Virtual 3D Human Cancer Tissues to Accelerate, Enhance Research
Three researchers from the University of Newcastle and the Hunter Medical Research Institute (HMRI) have now designed the world’s first online platform that houses 2D and 3D microscopy datasets of valuable clinical human cancer biopsy samples, revolutionising the way researchers access critical information needed to advance cancer treatment.
Jamie Flynn, Antony Martin and William Palmer, in collaboration with the Hunter Cancer Biobank, created a virtual database that displays 3D image datasets alongside traditional 2D micrographs used by pathologists and researchers. According to website information, each dataset is furnished with detailed, de-identified clinicopathological and technical metadata in order 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.
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.“It currently takes many months before researchers are able to obtain tissue samples from a physical biobank and carry out investigations with it. Once a researcher has performed their study, that sample typically cannot be reused. Each digital cancer sample in The Virtual Biobank is made up of high resolution microscopy images in both 2D and 3D, plus important clinical and molecular information that provides the foundation for virtual research into cancer.
“We’ve taken a tiny sample from tumor biopsies stored at the Hunter Cancer Biobank and converted them into a virtual copy, enabling anyone around the world with an internet connection to carry out research from their computers or easily request access to the physical sample they need.
“This process ensures the physical sample remains intact, but a 3D, digital copy with clinical and experimental information is kept online for future use. This is particularly critical for rare cancers, which are hard to study due to a limited number of samples,” Dr Flynn explained.
In the course of their work, the researchers used a hand-built laser microscope, engineered to create these advanced 3D images. Instead of analyzing a thin slice of the sample, the CLARITY light-sheet produces clear, detailed 3D images of the whole tissue at a cellular level in a process that only takes a few minutes.
The Biobank, further, includes a “Tissue Tracker” that automatically collects metadata so that all new tissue samples can be cataloged and experiments easily replicated.
While still in its early stages, the online platform holds promising future potential in areas of research, education and even virtual reality.
“The technology and tools that we’ve put together make this data available to anyone in the world. People in the fields of engineering or computer science can now easily apply their knowledge to questions surrounding cancer. Educators can also access the site and use real-world examples to teach pathology to the next generation of cancer clinicians and researchers.
“We’d also like to convert the 3D data into virtual reality for education and general awareness. Hopefully soon, anyone with a smartphone and Google Cardboard could experience the internal environment of cancer tissue and bring about new insights,” Dr Palmer said.
