How do I find my way around?#
What will I learn?
How to access QuPath’s tour
How to view the interactive help
How to find & copy log messages
How to change preferences to your liking
How to find & run menu commands (quickly)
QuPath’s many options, menus and buttons may seem overwhelming at first. Fortunately, there are tools and tricks to help.
QuPath’s tour#
What to do
Open an image (any image).
Choose .
Move through the tour with the left and right arrows, or jump slides by clicking numbers at the bottom.
QuPath has an built-in tour that guides you through the user interface.
It’s worth checking this out: screen space is limited, so if something is always visible (e.g., in the toolbar) then it’s probably important.
Fig. 19 The QuPath Tour#
Underappreciated toolbar buttons#
This section introduces some toolbar buttons that are often neglected by new QuPath users – because they are far more useful than they may first appear.
Interactive help#
What to do
Select
or open .Hover your mouse over buttons on the screen.
Watch the interactive help update with information about what you are hovering over.
If you are stuck or unsure when using QuPath, the interactive help is a very good place to look first.
If you don’t have the help tool open on screen, coloured notification dots will appear on the button to indicate suggestions or warnings are available. Examples of these can be seen below.
Fig. 20 QuPath’s context help#
Log viewer#
What to do
Click on the
button in the toolbar to open the Log.Highlight the first entry in the log viewer and copy it to the clipboard using Ctrl+C (or Cmd+C on Mac)
Paste the message into a text editor (e.g., Notepad, Notes, Microsoft Word)
Sometimes things go wrong in QuPath, the log viewer helps us figure out where things went wrong and what happened.
If you want to report a problem to the QuPath or get help with an error on the forum, we highly recommend you paste any warnings or errors that were reported in the log. If you don’t, the first response will probably be someone asking for them.
Not all logs are bad though: messages are logged when you do anything in QuPath, and most of the time we don’t need to worry about them. When we do need to take a look, you will usually be notified by a pop up and/or coloured notification dots will appear on the log button.
Fig. 21 QuPath’s log viewer#
Tip
Clicking on the warning or error count (if present) on the bottom left will cycle through warnings or errors. In general, warnings indicate possible problems, while errors usually suggest a definite problem.
Preferences#
What to do
Click on the
button in the toolbar to open the .Try changing QuPath’s theme – to make it dark or light.
QuPath has quite a few things that can be changed to your liking. It’s worth spending some time exploring the preferences to see what can be done.
For example, in the bar at the top, start typing color to see all colour-related things you might change (forgiving the non-British spelling as we try to accommodate a global audience…).
Fig. 22 QuPath preferences#
Puzzle
Imagine you are showing a screenshot of QuPath during a presentation. Which preference could you change to make the scalebar bigger, so it’s easier for people to see at a distance?
Command list#
What to do
Press Ctrl+L (or Cmd+L on Mac) or open .
Start typing
Preferences– the table of commands should get smallerDouble click the row with
Preferences...to run the command
QuPath has even more tools and features accessible under the menus and sub-menus at the top of the application. You might forget where they are or what they are called sometimes (we all do!).
is here to help: this makes it possible to both discover and run commands. It also tells you if they have any keyboard shortcuts.
The shortcut for the command list itself is Ctrl/Cmd+L. This is the same as the corresponding shortcut in ImageJ, to make it easier to remember for people who already use ImageJ.