Hinrich B Winther*, REPAIR-lab, Institute of Pathology, University Medical Centre, Koblenz, Germany Christoph Brochhausen*, REPAIR-lab, Institute of Pathology, University Medical Centre, Mainz, Germany C James Kirkpatrick, REPAIR-lab, Institute of Pathology, University Medical Centre, Mainz, Germany Track: Research Presentation Topic: Science 2.0/Collaborative Science Presentation Type: Poster presentation Submission Type: Single Presentation Last modified: 2014-06-09

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Background: Pate, a whole slide imaging (WSI) application was originally developed for teaching of medical students at the University Medical Center Mainz, Germany. It follows a closed source development model. Thus, cooperation with third parties in the development of Pate was not intended. Furthermore, no incentives for cooperation with third parties were present. In addition, the used file format “Zoomify” was problematic. It requires storing each WSI image as many small images called tiles, which made them hard to handle by non-computer experts. To ensure good performance, the image data were stored as tiles in a MySQL database. This made the setup more complicated and was hard to maintain if the amount of image data reached a critical level.
Objective: The aim of this presentation is to show how the technical development process can be modified to enable the participation of third parties in the development process.
Methods: The source code of Pate is managed with GIT and is published on the Github community plattform. The Tiled Tiff image data are handled by the iipsrv server. Pate is implemented in Python utilising the Flask microframework.
Results: As a crucial prerequisite for participation in the development process the source code of Pate on Github was published. This allows anyone to browse the code and to make changes to accommodate their specific requirements.
We changed the image file format to Tiled TIFF, which allows storage of the images in a filesystem. The image server (iipsrv) delivers “Zoomify” file format compliant data since the HTML5 client still expects this format. No image recompression or conversion is done as the image server only provides the tiles from the TIFF source. This enables low latency and high data output.
In order to create a WSI application instance high resolution image data are required. In order to assist in bootstrapping an instance of Pate, we are publishing image data under the "Creative Commons Attribution-ShareAlike 4.0 International" license.
Conclusions: Using modifications in the development process the transition of Pate to an open source development model was performed. This transition supports cooperation with other disciplines. In this context, a symbiotic relationship between informatics and medicine could be achieved, thus resulting in a productive cooperative developmental model.