Devices & Diagnostics, Health IT, Startups

Big data in pathology: 3Scan’s 3D tissue imaging platform offers reams of data on scale of gene sequencing

This one’s a big data play for the pathologist set: Bay Area startup 3Scan is […]

This one’s a big data play for the pathologist set: Bay Area startup 3Scan is developing an ultra high-res, 3-D tissue imaging platform that’s churning out data on the scale of whole-genome sequencing.

The startup just raised $6.7 million in a Series A round, led by Lux Capital. Before that, the four-year-old company raised about $350,000 from the Peter Thiel-backed Breakout Labs, and then $1.5 million in seed funding, CEO Todd Huffman said.

 

The company allows researchers – pathologists in particular – to get an extreme close-up of the 3-D structure of tissues and organ structures. 3Scan’s Knife Edge Scanning Microscope automatically sections and images tissue samples, spitting out ultra high-res data: It’s up to a terabyte per cubic centimeter.

“While medical science has made incredible advances in recent years, anatomic pathology has remained relatively stuck in the 19th century – a manual, analog, and highly qualitative discipline,” Huffman said.

 

Pathology is, after all, quite the hands-on activity: Once a tissue sample winds up in a lab, it’s sliced thinly by the scientist, preserved in formalin, then brushed onto slides. It takes days, and while it can show the microanatomy of a cell, very little is known about how that cell fits within the greater tissue structure.

3Scan, by contrast, is working on automating and digitizing the cross-sections of tissue in its original structure – without the human factor to slow things down or mess them up. The idea here is to look at these tissue slices in the context of an entire organ.

 

“We’re completely automating the process of slicing and imaging,” Huffman said. “By removing the human hand here, we speed up the tissue analysis 100-fold.”

Lots of diseases manifest at a tissue and organ scale, Huffman said, so a conventional microscope approach may not provide the same insights that a full-tissue analysis would. Having a 3D view of the microvasculature of a tumor, for instance, could actually help inform how drugs are working, Huffman said.

To examine larger swaths of tissue, the conventional methods of analysis are high resolution MRI and CT scans, but that just doesn’t have the same razor focus that light microscopy does, Huffman said. The KESM tech can process 3,600 slices per hour, imaging an entire mouse brain, for instance, he said.

The company was founded in 2011 – one of the first of Peter Thiel‘s Breakout Labs program. What sets it apart is that its diamond-edged knife serves a dual purpose: It’s also a light source. The knife shaves the tissue and illuminates it, so a camera that’s right behind it can take pictures of each slice.

3Scan’s device combines automated serial sectioning, machine vision and advanced optics to produce high throughput, quantified image analysis of tissue samples that are thinner than a micron – or smaller than a single red blood cell.

Other companies are operating in this space. Leica Biosystems, for instance, in 2013 used similar technology to digitize cross sections of Einstein’s brain in a similarly high-res manner.

But neither company is doing anything clinical – the appropriate regulatory clearances just aren’t there for these next-gen pathology technologies. And while the data’s there, the processing side has yet to catch up.

“There’s still a lot to do, especially on the computational side,” Huffman said.

The entire new field of bioinformatics had to be created, he said, to handle the data being created by gene sequencing. Similarly, there’s a lot of work to do, computationally, to understand what this 3D tissue data means.

“A human can’t look at a terabyte of imaging, much less make sense of it all,” Huffman said. “We have to develop new algorithms and techniques to visualize this.”

3Scan sold its first machine this past summer to Kettering University, Huffman said, and the company’s now building out a series of imaging services that it’ll do at the lab.

Most of 3Scan’s efforts are focused on helping scientists conduct basic disease research, drug discovery for these diseases, and developing high throughput screens for tissue structures. Updating tissue processing standards at your neighborhood path lab? That’s for another day.

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