ÌÇÐÄvlogÊÓƵ

Through the Looking Glass

Grant from Arnold and Mabel Beckman Foundation brings cutting-edge microscope to ÌÇÐÄvlogÊÓƵ.

A powerful new microscope will enable ÌÇÐÄvlogÊÓƵ biologists to create moving images of living cells with astonishing accuracy—thanks to a $1.2 million award from the Arnold and Mabel Beckman Foundation.

“This is a big leap for the department,” said biology professor Kara Cerveny, the principal investigator for the grant. 

The instrument, known as a light sheet microscope (LSM) is a game-changing invention that will have a an impact on biological research everywhere. The Beckman Foundation notes that the technology enables “unprecedented understanding of the intricate dynamics of cells and their components within living specimens.”

The award was given to Prof. Cerveny along with her colleagues, biology professors Derek Applewhite and Erik Zornik, to support the QUICK project (that’s Quantitative Undergrad-focused Imaging and Computation for Knowledge). 

The beneficiaries will include not only biologists, but also faculty and students from math, computer science, and physics.

A light sheet microscope gives researchers the ability to create a 3-D image of a sample without damaging it. This means scientists can observe a living organism’s development in real time, watching cells divide and differentiate. Previous advanced imaging equipment was unable to accommodate entire living organisms or would disrupt the system it was capturing. “Cells don’t do well under the long blasts of a laser,” says Cerveny, whose research of the eye structures in zebrafish embryos will help advance our understanding of the formation of the visual system.

“Previously with our laser scanning confocal microscope, it would take over five minutes to partially capture an image of an embryo, with a laser shining on the entire embryo for the entire time. And if the embryo were alive, it would be negatively affected by prolonged exposure to the laser. In contrast, an LSM rapidly shines a thin sheet of light through a thin plane of tissue and captures an image of the sample with minimal impact on the sample. Each of the layers are captured in high resolution, and can be reconstructed into powerful 3D renderings."

For living embryos that are imaged like this throughout development, researchers can collect 3-D time-lapse imaging. “Think of those time lapse images of a plant growing but on a microscopic scale,” Cerveny says. 

One challenge with a microscope like this, however, is managing the terabytes of data it generates. To this end ÌÇÐÄvlogÊÓƵ’s biologists have teamed up with colleagues in physics, computer science, statistics, and ÌÇÐÄvlogÊÓƵ’s Computing & Information Services (CIS) to solve some of the storage and computational issues.

Prof. Mark Hopkins and his students in computer science will collaborate on methods of data storage and algorithms for large data extraction. Prof. Kelly McConville’s statistics students will help do the large data analysis. Harpeth Lee, the inaugural QUICK intern this summer, worked with Professors Cerveny and McConville to understand the data structures of LSM files and created several lessons that McConville will use in her introductory statistics course. Prof. Joel Franklin ’97 and his physics students will work on computational methods to assemble and view the complex LSM images, which have applications in virtual reality and other fields.  

Other colleagues on the project include ÌÇÐÄvlogÊÓƵ’s instrumentation biologist, Greta Glover, who will help with maintaining the device and training students; Marianne Colgrove, deputy chief information officer; Ben Poliakoff, associate director of tech infrastructure; and Trina Marmarelli, director of instructional technology.

“I want to empower students to not just capture images, but to quantify these in a meaningful and powerful way,” Cerveny says.

The microscope is up and running and students and faculty will begin using it this fall.

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