Whole slide pathology images from excision specimens of cutaneous basal cell carcinomas (BCC) collected at the Department of Pathology at Sahlgrenska University Hospital, Sweden. The dataset contains 1832 WSIs from 479 excised BCCs and 261 punch biopsies representing BCCs annotated on a slide level. Furthermore the dataset contains 253 tumor-free skin biopsies.

Keywords: Pathology, Whole slide imaging, Weakly annotated, Basal cell carcinoma, Skin cancer.

Sample images

Sample images with reduced image quality. Please click to preview.

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Dataset information

Short name	BCCC
Origin	Clinical
Cite as	Noora Neittaanmäki, Kajsa Villiamsson, Jan Siarov, Filmon Yacob, Juulia T Suvilehto, Lisa Sjöblom, and Magnus Kjellberg (2023) Basal cell carcinoma classification doi:10.23698/aida/bccc [BibTeX format] @misc{ neittaanmäki_2023_bccc, author = { Noora Neittaanmäki and Kajsa Villiamsson and Jan Siarov and Filmon Yacob and Juulia T Suvilehto and Lisa Sjöblom and Magnus Kjellberg }, title = { Basal cell carcinoma classification }, year = 2023, publisher = { AIDA }, doi = { 10.23698/aida/bccc }, howpublished = { Available: AIDA Data Hub }, url = { https://datahub.aida.scilifelab.se/10.23698/aida/bccc } }
Field	Pathology
Organ	Skin
Age span	-
Title	Basal cell carcinoma classification
Author	Noora Neittaanmäki Kajsa Villiamsson Jan Siarov Filmon Yacob Juulia T Suvilehto Lisa Sjöblom Magnus Kjellberg
Year	2023
DOI	doi:10.23698/aida/bccc
Status	Completed
Version	1.0.1
Scans	1832
Annotations	0
Size	7.78TB
Resolution	x40
Modality	SM
Scanner	NanoZoomer S360 Hamamatsu
Stain	H&E (hematoxylin and eosin)
Phase
References	Yacob, F., Siarov, J., Villiamsson, K. et al. Weakly supervised detection and classification of basal cell carcinoma using graph-transformer on whole slide images. Sci Rep 13, 7555 (2023). https://doi.org/10.1038/s41598-023-33863-z
Copyright	Copyright 2023 University of Gothenburg, Noora Neittaanmäki
Access	Available under the following licenses, described in the License section below. Controlled access Free for use in legal and ethical medical diagnostics research. AIDA BY license Free for use within AIDA with attribution and co-authorship.

Annotation

The data is annotated on a slide level into four aggressivity tumour subtypes: low aggressive Ia (nodular) and Ib (superficial) and more aggressive subtypes II (medium aggressive) and III (high aggressive). Of these, types Ia and Ib represent low risk and II and III high risk tumors according to WHO classilification of skin tumors (4th Edition 2018).

File formats

The dataset consists of two types of images: Histopathological slides are stored as .ndpi (size per slide 1-5.5GB). Annotations are provided as .csv files (one for main data set, one for test set)

License

Controlled access

Free for use in legal and ethical medical diagnostics research. Please contact the dataset provider for terms of access.

You are invited to send an access request email from your institutional account.

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To: noora.neittaanmaki@vgregion.se
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Subject: Requesting access to dataset doi:10.23698/aida/bccc
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Dataset: https://datahub.aida.scilifelab.se/10.23698/aida/bccc

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AIDA BY license

Copyright 2023 University of Gothenburg, Noora Neittaanmäki

Permission to use, copy, modify, and/or distribute this data within Analytic Imaging Diagnostics Arena (AIDA) for the purpose of medical diagnostics research with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies, and that publications resulting from the use of this data cite the following works:

Noora Neittaanmäki, Kajsa Villiamsson, Jan Siarov, Filmon Yacob, Juulia T Suvilehto, Lisa Sjöblom, and Magnus Kjellberg (2023) Basal cell carcinoma classification doi:10.23698/aida/bccc

Yacob, F., Siarov, J., Villiamsson, K. et al. Weakly supervised detection and classification of basal cell carcinoma using graph-transformer on whole slide images. Sci Rep 13, 7555 (2023). https://doi.org/10.1038/s41598-023-33863-z

THE DATA IS PROVIDED “AS IS” AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS DATA INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR CHARACTERISTICS OF THIS DATA.