An Open Source Platform for Computational Histopathology

Abstract

Computational histopathology is a fast emerging field which converts the traditional glass slide based department to a new examination platform. Such a paradigm shift also brings the in silico computation to the field. Much research have been presented in the past decades on the algorithm development for pathology image analysis. On the other hand, a comprehensive software platform with advanced visualization and computation capability, large developer community, flexible plugin mechanism, and friendly transnational license, would be extremely beneficial for the entire community. In this work, we present SlicerScope: an open platform for whole slide histopathology image computing based on the highly successful 3D Slicer. We present rationale on the choice of such an architecture, introducing new modules/tools for giga-pixel whole slide image viewing, and four specific analytical modules for qualitative presentation, nucleus level analysis, tissue scale computation, and 3D pathology. The entire software is publicly available at https://slicerscope.github.io/, facilitating the algorithmic, clinical, and transnational researches.

Keywords

• Open-source platform
• computational pathology
• reproducibility