Viewing images
The Viewer is the main QuPath component in which images are shown.
This section describes the controls and shortcuts that can enable you to use the viewer efficiently to move around images and draw annotations. If you would like to know more about changing how pixels are displayed (including adjusting the brightness and contrast), check out the Changing colors section.
Select the Move tool , then click on the image and drag to move it.
If another tool is currently selected, press spacebar to temporarily activate the Move tool. Releasing the spacebar returns to the previously selected tool.
Alternatively, to move quickly to a specific region simply click on the area you wish to navigate to in the overview shown in the top right corner.
Use the scroll wheel to zoom in and out.
The location of the cursor determines where will be centered whenever zooming - so it is a good idea to put the cursor on top of the area that you would like to zoom to.
If everything seems inverted: In some cases, it may appear that scrolling makes things move in the opposite direction from what is expected. This can happen, for example, when using a Mac with Scroll direction: natural turned off in the System Preferences. If this affects you, open QuPath's Preferences panel (Edit → Preferences...) and change the setting for Invert scrolling. It should behave better afterwards.
Of course, the mouse controls also work with trackpads. However additional touchpad gestures can be activated under Tools → Multi-touch gestures. These can be used to turn on 'pinch-to-zoom', and free up the scrolling motion to navigate the slide. This can also enable rotation.
It is possible to use the at least some of the gestures with a touch-sensitive mouse, e.g. the Apple Magic Mouse. For example, turning on the scroll gestures only provides an efficient alternative method to navigate images. Just don't forget to hold down the Shift key when scrolling to zoom in and out.
For most images, scroll the image in the direction pressed. For a TMA image, select the next core in the direction pressed.
Zoom in or out.
In general, set the currently-selected object to the center of the viewer (think: 'center on enter').
If a TMA core is selected, or another object that supports adding notes, then a dialog box will appear to allow notes to be entered quickly.
Temporarily turn on the Move tool (as described above).
Gesture controls can also be applied to touchscreens.
If you have a 3D mouse, this can (possibly, with some luck) be used to navigate slides - tilting to move, and twisting to zoom. This requires an extension using https://github.com/jinput/jinput.
So far, 3D mouse support has only been tested successfully with a SpaceNavigator on a Mac. Tests have been less successful so far on Windows or using a SpacePilot - possibly because of this known issue with JInput.
If you have a pressure-sensitive graphics tablet, QuPath's Brush tool is able to adapt size according to pressure - with the help of an extension based on JPen.
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