QuPath:Open source software for digital pathology image analysis

Abstract QuPath is new bioimage analysis software designed to meet the growing need for a user-friendly, extensible, open-source solution for digital pathology and whole slide image analysis. In addition to offering a comprehensive panel of tumor identification and high-throughput biomarker evaluation tools, QuPath provides researchers with powerful batch-processing and scripting functionality, and an extensible platform with which to develop and share new algorithms to analyze complex tissue images. Furthermore, QuPath’s flexible design makes it suitable for a wide range of additional image analysis applications across biomedical research

Icytomine: A User-Friendly Tool for Integrating Workflows on Whole Slide Images

International audienceWe present Icytomine, a user-friendly software platform for processing large images from slide scanners. Icytomine integrates in one unique framework the tools and algorithms that were developed independently on Icy and Cytomine platforms to visualise and process digital pathology images. We illustrate the power of this new platform through the design of a dedicated program that uses convolutional neural network to detect and classify glomeruli in kidney biopsies coming from a multicentric clinical study. We show that by streamlining the analytical capabilities of Icy with the AI tools found in Cytomine, we achieved highly promising results