Improved support for using Qupath to analyse slides stored in Slide Score
QuPath is a free open-source image analysis software designed for analysing histopathology slides. It is very user-friendly but flexible and in some ways it works better than commercial software packages for image analysis. Its deceivingly simple user interface provides many advanced functions (cell and tissue detection, machine learning classification of cells or pixels, quantifications and more). It's also very extensible - it includes a scripting engine that helps automate image analysis across hundreds of slides.
Researchers can now run their image analysis in QuPath while the slides are safely stored on a single Slide Score server. Administrators don't have to share the actual files with, they can hide the slide names and labels and strictly control access protecting the privacy of the samples and avoid the need to copy the large files around.
Slide Score then works as a whole slide image management platform storing the pixel data, annotations, TMA core positions and scores and manages access to them in a unified manner. In the future we plan to support also importing annotations from QuPath and running QuPath scripts and analysis pipelines on the server directly.
To use QuPath integration you just need to enable it in the user settings and install the QuPath Slide Score plugin (for versions 0.2.0 and newer). You will then be able to download a QuPath project file for a study, open a slide by opening the link from Slide Score using File-Open URL command and import positions of TMA cores on a slide from Slide Score to avoid the need to perform the dearraying in QuPath.