Why choose Pathomation for digital microscopy research?

Take your microscopy data anywhere

Research projects take longer time, research teams are becoming larger, research exceeds geographical boundaries... Research is generally becoming more complex. With Pathomation's solutions, you can now share your microscopic data with anybody in your team, regardless from which source it originates.

A great way to get started with this is through PMA.biobank; our standard solution for hosting (historic) collections or complement existing biobanks.


It's a common occurrence: you've analyzed a couple of slide manually, or you've tried out a new algorithm on a sample set, and now you wish to repeat your experiment or automate your procedure on hundreds if not thousands of slides.

We offer a complete API (Application Programming Interface) that allows you to process your data sets in any programming language and framework. Through our API you can do just that: use your programming (scripting) language of choice to automate your workflow, or optimize operational parameters for a new protocol.

The image below shows an example of a Pyhton script that uses OpenCV to do tissue detection. The script goes through the following steps:

  • Image content is brought into Python,
  • The image content is converted into a GD image object,
  • The image is analyzed with OpenCV to identify tissue regions
  • The regions are fed back into the Pathomation platform as annotation objects for further analysis and evaluation


Consult our programmer's documentation to see how you can embed our platform into your software and how to build custom applications that display whole slide images.

Empower research with Pathomation's digital slide manager and enjoy possibilities that previously seemed impossible.


  • Customizable data capturing via configurable forms per slide, case and user
  • Image annotations
  • Plugins for popular image processing and analysis tools such as ImageJ, Fiji, Adobe Photoshop and Matlab
  • A complete API that allows you to process your data sets in any programming language and framework

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