QuPath is an open-source, extensible software platform primarily developed for whole slide pathology image analysis. It is developed and maintaned by Pete Bankhead’s Lab here at the IGC. Download it here.

QuPath was specifically developed to meet the need for an user-friendly, extensible open-source solution for digital pathology and whole slide analysis but has expanded hugely from this original aim. The facility recommends using QuPath for any analysis of whole-slide or large stitched images, both fluoresecent and colorimetric stains like H&E, due to its ability to cope with large images like this. This includes .CZI files created using the Zeiss Axioscan and the .NDPI files created using the Hamamatsu Nanozoomer. It can however also be used for many other types of analysis, for example, the way QuPath works makes it very nice for analysis of library type files, (e.g LIF files as produced by Bumbleebee or multipoint ND2 files created using the Nikon microscopes).

Facility Resources
  • A general guide to using QuPath as well as more specific protocols that we thought would be helpful for users can be found here or as videos here.
  • Analysis workflows can be automated in QuPath using scripts. Facility scripts can be found on our Github along with a short guide of how to utilise them. Scripts can be published and distributed.
  • More general information on image analysis concepts and terms can be found here.
  • If you would like to know if there is a relevant workshop coming up soon please check here.
External resources
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