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Metadata record for the manuscript: Unmasking the immune microecology of ductal carcinoma in situ with deep learning

posted on 2020-11-02, 12:59 authored by Priya Lakshmi Narayanan, Shan E Ahmed Raza, Allison H. Hall, Jeffrey R. Marks, Lorraine King, Robert B. West, Lucia Hernandez, Naomi Guppy, Mitch Dowsett, Barry Gusterson, Carlo Maley, E. Shelley Hwang, Yinyin Yuan


This metadata record provides details of the data supporting the claims of the related manuscript: “Unmasking the immune microecology of ductal carcinoma in situ with deep learning”.

The data consist of immunohistochemistry (IHC) haematoxylin and eosin (H&E) staining images of grade 2-3 pure ductal carcinoma in situ (DCIS) and DCIS adjacent to invasive cancer (adjacent DCIS) samples.

The related study aimed to characterise tissue spatial architecture and the microenvironment of DCIS via design and validation of a new deep learning pipeline.

Data access

All training data, including the fully anonymised raw H&E image tiles and pathological annotations as binary marks, as well as Python code, are available in the corresponding author’s GitHub: https://github.com/pathdata/HE_Tissue_Segmentation. Requests for data access for the Duke samples can be submitted to E. Shelley Hwang (shelley.hwang@duke.edu) and Yinyin Yuan (yinyin.yuan@icr.ac.uk). Data underlying Figures 4 and 6 are in the files “Ext_validData_DCIS_DAVE_Fig4_data.csv” and “Ext_validData_DCIS_DAVE_Fig6_data.csv”, included with this metadata record. The images used as representative examples in Figure 8 are listed in the file “Figure 8 image details.xlsx”, included with this metadata record.

Name of Institutional Review Board or ethics committee that approved the study

The study was approved by the institutional review board of Duke with a waiver of the requirement to obtain informed consent.


Co-evolution of the tumour microenvironment and cancer resistance to endocrine therapy

Breast Cancer Now

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Cancer Research UK (CRUK) - C45982/A21808

Breast Cancer Now (BCN)

Children’s Cancer and Leukaemia Group (CCLGA201906),, NIH U54 CA217376, CRUK Brain Cancer Award (TARGET-GBM), European Commission ITN (H2020-MSCA-ITN-2019), Wellcome Trust (105104/Z/14/Z)

NIH R01 CA185138

R01 CA170595

CDMRP Breast Cancer Research Program Award BC132057

NIH grants U2C CA17035, R01 CA170595, R01 CA185138 , CDMRP Breast Cancer Research Program Award BC132057, CRUK Grand Challenge Award


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This record was produced by Springer Nature’s Research Data Support service. This service focuses on maximising the findability and accessibility of the data, and does not involve peer review of data.

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