FAQs
This page contains answers to many QuPath-related questions.
Please check it first to see in your question has already been answered. If not, head on over to one of the following places:
- Google Groups, for questions about the software, or how to apply it to analyze your images
- GitHub issues, to report bugs or make feature requests
For the latest news, you can also see Pete's blog or follow him on Twitter.
Please avoid using GitHub for general 'how-to?' questions. It is rather, as the name suggests, for 'issues', and should operate like a todo list for things that need to be fixed.
One day someone shall go through the existing questions on GitHub and close them if they aren't really issues...
Please do! Be sure to reference the Scientific Reports paper.
See Citing QuPath.
The best thing to do is to check if it's already reported as issue on GitHub. If so, you can add your voice to the discussion - if not, you can add it. This will help keep the bug prominent and tracked until it is fixed.
It is extremely helpful if you can include the following information:
- the version of QuPath you are using (which should be the latest)
- the operating system you are running on (e.g. Windows 10, macOS 10.12, some flavor of Linux)
- steps to recreate the bug
- any error messages QuPath displays or logs (if none appear, try View → Show log to see if anything more subtle has been recorded)
As with bugs, it is best to add a new issue on GitHub, or to get in contact through one of the methods described here.
Sometimes features can be added easily with a small code change or a script... but often considerably more work would be required.
Please note that time and resources are limited, and it is not possible to offer custom development as a service. However feel free to contact @petebankhead if you want to discuss the possibility of collaborating on interesting projects.
Type Ctrl + L to bring up the Command List, and start typing the name of the command you want.
You can even select the command using the arrow keys, and press Enter to run it - making it possible to run commands quickly from the keyboard, without needing to resort to using a mouse.
On the Wiki here.
Be sure to check the System requirements - especially the need for a 64-bit computer.
There can be problems with some flavors of Linux, e.g. https://github.com/qupath/qupath/issues/51 and also with some older Macs.
Where there are incompatibilities, chances are these are related to the 'native libraries', which in this case means OpenSlide or OpenCV. If you are able to try to launch QuPath from a command line, you may see more informative error messages.
If you suspect attempts to load OpenSlide or OpenCV are causing trouble, you can hack your QuPath installation to remove/hide any file you see with 'openslide' or 'opencv' in the name. You'll lose some important functionality, but it may at least allow the software to run. If it does, you can get some of the missing functionality back with alternative commands that do similar tasks by installing the Bio-Formats extension and Weka extension.
Kind of... here are some relevant links:
- https://groups.google.com/d/msg/qupath-users/7cdsBsdy4HQ/faFXwPN3BgAJ
- https://groups.google.com/d/msg/qupath-users/pyHMY6-O0DM/vJA1Gta6BAAJ
- https://github.com/qupath/qupath/issues/94
- https://github.com/qupath/qupath/issues/173
For consistency. Lots of subtle and thorny issues can happen when representing numbers in different ways, in particular when switching between using dots or commas the decimal mark.
For example, 1,001 can either be a fairly large number or a small number depending upon where on the world it is read.
In some cases, QuPath has to use the 'dot' representation for decimals (e.g. when scripting), since this is Java's preferred form... and trying to work around this proved too difficult. However, forcing everyone to use US English for everything (e.g. including exporting results) isn't a perfect solution, especially if other software (e.g. your preferred spreadsheet application) is set up to use something else.
Therefore QuPath does not (currently) insist on its preference for US English... but gives a warning to be very cautious about how numbers are represented and interpreted.
There is a more detailed technical description about the issues involved here.
Begin with your First steps.
The fastest way is usually to just drag the file onto QuPath instead. This works for images, projects and scripts.
But, you really should put your images into a project to help keep all your files organized, see Projects.
Firstly, check out the supported formats here and check if your image is one of them.
Secondly, try downloading and installing the Bio-Formats extension to see if that helps.
If this does not lead to success, follow the steps for I've found a bug - including a check for any error log - in the hope that a solution may be found together.
Note: since QuPath uses a variety of other libraries to read images, image reading issues may not be solvable within QuPath, and may require either creating or modifying an extension.... but it is worth a try.
Is the extension .mrxs? Then see here.
(Or follow the link anyway, even if the file extension is different - the reason may be the same.)
Yes, see this answer.
This is an issue with v0.1.2 and earlier; see here for more information.
Double-clicking on the Min/Max display labels should work, as described here (and discussed here).
Currently no, but see here for a feature request and the latest information.
When I try to draw with a Brush or Wand tool inside another annotation, I end up just selecting the existing annotation.
This is intended; often this is desirable as it makes it easier to refine annotations with the Brush or Wand.
However, you can create new annotations inside if you lock the existing annotation first, see here.
See this blog post.
Not on its own, but see https://github.com/qupath/qupath/issues/165
If creating a detection classifier using the default Classify → Create detection classifier command doesn't work, there are two things you can do:
- Select a different classifier from the drop-down menu rather than the Random trees (default)
- Try the Weka extension for an alternative set of classifiers that may be more accommodating
This issue has been reported on a computer with an Intel Core i3 processor running Windows 64 here, although it is not clear if it occurs elsewhere.
Since it is not reproducible on any of my test systems, and there are two workarounds, unfortunately it is unlikely to be fixed... and so the use of a different classifier is required.
Start off with the CD3 tutorial.
That gives the general ideas. However for other kinds of scoring, you might need to exchange some steps for other ones; for example, instead of Fast cell counts you might run Positive cell detection and possibly train a detection classifier to end up with H-scores or positive cell % values.
Refer to Detecting objects and Classifying objects for more information.
See here.
This is a common question, to which the answer is 'not really' - this functionality would need to be created.
Currently, you can only view the consecutive sections side-by-side, and potentially transfer annotations between them... although this is only likely to be very meaningful/useful if you have already registered the images in some other software, and written out whole slide images that are 'perfectly' aligned.
Some places where this is discussed:
- https://github.com/qupath/qupath/issues/178
- https://github.com/qupath/qupath/issues/171
- https://github.com/qupath/qupath/issues/162
- https://github.com/qupath/qupath/issues/72
- https://groups.google.com/d/msg/qupath-users/OFSQMVkXTSg/zSujlnTzBAAJ
- https://groups.google.com/d/msg/qupath-users/5-JMvmCKRBo/64Iv5QcQBQAJ
- https://groups.google.com/d/msg/qupath-users/mj1smKg4dBw/T7I9cd0SCwAJ
- https://groups.google.com/d/msg/qupath-users/VLJL6UCXqEk/bicz5SsKBAAJ
Less easily than would be ideal; macros are currently not recorded in the workflow enabling them to be turned into scripts.
However, there are workarounds described here and further addressed here.
Be aware that the Send Overlay to QuPath ImageJ plugin doens't work in batch mode; see https://github.com/qupath/qupath/issues/136 for a description and workaround.
These docs are for QuPath ≤ v0.1.2.
For more up-to-date information, see https://qupath.readthedocs.io
- Video tutorials
- First steps
- Viewing images
- Drawing regions
- Counting cells
- Projects
- Multiple images
- Preferences
- Getting help
- Object-oriented analysis
- Types of object
- Object measurements
- Object classifications
- Object hierarchies
- Working with objects
- Workflows
- From workflows to scripts
- Writing custom scripts
- Advanced scripting with IntelliJ
- Scripting examples