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A new, custom-built microscope is capturing stunning views of the brain

‘ExA-SPIM’ microscope borrows from electronics industry to image incredible detail in an entire mouse brain


1 min read

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Using technology originally designed for defect detection in electronics manufacturing, the newly built “ExA-SPIM” microscope is showing scientists the mouse brain as it’s never been seen before. 

ExA-SPIM, developed by a team at the Allen Institute for Neural Dynamics, a division of the Allen Institute, is a one-of-a-kind microscope built for capturing images of the entire mouse brain at incredible resolution. The images coming off the scope allow the scientists to view individual neurons and their wiring in the context of the entire mouse brain, a jellybean-sized organ that houses nearly 80 million individual neurons. The researchers use special fluorescent tags to make certain neurons glow under the microscope — and the resulting images from the new technology are stunning in their clarity and definition.  

The new machine is a kind of light-sheet microscope, an emerging technology that uses 2D planes of light to illuminate tissues or cells with high definition; the 2D images are then stitched together to create a 3D view of entire mouse brains, in the case of ExA-SPIM. This new microscope also adds technology from the electronics manufacturing industry: “defect detection” cameras originally created to automatically detect minute imperfections in LED chips on conveyer belts in electronics factories. This camera technology enables both high resolution and speed in imaging. 

Watch scientist Adam Glaser, Ph.D., and his colleagues put together the world’s first  ExA-SPIM microscope in this time-lapse video. The researchers also recently published a pre-print publication how-to for building the equipment.

About Allen Institute for Neural Dynamics

Launched in 2021, the Allen Institute for Neural Dynamics is a division of the Allen Institute, an independent, 501(c)(3) nonprofit medical research organization founded by Paul G. Allen in 2003. The Allen Institute for Neural Dynamics is dedicated to answering fundamental questions about brain dynamics at the level of individual neurons, and the whole brain, to reveal how we interpret our environments to make decisions. Knowledge, data, and tools created by the Institute will be publicly shared to advance the field’s understanding of brain function and support the development of therapies for brain diseases and disorders.

Science Programs at Allen Institute