A074 - Integrated machine learning for scanned slides analysis with Qupath

Pierre Hener (pierre.hener@inci-cnrs.unistra.fr)
RĂ©my Flores-flores (remy.flores-flores@inserm.fr)

Since the last five years, various machine learning tools dedicated to the classification of pixels or objects have emerged (Ilastik, Trainable Weka Segmentation…). These tools are powerful but until now, it remains very difficult to analyze whole slide images or big tile scan images with these software. Few years ago, Qupath, an open source software dedicated to whole slide images was released. It integrates visualization and annotation tools, but also machine learning modules without the need of specific plugins installation or coding, helping users to simplify some image analysis workflows. These integrated modules are the pixels classifier for object detection and the objects classifier. They are easy to handle, efficient and versatile. This workshop will focus on these modules and how to use them on whole slide images. For the complete analysis workflow, we will as well explain how to display and export the parameters measured automatically by Qupath.