NEW YORK -- A software company that helped identify the remains of 9/11 victims is accusing the New York City Medical Examiner's Office of handing its secrets over to the FBI.

A Manhattan federal judge has been asked to decide if the lawsuit, filed in March by the Ann Arbor, Mich.-based Gene Codes, can go forward, The New York Times reported Saturday. New York City has filed a countersuit claiming Gene Codes didn't meet its contractual obligations.

Gene Codes' software, known as the Mass-Fatality Identification System, helped the city analyze and organize the DNA of victims of the terrorist attack. Both sides signed a three-year contract in 2002, for which the city said it paid $13 million.

The company claims that after the contract expired, New York refused to pay it to maintain the system, then gave the FBI proprietary information once the system crashed. The city claims Gene Codes had agreed to upgrade the system for free after the city's initial investment, and when the company didn't follow through, it was necessary to move the information to the FBI's database.

In court filings, the city claimed it had co-created the system by giving the company access to its database of 9/11 victims' DNA data and giving the company guidance on system updates.