UCSB Researchers Develop New Means of Tissue Cartography


Rishika Kenkre

Two postdoctoral students from the University of California, Santa Barbara Kavli Institute for Theoretical Physics (KITP), Sebastian Streichan and Idse Heemskerk, have developed a method for looking at tissues through processing data in a more efficient way than before.

Both researchers have produced a method that enables data reduction and examines the layered tissue. This new development can be used to identify and analyze curved tissues, such as the tissues of an animal, in order to identify many biological problems.

“For example, if you want to understand how an animal takes its shape, you need to be able to observe how they move,” said Streichan. “Then, you need to think about what frame these cells are moving; oftentimes, it turns out that the frame of the lab that we use in order to observe, like a microscope, is not the correct frame that the cells move. The cells actually move inside the tissue, and this software that we have created will allow the user to follow cells in that frame. You can also peel out a layer that you are interested in.”

They have created a general method that can be used for a wide variety of shapes. According to Streichan, it is much more complicated to use complex shapes, such as the shape of a beating heart, but the researchers behind the project have simplified the concept.

“We have generalized this concept of making something like a fish embryo look like large tissue surfaces,” said Streichan. “It’s almost every type of surface you can ascribe with a triangulation; that is a very big class surfaces that can be captured with our framework.”

Streichan has hopes that scientists will use this regularly. He acknowledges that it will help them handle the copious amounts of data at one observation.

“We hope that it’s going to become a way of how people work with daytime biology. The amount of data that is generated, especially the image-driven data that is currently generating biology, is increasing,” said Streichan. “Microscopes have become better,s and the surface tissue markers have become better. In that sense, people can generate much larger amounts of data, but they can’t quite handle that data because the surface itself is buried in something in three-dimensions … Think about a cube that contained so many layers inside, you’d have to rotate it to all sorts of angles, front and back. Our method is going to help to allow people, in one glance, to study most of their tissue, which is much faster and more efficient. By moving into the frame of the tissue itself, they’ll actually be able to describe the processes that are going on in their interest that they would like to characterize.”

Streichan plans to use the research to understand how a fruit fly embryo gets its shape. He uses the method to track the cells on the surface of the embryo, deducing how the cells move from one position to another, and how the genetic material deposited by the mother and father into the embryos is used to instruct cell movement.

The Bottom Line will continue to report on Streichan and Heemskerk’s findings.