Automating single cell studies in the brain

December 29, 2015

In order to understand the cells in the living brain, it is important to study them as individuals, one at a time. But doing this kind of individualized study at a large scale quickly becomes daunting, since examining each cell requires a researcher to position a pipette near a microscopic cell in a slice of brain – making time one of the most precious resources of all.

undefinedAllen Institute researchers are making strides toward automating the process of studying single cells, as they describe in research published this month in Scientific Reports. Their new method automatically positions pipettes near cells of interest so researchers can much more easily and quickly collect data from single cells.

“Targeting single cells in the living brain is challenging for a number of reasons, so even expert humans generate relatively low yield experiments,” says Hanchuan Peng, Ph.D., Associate Investigator at the Allen Institute. “Our method uses a combination of 3D visualization and automated pipette positioning to approach targeted cells automatically in a comparable time to a human researcher, freeing up time for researchers to conduct more experiments more accurately.”

The smartACT (smart, Adaptive Cell Targeting) method improves two phases of the experiment. First, the software can choose a target cell and identify its location in three dimensions, using Virtual Finger technology that lets researchers quickly and intuitively identify cells in 3D on a two-dimensional screen. Next, to move the pipette as close as possible to the cell of interest, the smartACT program calculates a path for the pipette to follow that will bring it near the cell while compensating for the displacement of the pipette and the target. 

The end result is a highly accurate pipette positioning that does not sacrifice experimental efficiency: the sweet spot for collecting large amounts of high quality data on many cells.

“Automated systems are essential for large-scale experiments since they help us collect the most accurate and consistent data possible,” says Peng. “smartACT helps researchers focus their attention and ultimately do more work, better.”