Tuesday May 18th 2021



Pathomation offers a software platform with both off the shelf products as well as individual components for custom-built solutions in digital pathology. In recent months, new file formats were added, bringing the total of supported file formats to 35 bright field, 16 fluorescent, and 16 z-stacked.

Digital pathology and virtual microscopy are steadily increasing and changing the world of microscopy and pathology alike.

Pathomation has developed a software platform with a set of components and plugins to build powerful and agile environments in this new exciting world. Key components in the Pathomation ecosystem are PMA.start (free desktop application) and PMA.core (server) to serve and view all types of whole slide images.

“In technical terms, PMA.start and PMA.core are both tile servers”, explains Angelos Pappas, senior software engineer, “A tile server chops up these huge gigapixel images in bite-size small tiles, so that the end-users gets a smooth viewing experience, just like you would when looking through a real microscope”.

A major challenge for many adaptors of the new virtual slide technology today is to cope with the variation in different file formats available to store whole slide images in. In its upcoming 2.0 software platform, Pathomation supports a range of new file formats, including:

  • Philips iSyntax file format (TIFF remains supported too)

  • Motic’s MDSX file format (MDS remains supported too)

  • Inspirata (formerly GE Omnyx) RTS file format

  • Unic Tech TMAP file format

  • KFBio KFB file format

New slides are being generated on new hardware constantly, but around the world, much content still exists on legacy infrastructure, too. The Pathomation platform therefore also still offers supports for several legacy platforms and image stacks, such as:

  • Olympus Webview

  • Microsoft Deepzoom DZI

  • Zoomify

In some instances, vendors have dropped support for these legacy formats. In the worst case, the original physical material that the virtual slides were derived from no longer exists. Ediz Güzel is a senior project manager at Pathomation and in charge of enterprise accounts. He elaborates: “PMA.core and PMA.start minimize the effort needed for organizations to migrate their existing slide collections, which isn’t always possible anyway. Remember that these can be patient sample data that cannot easily be replicated or obtained elsewhere.”

At the time of press, Pathomation supports 35 different bright field formats, 16 fluorescent and 16 z-stacked image file formats.

In addition to its tile server and various downstream presentation components, Pathomation’s platform also offers a range of plugins for content and learning management systems (CMS, LMS), as well as AI environments (FIJI, Anaconda, QuPath). The incorporation of historical data in novel applications like updated websites or image analysis pipelines is therefore secured.

The PMA.core component in the Pathomation software platform for digital pathology and virtual microscopy is a universal tile server for brightfield, fluorescence, and z-stacked imaging data acquired by over 30 different scanner systems. It can be installed on-premise as well as hosted by Pathomation in a SaaS model. The full list of supported file formats can be found at https://www.pathomation.com/formats

About Pathomation

Pathomation was founded in Belgium in 2012. Its free software, PMA.start, has global adaptation and is already used at 450+ sites each month. The company is organized around a virtual global team of collaborators, making it possible to offer around the clock global assistance. PMA.core is a commercial tile server product targeted at any organization that interacts with digital pathology and virtual microscopy data. Pathomation software supports over 30 different proprietary file formats. Visit us at https://www.pathomation.com/