3Scan announces milestones, plans to expand team in 2016

Renee Shenton
Breakout Ventures
Published in
4 min readJan 12, 2016


Breakout Lab_2014-47

This week, we’re proud to pass along some excellent news on the progress of 3Scan, one of Breakout Labs’ first portfolio companies.

Recently named as one of VentureBeat’s “15 interesting startups to watch in 2016,” 3Scan is developing automated 3-D digital reconstruction of complex tissues as a new tool for pathology and biological discovery. Combining machine vision, automated serial sectioning, micromachining, and advanced optics, their patented “Knife Edge Scanning Microscope” (KESM) captures and aligns images of tissue sections as they are sliced.

“It would take thousands of lab technicians to match our upcoming capability, and we’re excited and proud to be improving the investigation of biology.” — Todd Huffman

Since receiving their BOL grant in 2012, 3Scan has raised $7.5 million in Series A financing and made fantastic progress toward their goal of creating a data science that will translate discoveries into new diagnostic and therapeutic solutions.

In 2015, Todd and his team achieved some major milestones:

  • Expanded team from 10 to 21 members
  • Completed two six-figure contracts
  • Collected exciting new data.
  • Developed new microscopy techniques
  • Built two new versions of the microscope: full-color and fluorescence
  • Designed a new version of our microscope (12 new production-grade machines in production)

We recently asked COO and co-founder, Megan Klimen, to tell us about some of 3Scan’s recent achievements and long-term goals.

Megan Klimen

BOL: What are some of the recent research projects that have been using your technology to analyze 3D structures?

MEGAN KLIMEN: We have been very busy, which is exciting. We are using our unique ability to look at the 3D structure of tissue-scale biology to:

  • Quantify a variety of morphological endpoints for pharmaceutical preclinical work aimed at developing more effective treatments for pancreatic cancer
  • Aid in the understanding how neurons develop and differentiate in the brain to advance tissue engineering through true 3D quantitative comparisons of engineered vs. traditional tissue
  • Create teaching tools for medical students to learn about tissue anatomy through an entirely digital dissection table.

Those examples are just from what we are imaging this week. One of the most interesting things about our technology is that we are creating a platform for visualizing and understanding tissue-scale biology in 3D and this creates a virtually endless numbers of use cases. Every new scientist that I work with has a multitude of ideas for how to use our technology to help advance their research. It’s amazing to watch the uses grow to beyond things I could ever imagined myself.

BOL: 3Scan has been a passionate advocate for medical science becoming more automated, digitized and quantitative. Can you give a few examples of how your technology is helping medical research and biotechnology industry customers get close to that ideal?

MK: In the last 30 years, we’ve seen huge advances in molecular biology and genomics, largely because these types of analyses are easily understood by computers. As computing gets cheaper and more powerful, these fields have advanced alongside the rise in computing power.

Tissue-scale biology on the other hand, has remained largely unchanged in the last 150 years. This also has meant that the examination of tissue has continued to be an incredibly manual, slow, and error-filled process. The only way to move out of this archaic past is by automation and digitization so that we can use the power of modern computing to understand tissue-scale diseases.

3Scan is using the gains in speed and accuracy in the field of computer science to do things that have never been done before (or even been conceivable before) in medical research. We are mapping the full vasculature, down to the smallest capillaries of brains, so that we can completely understand what happens to blood flow during a stroke.

We are proving that automating histology leads to more accurate diagnoses and more effective treatments for cancer. In a single day, 3Scan’s automated sectioning microscope takes the same number of sections that a human histologist takes in a year. Every day, 3Scan is finding a new way to use that huge jump in throughput to provide insight in to a new area of medical research.

BOL: What are 3scan’s long-term goals?

MK: 3Scan wants to fundamentally change and improve the way we are able to see and understand tissue-scale biology. Until now, if you wanted to look at the detailed structures in tissue, you were stuck looking at a slide, a small two-dimensional picture, and trying to make guesses about how the 2D slice fit into the 3D structure.

Much like how a CT takes a stack of 2D pictures to allow a radiologist to view the 3D structure of the patient, 3Scan can take tens of thousands of 2D slides and allow us to look at the 3D structure of the underlying tissue. This means that anyone looking at tissue — whether it’s a researcher studying basic science, or a scientist developing a new drug, or a doctor diagnosing a patient — will be able to do their job better.

3Scan is creating a tool that will eliminate the manual and subjective practices of the past and is shepherding the field of pathology into the future.


This year, 3Scan will to continue to build their team and develop sales, distribution, and marketing workflows.

“We’re actively looking for introductions to movers and shakers in the preclinical drug discovery space,” says Huffman. “We always appreciate referrals to quality humans.”

If you know of some brilliant talent who would be interested in joining the 3Scan team, please send your suggestions to 3scan.com/opportunities.