After the Jenkins-Armat partnership was severed both men worked independently to improve the Phantoscope. In mid-December 1895 Jenkins showed his modified projector at the Franklin Institute Science Museum in Philadelphia. While a joint patent had been applied for, Jenkins told the Institute that the partners' joint attorneys advised him to file for a patent as sole inventor of the Phantoscope. He later learned, to his surprise, that Armat was not in agreement. “Interference proceedings” were declared, and an investigation went on for several months. The early days of invention and patents saw accusations, conspiracy theories and lawsuits thrown about quite feverishly. During the patent investigation a string of suspicious events occurred.

Armat notified Jenkins that he had sold the rights, interest and title covered by the contract between them to his business partner and cousin, T. Cushing Daniel. Weeks after the transaction was completed, Daniel approached Jenkins, telling him that Thomas Armat and his brothers would pay cash if Jenkins withdrew his opposition to the joint patent application. Without Jenkins’ knowledge, Armat had approached associates of Thomas Edison (Raff & Gammon) with his modified version of the projector, representing it as his own invention. They wanted to sell the Phantoscope to Edison, whom had shown interest in the projector, but needed to eliminate interference from Jenkins. Jenkins agreed to drop his opposition to the joint patent and received $2500. The joint patent recognizing both Jenkins and Armat for a modified Phantoscope was approved July 20, 1897. As he wrote in an archived letter to the Franklin Institute: “…a person more experienced in legal matters would have seen the inevitable result of so unequal financial resources. It’s the old story over again, the inventor gets the experience and the capitalist the invention. I’ll know better next time.”

This would not be the end of interference from the Armat camp. When the Franklin Institute was considering awarding Jenkins the Elliott Cresson Gold Medal for scientific achievement, Armat filed a formal protest with the institute, claiming he had invented the Phantoscope. When his claims fell on deaf ears, Armat was followed by Thomas Edison and Edison's attornies. The Institute dismissed Armat's complaints and awarded the medal to Jenkins and Jenkins alone in 1897. The institute cited the agreement that Armat had signed in March of '95 stating Jenkins was the inventor, as well as previous published interviews and articles by Jenkins, explaining his invention, which pre-dated their agreement. In addition, as Jenkins pointed out to the Franklin Institute in archived letters, Armat made several attempts in civil courts to discredit Jenkins and Armat lost all of those legal battles.

Daniel, Armat's cousin & partner, filed for an injunction to prevent Jenkins' use of the motion picture projector in the future. This was in an effort to prevent competition from Jenkins in the showing of motion pictures and the selling of the projector to theaters. (A practice not uncommon with Thomas Edison.) Associate Justice Hagner, Supreme Court, Washington D.C. wrote: "The evidence filed by both parties, proves, as far as it proves anything, that Jenkins is the sole inventor and that the bill to enjoin him should be dissolved, and it is so ordered".

In 1913, Jenkins was also awarded the Scott Medal by the Franklin Institute and again Armat complained...11 years after the awardment.

When a variety of "Jenkins' inventions" were displayed at the Smithsonian Institution, Armat protested the sole acknowledgement of Jenkins as the inventor, after almost twenty years on display. Armat wanted the entire display swept from the Smithsonian's floor. Some items were removed, others remained.

Meanwhile, Armat continued a short relationship with Thomas Edison. Armat and Edison's staff made modifications to the machine and began selling it as a patented Vitascope. It is with the Vitascope that Edison began his theater showings. Armat eventually cut his ties with Edison, whom he later sued, over copyright issues. Jenkins was brought into the Armat vs Edison dispute as well. Jenkins continued to modify, enhance and patent a variety of motion picture cameras, projectors and devices that improved the projection of motion pictures and are still used today.

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