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Whole slide images and patches of clear cell renal cell carcinoma tissue sections counterstained with Hoechst 33342, CD3, and CD8 using multiple immunofluorescence

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Wolflein_2023_Data_Whole_slide_images_CC.pdf (2.312Mb)
Date
15/02/2023
Author
Wolflein, Georg
Um, In Hwa
Harrison, David James
Arandelovic, Oggie
Funder
European Commission
Innovate UK
Grant ID
101017453
TS/S013121/1
Keywords
Cancer
Digital pathology
Machine learning
Computer vision
Virtual staining
Segmentation
RC0254 Neoplasms. Tumors. Oncology (including Cancer)
RB Pathology
QA75 Electronic computers. Computer science
3rd-DAS
MCC
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Abstract
In recent years, there has been an increased effort to digitise whole-slide images of cancer tissue. This effort has opened up a range of new avenues for the application of deep learning in oncology. One such avenue is virtual staining, where a deep learning model is tasked with reproducing the appearance of stained tissue sections, conditioned on a different, often times less expensive, input stain. However, data to train such models in a supervised manner where the input and output stains are aligned on the same tissue sections are scarce. In this work, we introduce a dataset of ten whole-slide images of clear cell renal cell carcinoma tissue sections counterstained with Hoechst 33342, CD3, and CD8 using multiple immunofluorescence. We also provide a set of over 600,000 patches of size 256 × 256 pixels extracted from these images together with cell segmentation masks in a format amenable to training deep learning models. It is our hope that this dataset will be used to further the development of deep learning methods for digital pathology by serving as a dataset for comparing and benchmarking virtual staining models.
Citation
Wolflein , G , Um , I H , Harrison , D J & Arandelovic , O 2023 , ' Whole slide images and patches of clear cell renal cell carcinoma tissue sections counterstained with Hoechst 33342, CD3, and CD8 using multiple immunofluorescence ' , Data , vol. 8 , no. 2 , 40 . https://doi.org/10.3390/data8020040
Publication
Data
Status
Peer reviewed
DOI
https://doi.org/10.3390/data8020040
ISSN
2306-5729
Type
Journal article
Rights
Copyright: © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).
Description
Funding: G.W. is supported by Lothian NHS. This project received funding from the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No. 101017453 as part of the KATY project. This work is supported in part by the Industrial Centre for AI Research in Digital Diagnostics (iCAIRD) which is funded by Innovate UK on behalf of UK Research and Innovation (UKRI) (project number 104690).
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  • University of St Andrews Research
URI
http://hdl.handle.net/10023/26986

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