 4, 8
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Leibe, Bastian
(Other)9
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Hölzle, Frank
(Other)1
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Hermans, Alexander
(Other)9
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Puladi, Behrus
(Contact person)1, 2
- 1. Department of Oral and Maxillofacial Surgery, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany
- 2. Institute of Medical Informatics, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany
- 3. Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen (AöR), Girardetstraße 2, 45131 Essen, Germany
- 4. Cancer Research Center Cologne Essen (CCCE), West German Cancer Center Essen, University Hospital Essen (AöR), Hufelandstr. 55, 45147 Essen, Germany
- 5. Institute of Pathology, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany
- 6. Institute of Pathology, Ludwig Maximilian University of Munich, Thalkirchner Str. 36, 80337 Munich, Germany
- 7. Department of Physics, TU Dortmund University, August-Schmidt-Str. 4, 44227 Dortmund, Germany
- 8. Center for Virtual and Extended Reality in Medicine (ZvRM), University Hospital Essen, University Medicine Essen, Hufelandstraße 55, 45147 Essen, Germany
- 9. Visual Computing Institute (Computer Vision), RWTH Aachen University, Mies-van-der-Rohe Str. 15, 52074 Aachen, Germany
Description
This is the dataset from the preprint "Cyto R-CNN and CytoNuke Dataset: Towards reliable whole-cell segmentation in bright-field histological images" by Raufeisen et al. (2024). It contains 6,683 annotations (3,991 nuclei and 2,607 whole cells) of head and neck squamous cell carcinoma cells in hematoxylin and eosin stained histological images. The annotations are in COCO format and distributed over 83 PNG images. Cyto R-CNN was trained on this dataset and compared with other state-of-the-art methods. The CytoNuke dataset is released under the CC BY-NC-SA 4.0 license.
The histological images are from the CPTAC dataset:
National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2018). The Clinical Proteomic Tumor Analysis Consortium Head and Neck Squamous Cell Carcinoma Collection (CPTAC-HNSCC) (Version 15) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2018.UW45NH81
Funding: Behrus Puladi was funded by the Medical Faculty of RWTH Aachen University as part of the Clinician Scientist Program. We acknowledge FWF enFaced 2.0 [KLI 1044, https://enfaced2.ikim.nrw/] and KITE (Plattform für KI-Translation Essen) from the REACT-EU initiative [https://kite.ikim.nrw/, EFRE-0801977]. Fabian Hörst, Jianning Li, Jens Kleesiek and Jan Egger received funding from the Cancer Research Center Cologne Essen (CCCE).
Files
CytoNuke Dataset.zip
Files
(12.8 MB)
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Additional details
Related works
- Is published in
- Journal article: 10.1016/j.cmpb.2024.108215 (DOI)
- Preprint: arXiv:2401.15638 (arXiv)
Dates
- Available
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2024-01-30