New brain imaging facility offers high-end preclinical MRI services to research community


By Nicholas Weiler

On September 1, the Wu Tsai Neurosciences Institute officially launches the Neuroscience Preclinical Imaging Laboratory, a new shared facility for top-of-the-line magnetic resonance imaging (MRI) of model organisms, housed in the Stanford Neurosciences Building.

“We want to make brain imaging accessible throughout the neuroscience community, even to people who have never done MRI research before,” said Jin Hyung Lee, PhD, an associate professor of neurology, bioengineering, and neurosurgery, and chair of the facility’s faculty advisory committee.

The facility features a brand-new 7 Tesla Bruker MRI scanner specially designed with an extra-large 40 cm central bore, the first of its kind in the United States. The extra space will enable researchers to study a wider range of model organisms than in a standard preclinical MRI and to incorporate specialized research equipment within the scanner itself.

Lee offered an example from her own group, which has pioneered a platform for controlling the activity of specific classes of neurons while simultaneously imaging their contributions to brain-wide circuit function. The spacious new shared scanner will make it easier to set up these experiments — termed optogenetic functional MRI (ofMRI) — in awake, behaving animals, which will in turn enable easier deployment of the technology. 

Other researchers, Lee suggested, may be eager to take advantage of the custom-designed scanner to incorporate bulky electrophysiological equipment or to non-invasively study brain anatomy and connectivity in larger model organisms.

“I believe having this powerful, versatile technology on campus has the potential to transform a lot of people's research and accelerate neuroscience discovery,” Lee said.

Images of a rodent brain captured during an August test session with the new MRI system located in the Neuroscience Preclinical Imaging Lab. Credit: Jieun Kim.

As part of the institute’s Neuroscience Community Labs program, access to the new scanner, expert training on its use and consultation on experimental design will be available to all members of the Stanford community. The facility aims to be usable and affordable by researchers of all experience levels, in part through a tiered service system where users pay only for the level of support they require, from end-to-end project support to independent operation.

Take a Tour
Neuroscience Preclinical Imaging Laboratory director Jieun Kim, PhD, will be leading tours of the new facility the week of Aug 30 – Sept 3, 2021, to mark the facility's official launch as a Stanford Service Center.
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This support will come primarily from the lab’s new director, Jieun Kim, PhD, who joined the institute in January, 2021, with more than a decade of experience in the MRI field — from developing MR data analysis software during her PhD at University College London to long-time management of a preclinical imaging facility at St. Jude Children’s Hospital in Memphis.  


Years of advance planning conclude with epic journey

Expanding the availability of high-end preclinical MRI on campus has been a mission for Lee since she joined the Stanford faculty in 2012 and recognized the intense demand for access to the existing preclinical MRI system housed in the Clark Center and operated by the Molecular Imaging Program at Stanford (MIPS) and the Department of Radiology.

Jieun Kim, PhD, who joined the institute in January, 2021, with more than a decade of experience in the MRI field — from developing MR data analysis software during her PhD at University College London to long-time management of a preclinical imaging facility at St. Jude Children’s Hospital in Memphis.  

“The scanner was booked for weeks, and people were imaging through the night, on weekends, every week,” said Tim Doyle, DPhil, Wu Tsai Neuro’s associate director in charge of the Neuroscience Community Laboratories, who previously oversaw the Clark Center preclinical imaging facility.

After spearheading a partnership between Wu Tsai Neuro, Stanford BioX, and multiple Stanford Medicine departments to upgrade the Clark Center scanner — work which was completed in 2015 — Lee, Doyle, and colleagues moved on to planning for the acquisition of a second scanner, to reside in the planned Stanford Neurosciences Building.

"Günther", a custom-designed magnetic resonance imaging (MRI) scanner for preclinical brain imaging research, arrives at the Stanford Neurosciences Building in April, 2021.

Beyond simply reducing demand, the team developed a plan for a welcoming, efficient facility where researchers of all backgrounds could do MRI research without breaking the bank — just like a researcher might book time at the Neuroscience Microscopy Facility, one of the institute’s other community laboratories, and quickly start gathering data with expert support from the facility.

Finally, in 2018, with funding from the National Institutes of Health S10 Instrumentation Grant awarded to Lee and generous support from the Wu Tsai Neurosciences Institute and additional support from the departments of Neurology, Neurosurgery, Psychiatry, and Radiology and Wu Tsai Neuro’s NeuroChoice Initiative — the $4.25 million magnet was ordered from German manufacturer Bruker. 

Since January 2021, Lee, Kim, and Doyle met every 2 weeks to plan for the magnet’s eventual delivery and the setup of the new imaging facility. “We put extra effort into making sure the facility can be most efficiently utilized to support research and to provide a flexible, lean, transparent, and respectful research environment,” Lee said.

All was in preparation to deliver the magnet to Stanford in early 2020, but then COVID-19 shut down the process — and the newly opened Neurosciences Building — leaving the magnet stranded in a warehouse in the German city of Ettlingen.

When the green light finally came in April for delivery of the magnet from the County of Santa Clara’s public health department, the team leapt into action. Bruker engineers filled the 10-ton magnet with liquid hydrogen and helium to bring its electromagnetic coils to a superconducting temperature of 4 degrees Kelvin, then loaded it onto an oversized freight airplane for a trip half-way around the world.

Finally, one sunny day in mid-April, delivery day came. Campus Drive to the east of the Stanford Neurosciences Building was closed down as movers and riggers unloaded the room-sized magnet, then lowered it via a 100 foot-tall crane through a 30-foot-deep concrete hatch — designed six years earlier during initial planning for the Neurosciences Building.

“It was great to see the magnet get unboxed right on Campus Drive,” said Doyle. “I kind of felt sorry for it as it had its last bit of daylight as it dropped through the hole.”

The rigging team maneuvered the magnet slowly through the tunnels below Campus Drive then raised it a final 6 feet to the basement level of the Neurosciences Building and into its new home in the custom-designed Neuroscience Preclinical Imaging Laboratory.

“Our baby is finally here!” Kim remembers thinking at the time. “Granted I’d only been waiting four months, not 10 years, but I couldn’t wait to get started.”

But the magnet — which Kim has nicknamed “Günther” after Bruker founder Günther Laukien — was still not yet ready for its public unveiling. Since April, Kim and Bruker engineers have been methodically testing its powerful electromagnetic coil. They brought the magnet up to full power for the first time in June, and in August, “Günther” acquired its first brain images.

“I’m very excited for the whole neuroscience community,” said Lee. “It’s taken a long time to get here, but really we’re just at the beginning of the journey.”

The Neuroscience Preclinical Imaging Lab is supported by the Wu Tsai Neurosciences Institute and by NIH grant S10OD025176 to Jin Hyung Lee. Additional funds for the facility were raised by the Vice Provost and Dean of Research, the Dean of the School of Medicine and the generous support of the departments of Neurology, Neurosurgery, Psychiatry and Radiology.