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ZENODO
Dataset . 2022
License: CC BY
Data sources: Datacite
ZENODO
Dataset . 2022
License: CC BY
Data sources: Datacite
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Training data for the "Computational textural mapping harmonises sampling variation and reveals multidimensional histopathological fingerprints"

Authors: Otso Brummer; Oscar Brück;

Training data for the "Computational textural mapping harmonises sampling variation and reveals multidimensional histopathological fingerprints"

Abstract

There are two ZIP-files consisting of small histological image tiles that have been used to detect and quantify distinct tissue textures and lymphocyte proportions from H&E-stained clear cell renal cell carcinoma (KIRC) digital tissue sections of the Cancer Genome Atlas (TCGA) image archive and the Helsinki dataset. The tissue_classification file contains 300x300px tissue texture image tiles (n=52,713) representing renal cancer (“cancer”; n=13,057, 24.8%); normal renal (“normal”; n=8,652, 16.4%); stromal (“stroma”; n= 5,460, 10.4%) including smooth muscle, fibrous stroma and blood vessels; red blood cells (“blood”; n=996, 1.9%); empty background (“empty”; n=16,026, 30.4%); and other textures including necrotic, torn and adipose tissue (“other”; n=8,522, 16.2%). Image tiles have been randomly selected from the TCGA-KIRC WSI and the Helsinki datasets. The binary_lymphocytes file contains mostly 256x256px-sized but also smaller image tiles of Low (n=20,092, 80.1%) or High (n=5,003, 19.9%) lymphocyte density (n=25,095). Image tiles have been randomly selected from the TCGA-KIRC WSI dataset. All accuracy of all annotations have been double-checked. However, the classification between multiple tissue textures or lymphocyte density can be sometimes ambiguous. The deep learning model parameters trained with the ResNet-18 infrastructure for (1) lymphocyte and (2) texture classification are named as (1) resnet18_binary_lymphocytes.pth and (2) resnet18_tissue_classification.pth. Codes and instructions to use these are found in https://github.com/vahvero/RCC_textures_and_lymphocytes_publication_image_analysis. If you use either work, please cite the publication by Brummer O et al (1) AND the TCGA Research Network (2):(1) Brummer, O., Pölönen, P., Mustjoki, S. et al. Computational textural mapping harmonises sampling variation and reveals multidimensional histopathological fingerprints. Br J Cancer 129, 683–695 (2023). https://doi.org/10.1038/s41416-023-02329-4 (2) The results shown here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.

Keywords

H&E, Tissue textures, clear-cell renal-cell carcinoma, Lymphocytes, TCGA

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
views
OpenAIRE UsageCountsViews provided by UsageCounts
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