Peter and Rex Swann incorporated Gatan in Pennsylvania in 1964. For the first fifteen years, the Company focused on contract manufacturing involving high-precision machining. In 1979, Gatan introduced its first major product for the electron microscope market, the DuoMill, a high-precision ion-milling system used to thin a specimen to electron transparency so that it could be successfully viewed in an electron microscope. 

During the next five years, Gatan continued to expand its specimen preparation and manipulation product offerings, becoming the preeminent supplier to microscope manufacturers and end users. Also, the highly successful TV-rate camera for surveying and imaging specimens electronically was conceived and introduced. This served as Gatan's entry into the imaging market. In 1983, Gatan opened a research and development facility in Pleasanton, California, 40 miles southeast of San Francisco and hired Dr. Ondrej Krivanek as Chief Scientist responsible for electron optics design. The Pleasanton facility also became the anchor for the sales and support team covering the rapidly growing Pacific Rim and Western United States. Later the same year, Gatan formed a German subsidiary, Gatan GmbH, which currently handles direct sales in Germany and supports the Company's distribution network throughout Europe. A similar subsidiary was established in the United Kingdom in 1988. 

Gatan substantially expanded its technology and products into analytical applications with the introduction of the first parallel electron energy loss spectrometer (PEELS) in 1985. Computer automation was added in 1995 with the introduction of DigiPEELS. These products provide extremely useful compositional information in the form of elemental mapping of a specimen. In 1989, Gatan introduced the first Gatan Imaging Filter (GIF) and an improved version followed in 1995 (GIF100). The GIF offers significant advantages in improving image contrast and quality through energy filtering of the electron image while at the same time offering enhanced compositional information and elemental mapping. In 1990, Gatan established itself as the leader in TEM digital imaging by introducing the first commercial 1kx1k slow-scan CCD (SSC) camera. This has greatly changed the way that electron microscopy was done, allowing TEM users to view, process and analyze their sample images on-line. In 1995, Gatan introduced the second generation of the CCD cameras, called Multi-scan CCD (MSC) cameras. The MSC cameras can be operated in various speeds, thus allowing users to view samples in fast survey mode and record final high-quality images in standard mode. Gatan now offers a wide range of CCD cameras (1kx1k and 2kx2k) suitable for any TEM applications. 

In June 2000 Gatan was pleased to announce its acquisition of the EM Products Group from Oxford Instruments. The new business is known as Gatan UK and operates as a self-standing UK manufacturing unit, with enhanced facilities to provide specialist products for SEM and TEM. The acquisition coincided with a move for the existing team to a modern, (6000 sq. ft.) factory unit in Oxford, with purpose-built facilities , such as a clean room for assembly and a large EM Applications laboratory. Bob Buchanan, president of Gatan Inc, stated, "The acquisition of Oxford Instruments will fulfill a long-held objective of Gatan: to add a world-class range of SEM products to the Gatan range of products, as well as an even wider portfolio of systems for the TEM. The leading reputation of the Oxford-based team in techniques such as cryo-transfer and cathodoluminescence will allow us to offer a still better service to the microscopy community." 

Gatan, the market leader in TEM automation, develops software and CCD cameras to enhance and optimize TEM performance by providing the capability for viewing and processing images on-line.