Commands
File
Create project
Create a new project. Usually it’s easier just to drag an empty folder onto QuPath to create a project, rather than navigate these menus.
Open project
Open an existing project. Usually it’s easier just to drag a project folder onto QuPath to open it, rather than bother with this command.
Close project
Close the current project, including any images that are open.
Add images
Add images to the current project. You can also add images by dragging files onto the main QuPath window.
Export image list
Export a list of the image paths for images in the current project.
Edit project metadata
Edit the metadata for the current project. By adding key-value properties to images, they can be sorted and queried more easily.
Check project URIs
Check the ‘Uniform Resource Identifiers’ for images in the current project. This basically helps fix things whenever files have moved and images can no longer be found.
Import images from v0.1.2
mport images from a legacy project (QuPath v0.1.2 or earlier). Note that it is generally a bad idea to mix versions of QuPath for analysis, but this can be helpful to recover old data and annotations.
The original images will need to be available, with the paths set correctly in the project file.
Open…
- Ctrl+O
Open an image in the current viewer, using a file chooser. You can also just drag the file on top of the viewer.
Open URI…
- Shift+Ctrl+O
Open an image in the current viewer, by entering the path to the image. This can be used to add images that are not represented by local files (e.g. hosted by OMERO), but beware that a compatible image reader needs to be available to interpret them.
Reload data
- Ctrl+R
Reload any previously-saved data for the current image. This provides a more dramatic form of ‘undo’ (albeit without any ‘redo’ option).
Save As
- Shift+Ctrl+S
Save a .qpdata file for this image, specifying the file path. Warning! It is usually much better to use projects instead, and allow QuPath to decide where to store your data files.
Save
- Ctrl+S
Save a .qpdata file for this image. This command is best used within projects, where QuPath will choose the location to save the file.
Original pixels
Export an image region, by extracting the pixels from the original image
Rendered RGB (with overlays)
Export an image region, as an RGB image matching how it is displayed in the viewer
OME TIFF
Write regions as OME-TIFF images. This supports writing image pyramids.
Rendered SVG
Export the current selected region as a rendered (RGB) SVG image. Any annotations and ROIs will be stored as vectors, which can later be adjusted in other software.
Main window screenshot
Export the area of the screen corresponding to the main QuPath window to the clipboard. This includes any additional overlapping windows and dialog boxes.
Main window content
Export the contents of the main QuPath window to the clipboard. This ignores any additional overlapping windows and dialog boxes.
Current viewer content
Export the contents of the current viewer to the clipboard. Note that this creates an RGB image, which does not necessarily contain the original pixel values.
Current viewer content (SVG)
Export an RGB snapshot of the current viewer content as an SVG image. Any annotations and ROIs will be stored as vectors, which can later be adjusted in other software.
Import objects from file
Import objects from GeoJSON or .qpdata files
Export objects as GeoJSON
Export objects in GeoJSON format to file
Import TMA map
Import a TMA map, e.g. a grid containing ‘Case ID’ values for each core
Export TMA data
Export TMA data for the current image, in a format compatible with the ‘TMA data viewer’
Launch TMA data viewer
Launch the ‘TMA data viewer’ to visualize TMA core data that was previously exported
Quit
Quit QuPath
Edit
Undo
- Ctrl+Z
Undo the last action for the current viewer. Note QuPath’s undo is limited, and turns itself off (for performance reasons) when many objects are present. The limit can be adjusted in the preferences.
Redo
- Shift+Ctrl+Z
Redo the last action for the current viewer.
Selected objects
Copy the selected objects to the system clipboard as GeoJSON
Annotation objects
Copy all annotation objects to the system clipboard as GeoJSON
Current viewer
Copy the contents of the current viewer to the clipboard. Note that this creates an RGB image, which does not necessarily contain the original pixel values.
Main window content
Copy the contents of the main QuPath window to the clipboard. This ignores any additional overlapping windows and dialog boxes.
Main window screenshot
Copy the area of the screen corresponding to the main QuPath window to the clipboard. This includes any additional overlapping windows and dialog boxes.
Full screenshot
Make a screenshot and copy it to the clipboard.
Paste
Paste the contents of the system clipboard, if possible. If the clipboard contents are GeoJSON objects, the objects will be pasted to the current image. Otherwise, any text found will be shown in a the script editor.
Paste objects to current plane
Paste GeoJSON objects from the system clipboard to the current z-slice and timepoint, if possible. New object IDs will be generated if needed to avoid duplicates.
Preferences…
- Ctrl+','
Set preferences to customize QuPath’s appearance and behavior
Reset preferences
Tools
Move
- M
Move tool, both for moving around the viewer (panning) and moving objects (translating)
Rectangle
- R
Click and drag to draw a rectangle annotation. Hold down ‘Shift’ to constrain shape to be a square.
Ellipse
- O
Click and drag to draw an ellipse annotation. Hold down ‘Shift’ to constrain shape to be a circle.
Line
- L
Click and drag to draw a line annotation. Right-click the toolbar button to optionally switch to use arrowheads.
Polygon
- P
Create a closed polygon annotation. You can either click individual points (with double-click to end) or click and drag (and release the mouse button to end).
Polyline
- V
Create a polyline (i.e. open polygon) annotation. You can either click individual points (with double-click to end) or click and drag (and release the mouse button to end).
Brush
- B
Click and drag to paint with a brush. By default, the size of the region being drawn depends upon the zoom level in the viewer.
Points
- '.'
Click to add points to an annotation
Selection mode
- Shift+S
Turn on/off selection mode - this converts drawing tools into selection tools
View
Show analysis pane
- Shift+A
Show the analysis pane. This contains the main tabs for managing projects, images and objects.
Show command list
- Ctrl+L
Show the command list (much easier than navigating menus…)
Show recent commands
- Ctrl+P
Show a list containing recently-used commands
Brightness/Contrast
- Shift+C
Show the brightness & contrast dialog. This is also used to adjust channels and colors. It makes it possible to change how the image is displayed, but does not change the image itself.
Grid 1 x 1 (single viewer)
Set the viewer grid to contain a single viewer
Grid 1 x 2 (horizontal)
Set the viewer grid to contain 2 viewers, arranged horizontally
Grid 2 x 1 (vertical)
Set the viewer grid to contain 2 viewers, arranged vertically
Grid 2 x 2
Set the viewer grid to contain 4 viewers, arranged in a 2x2 grid
Grid 3 x 3
Set the viewer grid to contain 9 viewers, arranged in a 3x3 grid
Add row
Add a new row of viewers to the multi-view grid. This makes it possible to view two or more images side-by-side (vertically).
Add column
Add a new column of viewers to the multi-view grid. This makes it possible to view two or more images side-by-side (horizontally).
Remove row
Remove the row containing the current viewer from the multi-view grid, if possible. The last row cannot be removed.
Remove column
Remove the column containing the current viewer from the multi-view grid, if possible. The last column cannot be removed.
Reset viewer sizes
Reset the multi-view grid so that all viewers have the same size
Synchronize viewers
- Alt+Ctrl+S
Synchronize panning and zooming when working with images open in multiple viewers
Match viewer resolutions
Adjust zoom factors to match the resolutions of images open in multiple viewers
Close viewer
Close the image in the current viewer. This is needed before it’s possible to remove a viewer from the multi-view grid.
Detach viewer from grid
Detach the selected viewer from the viewer grid, into its own window
Attach viewer to grid
Add the detached viewer back to the viewer grid (if there is space for it)
Show channel viewer
Open a viewer window that shows individual channels of an image size by side. This is useful when working with multiplexed/multichannel fluorescence images. Right-click on the viewer to adjust settings.
Show mini viewer
Open a viewer window that shows a view of the pixel under the cursor. This is useful for viewing the image booth zoomed in and zoomed out at the same time.
400%
Set the zoom factor to 400% (downsample = 0.25)
100%
Set the zoom factor to 400% (downsample = 1)
10%
Set the zoom factor to 400% (downsample = 10)
1%
Set the zoom factor to 400% (downsample = 100)
Zoom in
Zoom in for the current viewer
Zoom out
- '-'
Zoom out for the current viewer
Zoom to fit
Set the current viewer’s zoom to fit the image
Rotate image
Rotate the image visually (this is only for display - the coordinate system remains unchanged)
Cell boundaries only
Display cells by drawing the cell boundary ROI only
Nuclei only
Display cells by drawing the cell nucleus ROIs only
Nuclei & cell boundaries
Display cells by drawing both the cell boundary and nucleus ROIs, where available
Cell centroids only
Display cells by drawing the cell centroids only. The shape and color will depend upon the classification.
Show annotations
- A
Show/hide annotation objects
Fill annotations
- Shift+F
Fill/unfill annotation object ROIs for display
Show annotation names
- N
Show/hide annotation names (where available)
Show TMA grid
- G
Show/hide the tissue microarray grid (where available)
Show TMA grid labels
Show/hide the tissue microarray core labels (where available)
Show detections
- D
Show/hide detection objects
Fill detections
- F
Fill/unfill detection object ROIs for display
Show object connections
Show connections between objects, if available. This can be used alongside some spatial commands, such as to display a Delaunay triangulation as an overlay.
Show pixel classification
- C
Show/hide the pixel overlay (used for pixel classification)
Show slide overview
Show/hide the viewer overview image. This is a clickable thumbnail used for navigation.
Show cursor location
Show/hide the cursor location text
Show scalebar
Show/hide the viewer scalebar
Show grid
- Shift+G
Show/hide the counting grid overlay
Set grid spacing
Set the spacing for the counting grid
Show view tracker
Record zoom and panning movements within a viewer for later playback and analysis
Show slide label
Show the slide label associated with the image in the active viewer (if available)
Show input display
Show mouse clicks and keypresses on screen. This is particularly useful for demos and tutorials.
Show memory monitor
Show a dialog to track memory usage within QuPath, and clear the cache if required
Show log
- Shift+Ctrl+L
Show the log. This is very helpful for identifying and debugging errors. If you wish to report a problem using QuPath, please check the log for relevant information to provide.
Turn on all gestures
Turn on all multi-touch gestures for touchscreens and trackpads
Turn off all gestures
Turn off all multi-touch gestures for touchscreens and trackpads
Use scroll gestures
Toggle scroll gestures for touchscreens and trackpads
Use zoom gestures
Toggle zoom gestures for touchscreens and trackpads
Use rotate gestures
Toggle rotate gestures for touchscreens and trackpads
Objects
Delete selected objects
Delete the currently selected objects
Delete all objects
Delete all objects for the current image
Delete all annotations
Delete all annotation objects for the current image
Delete all detections
Delete all detection objects for the current image
Reset selection
- Alt+Ctrl+R
Reset the selected objects for the current image
Select TMA cores
- Alt+Ctrl+T
Select all TMA cores for the current image
Select annotations
- Alt+Ctrl+A
Select all annotation objects for the current image
Select all detections
- Alt+Ctrl+D
Select all detection objects for the current image (this includes cells and tiles)
Select cells
- Alt+Ctrl+C
Select all cell objects for the current image
Select tiles
Select all tile objects for the current image
Select objects by classification
Select objects based upon their classification
Select objects on current plane
Select all objects on the current plane visible in the viewer
Lock selected objects
- Shift+Ctrl+K
Lock all currently selected objects
Unlock selected objects
- Alt+Ctrl+K
Unlock all currently selected objects
Toggle selected objects lock
- Ctrl+K
Toggle the ‘locked’ state of all currently selected objects
Show object descriptions
Show descriptions for the currently-selected object, where available. Descriptions can be any plain text, markdown or html added as the ‘description’ property to an object (currently, only annotations are supported).
Specify annotation
Create a rectangle or ellipse annotation with the specified properties
Create full image annotation
- Shift+Ctrl+A
Create an annotation representing the full width and height of the current image
Insert into hierarchy
- Shift+Ctrl+I
Insert the selected objects in the object hierarchy. This involves resolving parent/child relationships based upon regions of interest.
Resolve hierarchy
- Shift+Ctrl+R
Resolve the object hierarchy by setting parent/child relationships between objects based upon regions of interest.
Transform annotations
- Shift+Ctrl+T
Interactively translate and/or rotate the current selected annotation.
Duplicate selected annotations
- Shift+D
Duplicate the selected annotations
Copy annotations to current plane
- Shift+Ctrl+V
Duplicate the selected objects and paste them on the current plane (i.e. the z-slice and timepoint visible in the viewer). This avoids using the system clipboard. It is intended to help transfer annotations quickly across multidimensional images.
Transfer last annotation
- Shift+E
Transfer the last annotation to the current image. This can be used to bring annotations from one viewer to another, or to recover an annotation that has just been deleted.
Expand annotations
Expand (or contract) the selected annotations, optionally removing the interior.
Split annotations
Split complex annotations that contain disconnected pieces into separate annotations
Split annotations by lines
Split area annotations along lines defined by line annotations
Remove fragments & holes
Remove small fragments of annotations that contain disconnected pieces
Fill holes
Fill holes occurring inside annotations
Make inverse
Make annotations corresponding to the ‘inverse’ of the selected annotation. The inverse annotation contains ‘everything else’ outside the current annotation, constrained by its parent.
Merge selected
Merge the selected annotations to become one, single annotation.
Simplify shape
Simplify the shapes of the current selected annotations. This removes vertices that are considered unnecessary, using a specified amplitude tolerance.
Refresh object IDs
Update all object IDs to ensure they are unique
Refresh duplicate object IDs
Update all duplicate object IDs to ensure they are unique
TMA
TMA dearrayer
Identify cores and grid arrangement of a tissue microarray
Specify TMA grid
Create a manual TMA grid, by defining labels and the core diameter. This can optionally be restricted to a rectangular annotation.
Add TMA row above selected
Add a row to the TMA grid before (above) the row containing the current selected object
Add TMA row below selected
Add a row to the TMA grid after (below) the row containing the current selected object
Add TMA column before selected
Add a column to the TMA grid before (to the left of) the column containing the current selected object
Add TMA column after selected
Add a column to the TMA grid after (to the right of) the column containing the current selected object
Remove TMA row
Remove the row containing the current selected object from the TMA grid
Remove TMA column
Remove the column containing the current selected object from the TMA grid
Relabel TMA grid
Relabel the cores of a TMA grid. This is often needed after adding or deleting rows or columns.
Reset TMA metadata
Remove all the metadata for the TMA grid in the current image
Delete TMA grid
Delete the entire TMA grid for the current image
Find convex hull detections (TMA)
Find all detections occurring on the convex hull of the detections within a TMA core. This can be used to find cells occurring towards the edge of the core, which can then be deleted if necessary. Often these cells may yield less reliable measurements because of artifacts.
Measure
Show measurement maps
- Shift+Ctrl+M
View detection measurements in context using interactive, color-coded maps
Show measurement manager
View and optionally delete detection measurements
Show TMA measurements
Show a measurement table for tissue microarray (TMA) cores
Show annotation measurements
Show a measurement table for annotation objects
Show detection measurements
Show a measurement table for detection objects
Show annotation grid view
Show annotation measurements in a grid view
Show TMA core grid view
Show tissue microarray (TMA) core measurements in a grid view
Export measurements
Export summary measurements for multiple images within a project
Automate
Script editor
- Ctrl+'['
Open the script editor
Script interpreter
Open a script interpreter to run scripts interactively, line by line. (In general, the Script Editor is more useful).
Show workflow command history
- Shift+Ctrl+W
Show a history of the commands applied to the current image. Note that this is not fully exhaustive, because not all commands can be recorded. However, the command history is useful to help automatically generate batch-processing scripts.
Create command history script
Create a script based upon the actions recorded in the command history
Analyze
Estimate stain vectors
Estimate stain vectors for color deconvolution in brightfield images. This can be used when there are precisely 2 stains (e.g. hematoxylin and eosin, hematoxylin and DAB) to improve stain separation.
Create tiles
Create tiles. These can be useful as part of a larger workflow, for example by adding intensity measurements to the tiles, training a classifier and then merging classified tiles to identify larger regions.
SLIC superpixel segmentation
Create superpixel tiles using the SLIC method
DoG superpixel segmentation
Create superpixel tiles using a Difference of Gaussians method
Tile classifications to annotations
Merge tiles sharing the same classification to become annotations
Cell detection
Default cell detection in QuPath. Note that this is general-purpose method, not optimized for any particular staining.
It is essential to set the image type first (e.g. brightfield or fluorescence) before running this command.
Positive cell detection
Equivalent to ‘Cell detection’, with additional parameters to set a threshold during detection to identify single-positive cells.
Subcellular detection (experimental)
Identify subcellular structures (e.g. spots of all kinds) within detected cells.
Fast cell counts (brightfield)
Fast cell counting for hematoxylin and DAB images
Add smoothed features
Supplement the measurements for detection objects by calculating a weighted sum of the corresponding measurements from neighboring objects
Add intensity features
Add new intensity-based features to objects
Add shape features
Distance to annotations 2D
Calculate distances between detection centroids and the closest annotation for each classification, using zero if the centroid is inside the annotation. For example, this may be used to identify the distance of every cell from ‘bigger’ region that has been annotated (e.g. an area of tumor, a blood vessel).
Signed distance to annotations 2D
Calculate distances between detection centroids and the closest annotation for each classification, using the negative distance to the boundary if the centroid is inside the annotation. For example, this may be used to identify the distance of every cell from ‘bigger’ region that has been annotated (e.g. an area of tumor, a blood vessel).
Detection centroid distances 2D
Calculate distances between detection centroids for each classification. For example, this may be used to identify the closest cell of a specified type.
Delaunay cluster features 2D
Apply a Delaunay triangulation to detection objects based on their centroid locations. This helps identify clusters of objects neighboring one another.
Note this command is likely to be replaced in a future version.
Create density map
Create a density map to identify regions containing a high density of detections (e.g. cells), optionally with specified classifications
Load density map
Load a density map previously generated with ‘Create density map’
Classify
Reset detection classifications
Reset the classifications of all detections
Load object classifier
Load an existing object classifier. This can be used to apply the classifier to new objects, but not to continue training.
Train object classifier
- Shift+Ctrl+D
Interactively train an object classifier using machine learning. This is useful whenever objects cannot be classified based on one measurement alone.
Create single measurement classifier
Create a simple object classifier that applies a threshold to a single measurement
Create composite classifier
Combine multiple classifiers together to create a single classifier by applying them sequentially
Set cell intensity classifications
Set cell intensity classifications based upon a single measurement. This is useful to calculate densities/percentages of positive cells or H-scores.
Load pixel classifier
Load an existing pixel classifier. This can be used to apply the classifier to new images, but not to continue training.
Train pixel classifier
- Shift+Ctrl+P
Train a pixel classifier. This can be used to quantify areas, or to generate or classify objects.
Create thresholder
Create a simple pixel classifier that applies a fixed threshold to an image
Create region annotations
Create annotations of fixed-size regions. This can be used to select representative regions of multiple images to train (usually pixel) classifier, in combination with ‘Create training image’.
Create training image
Create an image comprised of regions extracted from multiple images in a project. This can be useful for interactively training a classifier across a varied dataset.
Create duplicate channel training images
Duplicate an image in a project so that there is one duplicate for each channel of the image.
This can be used to train separate classifiers for different channels in multiplexed images, which are then merged to form a composite classifier.
Split project train/validation/test
Split images within a project into training, validation and test sets
Extensions
Manage extensions
Manage the list of installed QuPath extensions
Send region to ImageJ
Extract the selected image region and send it to ImageJ
Send snapshot to ImageJ
Create a rendered (RGB) snapshot and send it to ImageJ
Import ImageJ ROIs
Import ImageJ ROIs from .roi or .zip files, converting them QuPath objects
Set plugins directory
Set the plugins directory to use with QuPath’s embedded version of ImageJ.
This can be set to the plugins directory of an existing ImageJ installation, to make the plugins associated with that installation available within QuPath.
ImageJ macro runner
Run ImageJ macros within QuPath
Help
Show welcome message
Show the welcome message that appears when QuPath is first launched
Show interactive help
Show interactive help info based on the cursor location and QuPath’s current state
Documentation (web)
Open the main QuPath documentation in a web browser
YouTube channel (web)
Open the QuPath YouTube channel in a web browser for demo videos & tutorials
Check for updates (web)
Check online for updates to QuPath & supported extensions
Cite QuPath in a paper (web)
Please cite the QuPath publication if you use the software! This command opens a web page to show how.
Report a bug (web)
Open QuPath’s issues page in a web browser to report a bug. Please follow the bug report template - and use the forum instead for general questions.
View user forum (web)
Visit the user forum at image.sc. This is the place to ask questions about QuPath - and to give answers to help other users.
View source code (web)
View QuPath’s source code on GitHub
License
View license information for QuPath and its third-party dependencies
System info
View technical information about this QuPath installation