This dataset consists of 361 whole slide images (WSI) - 296 malignant from women with invasive breast cancer (HER2 neg) and 65 benign. The tumours have been classified with four SNOMED-CT categories based on morphology: invasive duct carcinoma, invasive lobular carcinoma, in situ carcinoma, and others. 4144 separate annotations have been made to segment different tissue structures connected to ontologies.

Keywords: Pathology, Breast, Cancer, Whole slide imaging, Annotated.

Sample images

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

• 
• 
• 
• 

Dataset information

Short name	DRBR
Origin	Clinical
Cite as	Anna Bodén, Jerónimo F. Rose, Martin Lindvall, and Caroline Bivik Stadler (2019) Breast data from the Visual Sweden project DROID doi:10.23698/aida/drbr
Field	Pathology
Organ	Breast
Age span
Title	Breast data from the Visual Sweden project DROID
Author	Anna Bodén Jerónimo F. Rose Martin Lindvall Caroline Bivik Stadler
Year	2019
DOI	doi:10.23698/aida/drbr
Status	Completed
Version	1.1.0
Scans	361
Annotations	4144
Size	500.8GB
Resolution	40X single plane, scanned in NDP format
Modality	SM
Scanner	Hamamatsu NanoZoomer-XR C12000 series 2013 Hamamatsu NanoZoomer 2.0 HT C9600 series 2013
Stain	H&E (hematoxylin and eosin)
Phase
References	Stadler, C.B., Lindvall, M., Lundström, C. et al. Proactive Construction of an Annotated Imaging Database for Artificial Intelligence Training. J Digit Imaging (2020). https://doi.org/10.1007/s10278-020-00384-4
Copyright	Copyright 2019 Linköping University, Claes Lundström
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.

Annotation

The breast tumours were classified with four SNOMED-CT categories based on morphology: invasive duct carcinoma, Invasive lobular carcinoma, in situ carcinoma and others. 4144 separate annotations were made to segment different tissue structures connected to ontologies. One physician were responsible for the manual annotations controlled by a second pathologist.

File formats

Pixel position scaling

Coordinates given are relative to the image width. To get the correct pixel position, X coordinates (and Y coordinates!) should therefore be multiplied with the image width.

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.

Clicking the access request email link above should open a draft email message in a new window, to help you provide relevant information for efficient request evaluation. If the above link does not work for you, then please click to view the suggested email text.

To: claes.lundstrom@liu.se
cc: Anna.C.Boden@regionostergotland.se,aida-data@nbis.se
Subject: Requesting access to dataset doi:10.23698/aida/drbr
Hi!

I work at INSTITUTION in COUNTRY, emailing from my institutional account.

I would like to access the dataset doi:10.23698/aida/drbr, for use in ethical and legal medical diagnostics research. Could you please send me a data sharing agreement template?

Our planned use of the data can be summarized as:

BRIEF_DESCRIPTION_OF_PLANNED_ACTIVITIES

Dataset: https://datahub.aida.scilifelab.se/10.23698/aida/drbr

Example agreement template: https://datahub.aida.scilifelab.se/sharing/templates/

Template placeholders:

Name of research PI ("Recipient Scientist"): PI_NAME (cc here)
Title of research PI: PI_TITLE (ph d or better, in relevant field)

Name of institution: INSTITUTION_NAME
Name of department: DEPARTMENT_NAME
Institution postal address: POSTAL_ADDRESS

Name of authorized signatory: SIGNATORY_NAME (cc here)
Title of authorized signatory: SIGNATORY_TITLE

Also, I would like to ALTERNATIVELY_WOULD_NOT_LIKE_TO be included in the public record of data sharing facilitated by AIDA:

https://docs.google.com/spreadsheets/d/1fl2BwZJ4rivOKzOCy5pAnxU8N1CyoF86BTCnH-rBV04

which is used to facilitate scientific discussion, and to show what good AIDA has been to the global research community.

(If "not", then only institution/department information will be included.)

/MY_NAME

Click to create draft email (new window). Use your institutional account.

AIDA BY license

Copyright 2019 Linköping University, Claes Lundström

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:

Anna Bodén, Jerónimo F. Rose, Martin Lindvall, and Caroline Bivik Stadler (2019) Breast data from the Visual Sweden project DROID doi:10.23698/aida/drbr.

Stadler, C.B., Lindvall, M., Lundström, C. et al. Proactive Construction of an Annotated Imaging Database for Artificial Intelligence Training. J Digit Imaging (2020). https://doi.org/10.1007/s10278-020-00384-4

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.