Low-cost DNA sequencing has helped to create a boom in bioinformatics, whose main purpose is to speed up the medical diagnostics process. Now a new, cutting-edge technique being used by 3Scan enables automation of microscopy.

The team at US startup 3Scan see their mission as taking the science of biology to the next level, shifting it away from a basically qualitative approach, with biologists working manually on individual tissue samples, to one is that is able to draw on quantitative data and 3D modelling techniques. The 3Scan microscope enables researchers to capture thousands of images in a few hours. Powerful scanners are in widespread use in the field of radiology and 3Scan has set out to provide a high-performance tool for examining organic tissue at the microscopic level as well.

The 3Scan proposition is however about much more than just saving time. Being able to perform 3D modelling of an organ using a microscope can basically change the way a biologist works. Low-cost DNA sequencing has in recent years made it more feasible to customise diagnostics and treatment, and bioinformatics in general has become an essential driver in the paradigm shift which life sciences are undergoing. The potential to work on virtual models should enable the science of biology to free itself from constraints – such as the gestation period and the time needed for cells to degenerate – that slow down new discoveries.

Bringing an engineering approach to biology

The process of studying living tissue under a microscope has basically not changed much since the 19th century. However, in the meantime medical science has made great strides, from DNA sequencing to the understanding of the overall immunity system. 3Scan is now looking to automate microscope-based analysis and bring biology into the era of automation, doing away with cumbersome human interventions in the data collection process.

So the San Francisco-based startup has come up with a – literally – cutting-edge microscope plus special software to model organ tissue in 3D. The patented technology, known as Knife Edge Scanning Microscope (KESM), slices and scans an organ, building up a picture layer by layer. As the scanner is able to register an image of a one-micron thick slice, the reconstructed model is sufficiently realistic to makes it unnecessary to work on actual tissue samples. The 3Scan approach greatly reduces the time it takes to model and analyse an organ compared with previous techniques.

On the diagnostic front, 3Scan enables quantitative analysis and also the use of tissue coloration techniques to highlight the development of cancerous tissue or damage to neuron tissue. Being able to record and keep 3D models of organic tissue means that scientists are at last able to progressively track the advance of a degenerative disease.

Diagnostics: from organic tissue to carbon products

3Scan CEO Todd Huffman reckons that with this advanced technology, biologists will now be able to work more like engineers, automating a process which has hitherto been rendered very slow by the need for direct human intervention on individual samples. Increasing the number of slices which can be analysed within a short period of time looks set to change the nature of the biologist’s day-to-day work. Decisions and diagnostics traditionally based on purely qualitative interpretation will henceforth benefit from high-volume statistics, he points out.

Bioinformatics is part and parcel of the Big Data phenomenon. Scientific methodology is being shaken up by the way IT systems are able to draw on masses of collected data to enhance our understanding in all kinds of fields. For example, researchers working in areas from neurobiology to artificial intelligence now use fast modelling of the brain to gain insights into inter alia the nervous system and the learning process.
Huffmann is already looking beyond the medical field and expects soon to extend the use of the KESM techniques to the study of carbon-based materials.  It is not hard to envisage the 3Scan slicing-scanning approach being applied to materials and products quality control, potentially helping to spot any imperfections in a manufactured part at a much lower cost.




By Simon Guigue