The Virtual Biobank

Welcome to The Virtual Biobank

The Virtual Biobank is an online platform that houses 2D and 3D microscopy datasets of valuable clinical biopsy samples. The recent advance of 3D tissue clearing technology has allowed us to produce and display 3D image datasets alongside traditional 2D micrographs used by pathologists and researchers. Each dataset is furnished with detailed, de-identified clinicopathological and technical metadata to provide context for further research. Physical samples associated with each dataset can also be obtained from the source biobank, using provided contact details. Importantly, the datasets have been made available to both researchers and the general public to encourage greater utilisation of clinical data.

We have also developed a free toolkit for contributors, which includes Tissue Tracker for collecting accurate experimental metadata, and a Terastitcher Pipeline for stitching overlapping image z-stacks for 3D visualisation and analysis. The toolkit is currently accessible to UoN affiliates and research partners. For information on becoming a research partner, please email

The Virtual Biobank was developed by The 3D Tissue Clearing and Lightsheet Microscopy Facility, based at the Hunter Medical Research Institute, University of Newcastle (Australia).

Current Projects

  • Breast Cancer Subtype Study in collaboration with The Hunter Cancer Biobank
  • Conversion of 3D datasets into Virtual Reality compatible files


15/1/18 High resolution 2D slidescans uploaded for all samples in the Breast Cancer Repository

8/2/18 A further 60 Gb of 3D microscopy data added to the Breast Cancer Repository

22/5/17 - The first datasets of The Virtual Biobank are currently being uploaded to MyTardis

20/5/17 - New 3D images for our breast cancer study are being collected and processed with help from The Bosch Institute in collaboration with the 3D Tissue Clearing and Lightsheet Microscopy Facility.

20/9/17 - Contributor toolkit (Tissue Tracker and 3D Terastitcher Pipeline) now available to UoN staff, students and affiliates


Support The Virtual Biobank

The Virtual Biobank is not-for-profit, and has a singular goal to provide better access to research grade datasets for the scientific community and general public. If you would like to see this resource maintained and improved, please donate today.


All data is released to the general public under the Creative Commons 'Attribution-NonCommerical-ShareAlike' license. As such, users must appropriately attribute the authors from which data is derived, not use data for commercial purposes and must release derived data under the identical license. Users must acknowledge the rights of study Participants to their privacy and must not attempt to re-identify Participants under any circumstances. Please refer to the Access Policy for further information regarding the viewing, use and attribution for datasets within The Virtual Biobank.

Sponsors and Collaborators

University of Newcastle
Hunter Medical Research Institute
Australian National Data Service
Hunter Cancer Biobank
The Bosch Institute