QuPath: Advanced open platform for next generation bioimage analysis

Bioimage analysis helps answer scientific questions by applying computational methods to images comprising millions – or, increasingly, billions – of pixels. As imaging technologies advance, new software tools are required to interpret these complex images.

QuPath (http://qupath.github.io) was created specifically to address the image analysis challenges of one emerging imaging modality: whole slide imaging.

Whole slide images (WSI) are ultra-large digital scans (up to 50 GB), typically representing histological samples containing a wealth of information relating to health and disease.

QuPath’s native support for WSI and intuitive combination of image processing and AI have established the software as a de facto standard for digital pathology and an essential tool for basic research.

The aims of this project are to: - Expand the range of algorithms available in QuPath to maximize the value of imaging data - Improve workflow development, validation and sharing to aid the translation of image analysis and AI towards clinical practice - Extend QuPath to new imaging modalities and applications to address unmet needs across a wide range of bioimaging applications Together these represent a major upgrade to the software, transitioning QuPath from being primarily 2D and pathology-focussed into becoming an advanced bioimage analysis platform for next generation multidimensional imaging.