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Sound Transit would pay the University of Washington $43 million to move some college labs to a new lab space, across campus and away from an underground light-rail tunnel, under a new deal being considered by both agencies this month.

The concern: That construction and operation of Sound Transit’s Northgate Link extension will cause electromagnetic interference in four UW buildings, where delicate instruments such as electron microscopes are used in research.

That concern first arose many years ago, when Sound Transit began mapping an underground route through the UW campus. In 2007, the UW and Sound Transit agreed the transit agency would pay the university to mitigate the possible effects of electromagnetic interference.

The amended agreement includes the price of mitigation and puts an upper limit

on the level of vibration and electromagnetic interference that’s acceptable. If the agreement is approved, the university plans to use the money to nearly double the size of its Molecular Engineering & Sciences building, which opened in October 2012 just south of Gerberding Hall.

The UW Board of Regents will vote on the agreement during a meeting Thursday, and Sound Transit’s board will vote on it in two weeks.

The $43 million in mitigation was about what transit-agency officials expected to pay, said Sound Transit spokesman Bruce Gray.

“Given the importance of what goes on in the campus, and in these labs, we don’t feel like it’s out of line,” he said.

The money would come from the $1.8 billion budget for the first section of the line, running from Capitol Hill to Husky Stadium.

Tunnel boring will launch soon at Northgate for the section between the stadium and Northgate, with two machines boring south to the stadium, arriving in early- to mid-2016, Gray said.

He said the segment that goes through the University District will be about 80 feet below ground, and will go still deeper — about 140 feet below ground — as it travels across campus.

At first, the university was concerned primarily with vibrations, but Sound Transit “has done a wonderful job of finding the latest technology” to reduce ground vibrations, said Richard Chapman, the UW’s associate vice president for capital projects.

That technology includes train tracks built on slabs of concrete that sit on big rubber doughnuts at the bottom of the tunnel, a kind of track known as a floating-slab track.

Electromagnetic interference, however, remained a concern.

Four buildings on campus, adjacent to the train line, house a variety of sensitive equipment, including electron microscopes, which are “really, really, really high resolution — so when the trains come by, they generate a magnetic field, and that distorts the imaging, and you get bad results,” Chapman said.

The buildings that could be affected are Wilcox Hall, Roberts Hall, Mechanical Engineering Building and the Engineering Annex, all on the southeast side of campus.

Research and related activities that take place in those buildings would be moved into a newly constructed addition to the Molecular Engineering building. The building was designed from the beginning to house sensitive instruments and has an unusually large foundation to block vibrations and electromagnetic interference, Chapman said.

The money would be used to build a 78,000-square-foot addition to Molecular Engineering, roughly doubling its size. The project is estimated to cost $53 million, with most of the rest of the money coming from university funding.

The UW isn’t the only research university that has had to deal with interference from light rail.

A similar issue arose at the University of Minnesota, where university officials feared that an aboveground light-rail line being built through the Minneapolis campus could interfere with delicate instrumentation.

The university had to move several labs, including one with a nuclear magnetic resonance imaging (MRI) machine, said Leslie Krueger, chief of staff for university services. The city’s transit agency also built a floating-slab track and made power-line adjustments to reduce electromagnetic interference, she said. The line is being tested and is set to open for service in June.

Seattle’s light-rail line will run directly underneath several buildings that won’t be affected by vibrations or electromagnetic interference, including Kane, Savery, Smith, Loew, Husky Union Building, the engineering library and the power plant.

The trains will follow a gently curving path underneath the university, running between the U District Station on Brooklyn Avenue Northeast — between Northeast 45th and Northeast 43rd streets — and the UW Station in front of Husky Stadium on Montlake Boulevard Northeast.

The first phase of the line, which will connect Capitol Hill to the UW Station at Husky Stadium, is expected to open for service in 2016.

Katherine Long: 206-464-2219 or On Twitter @katherinelong.