Download & install
QuPath isn’t currently a signed application. This means that, after you download it for your platform (Windows, Linux, macOS) from GitHub, you may need to take a few extra steps to get it to run:
On Windows, if you downloaded an
.msifile then double-click on it to launch the installer
If you see a warning, choosing More info and Run anyway should let you proceed
On Windows, if you downloaded a
.zipthen extract its contents and run the
On macOS, right-click the
.pkgfile, then choose ‘Open’ (you might need to do this twice)
If you’re using an M1/M2 Mac, please check out the notes on Apple silicon
On Linux, download and extract the
You’ll probably have to use
chmod u+x /path/to/QuPath/bin/QuPathto make the launcher executable
See Troubleshooting for more information.
What is QuPath (console).exe?
On Windows, you will see two executable files: QuPath.exe and QuPath (console).exe – perhaps with version numbers incorporated.
You can use either. The only difference between these is that the console version also shows a console that prints text as QuPath runs. This is useful when using the Command line.
If you have trouble installing at all, please see below…
If QuPath does not start, make sure that you are not trying to run it directly from within the
.zip file that you downloaded.
It is important to first extract the files into their own ‘QuPath’ folder, and then run
QuPath.exe from within that.
The QuPath installer gives a scary warning
It is expected that Windows will give a scary-looking warning whenever the QuPath installer is first run, as it tries to protect you from software it does not know.
If you would like to get past this screen, press ‘More info’ and the option to ‘Run anyway’ appears.
The QuPath installer does not start
If the QuPath installer does not start at all, you may not have administrator privileges on your computer - and therefore cannot install it. Try downloading the
.zip file instead, which should not need such privileges.
Running QuPath on 32-bit Windows is not supported.
Mac users may also see security messages when running the QuPath pkg installer.
QuPath cannot be opened
If you see the message that QuPath cannot be opened because the developer cannot be verified, you can try right-clicking on the QuPath icon and select Open from the popup menu that appears.
You should then see an option to open QuPath that should work.
You may also need to right-click and choose open the first time you run the QuPath app after installation. Double-clicking should work as normal once it has been run once.
Since macOS (presumably) has your best interests at heart, circumventing its security settings routinely is probably not advisable.
However, as an open source project, we don’t currently have the time and resources needed to distribute QuPath as a signed/notarized app and avoid these warnings.
v0.4.0 introduces a new (experimental) QuPath build specifically for Apple Silicon.
If you have a new Mac with an M1/M2 processor, this is likely to run much faster than the alternative Intel build.
However, there are a few significant disadvantages:
OpenSlide is missing. You can add it separately with the help of Homebrew - see https://github.com/petebankhead/homebrew-qupath for details
Images opened with Bio-Format may not work if they require a native library, e.g.
some .ndpi files (e.g. the OS-1/OS-2/OS-3.ndpi sample images)
some .czi files (with JPEG-XR compression)
TensorFlow for Java doesn’t work. But it doesn’t work on Apple Silicon even if you use the Intel build (this will hopefully be fixed by the TensorFlow Java maintainers in the future).
QuPath for Linux was compiled on Ubuntu, with best efforts made to include all dependencies, although in the case of OpenSlide this wasn’t entirely successful. You may need to install OpenSlide separately through your package manager.
Known issues are:
Black/white tiles can appear in some images reading using OpenSlide; updating libpixman can resolve this (see Issue #355), or alternatively you can try the alternative bash script
/path/to/QuPath/bin/QuPath.shto launch the software.
QuPath (like other Java applications) cannot be started if its installation path contains a directory named
bin; moving to another directory resolves this (see Issue #614)
Some sub-dependencies might not be found (reported on the forum)
If you still have trouble getting OpenSlide to work, you could also try installing OpenSlide Java using Homebrew.