Virtual cancers aid researchers


A not profit online biobank brings cell-level detail to cancer study. Geetanjali Rangnekar reports.


A 3D images showing a breast cancer biopsy, available on the Virtual Biobank site.
A 3D images showing a breast cancer biopsy, available on the Virtual Biobank site.
University of Newcastle

In a world first, three scientists from the University of Newcastle and the Hunter Medical Research Institute, in New South Wales, Australia, have created an online repository containing 3D images of human cancer tissues in unprecedented detail.

Data on the platform, called the Virtual Biobank, allows rapid access to images that map each tumour down to cellular level, and provides case-specific clinical details while preserving patient anonymity.

This opens doors to new possibilities for researchers, educators, and anyone interested in or affected by cancer. The project is non-profit, and relies on donations to stay in operation.

Jamie Flynn, Antony Martin and William Palmer, in collaboration with the Hunter Cancer Biobank, have so far created high-resolution digitised 2D and 3D images of 20 breast cancer samples obtained from patients.

Currently, tumour samples can be obtained from physical biobanks to conduct investigations. But the process is riddled with obstacles, including lengthy ethics applications, long wait times and high costs. Once a sample is obtained, it can only be used for a single experiment. This is acknowledged as less than satisfactory, especially in the case of rare tumours, where samples are hard to source.

Virtual Biobank overcomes these hurdles and comes loaded with some nifty features, thanks to specialised software tools that have been embedded in its program. Working with developer Bill Pascoe and the Academic Research Computing Support team at the university, the scientists came up with Tissue Tracker. This feature allows other scientists to log their own samples, keeping accurate records of all new tissues entering the system. It also circumvents the need for deciphering hand-written clinical or research notes.

There is also the Terastitcher Pipeline feature, which lets external researchers create full 3D images from tissue specimens collected during their studies.

The feature relies on a custom-made laser microscope designed and built by Flynn, Martin and Palmer (using, believe it or not, spare parts and advice from the internet), which provides a cost-effective way of stitching together various incongruent images to produce ‘see through’, seamless 3D ones.

The trio now aim to increase the number of cancer tissue images on the platform, and are looking at adapting the data to virtual reality applications.

  1. https://virtualbiobank.newcastle.edu.au
  2. https://hmri.org.au/news-article/hand-built-laser-microscope-give-greater-clarity
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