August 25th 13:00 Finnish time

Open online lecture: https://oulu.zoom.us/j/64556587648 QuPath: Open-source software for bioimage analysis and digital pathology

Reader, Peter Bankhead Institute of Genetics and Cancer University of Edinburgh

[cid:image001.jpg@01D8B79C.C9F24A70] Dr Peter Bankhead - Reader

Realising the potential of image analysis and AI for biology and pathology is hard, and requires software. Firstly, we need open and adaptable software tools that help specialists in different areas work together to devise meaningful algorithms. We then need user-friendly and accessible software platforms to make these algorithms widely available, so that others can validate and apply them in practice.

QuPath (http://qupath.github.io) is free and open-source software designed to help address these needs. Since its release in 2016, QuPath has been downloaded more than 240,000 times and applied in well over 1,000 published studies by groups throughout the world. A growing community of users and developers are now using the platform to create innovative ways of exploring complex biomedical images, with over 2,300 QuPath-related discussions on the Scientific Community Image Forum at https://image.sc.

This talk will describe QuPath’s background and current status, what the future holds, and how the software can be useful for a wide range of different groups working with whole slide and microscopy images today.

Bio Pete completed his PhD at Queen’s University Belfast, focussing on the analysis of retinal images and calcium signals in retinal arterioles. He then moved to Germany, becoming a postdoc in the Nikon Imaging Center at Heidelberg University where he spent much of his time helping microscope users interpret their imaging data using open-source software. During this time he wrote a bioimage analysis handbook for biologists. This has recently been rewritten and released as a new open, interactive, executable book at https://bioimagebook.github.io.

Upon returning to Belfast as a postdoc at the end of 2012, Pete encountered digital pathology for the first time. After trying to apply existing open software tools to whole slide images with limited success, he wrote his own: QuPath. After a short time in industry, Peter is now Reader (Associate Professor) at the University of Edinburgh, where he is building a group dedicated to developing open AI and bioimage analysis methods for pathology and other imaging data.

Welcome to join and please feel free to share with colleagues.