Transportation agencies outlined potential routes and made the case for a controversial high-speed rail from the Twin Cities to Rochester in a plan released Tuesday.

It will provide the framework for future studies of the Zip Rail that would connect the fast-growing biomedical hub to the Twin Cities. The plan also listed hundreds of concerns from residents and communities — from impacts of vibrations to a lack of stations along the way.

The completion of this so-called “scoping decision document” allows the Minnesota Department of Transportation and its partners on the project, the Federal Railroad Administration and Olmsted County, to move on to the next phase of research. By this summer or fall, they will pick the preferred route for the rail, said Praveena Pidaparthi, a planning director with MnDOT’s Passenger Rail Office.

It will be years before passengers will be able to board the train.

“If all the pieces of the puzzle fall into place, 10 to 15 years would be a very optimistic” estimate of when riders could start using the line, Pidaparthi said.

The first phase of studies costs $2.3 million and has been paid for by the state and Olmsted County Regional Rail Authority. No other funding has been secured for the project, Pidaparthi said.

The Zip Rail would connect Rochester, home of the Mayo Clinic, to either the Minneapolis-St. Paul International Airport or St. Paul Union Depot. It would make a 100-mile trip in 45 to 50 minutes and travel at speeds up to 186 miles per hour, according to the plan.

“The purpose of the project is to provide a reliable and safe passenger rail transportation alternative that is convenient and cost effective and will serve the forecast population and economic growth demands in the corridor,” the document reads.

The agencies received 541 comments on their draft of the scoping decision document. But they made only one major change in the final version, Pidaparthi said. That alteration moves a section of the rail between Coates and Pine Island closer to Hwy. 52.

The final report included many other community concerns, like Dakota County’s, where officials are worried about noise and effects on protected farmlands. They also stressed the need for a station in the county.

Further Zip Rail study will look into a potential stop at County Road 42 and Hwy. 52 near UMore Park in Rosemount.

The city of Hampton’s letter acknowledged that adding stations would lengthen the journey. Nonetheless, city officials requested a stop, possibly in Rosemount or Inver Grove Heights, that “would open up Hampton residents to some of the benefits of rail access instead of being completely passed over.”

The mayors of Zumbrota and Pine Island said the Zip Rail appears to cut off local roads and highways. Pine Island Mayor Rod Steele said the city would be more receptive to the project if it included a stop in Pine Island.

Many places want a stop, but placement will be based on analysis and ridership data, Pidaparthi said.

There will be more opportunities for people to share their opinions after the Tier 1 environmental impact statement is completed this summer or fall, she said. In the next two or three weeks, MnDOT will also announce the creation of a citizen advisory committee for the project, she said, and will begin take applications.