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 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 the current project, including any images that are open.
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
Import 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 an image in the current viewer, using a file chooser. You can also just drag the file on top of the viewer.
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 any previously-saved data for the current image. This provides a more dramatic form of ‘undo’ (albeit without any ‘redo’ option).
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 a .qpdata file for this image. This command is best used within projects, where QuPath will choose the location to save the file.
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.
Write regions as OME-TIFF images. This supports writing image pyramids.
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 ‘Unique 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.
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 the last action for the current viewer.
Copy the selected objects to the system clipboard as GeoJSON.
Copy all annotation objects to the system clipboard as GeoJSON.
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.
Make a screenshot and copy it to the clipboard.
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.
Set preferences to customize QuPath’s appearance and behavior.
Reset preferences to their default values - this can be useful if you are experiencing any newly-developed persistent problems with QuPath.
Move tool, both for moving around the viewer (panning) and moving objects (translation).
Click and drag to draw a rectangle annotation. Hold down ‘Shift’ to constrain shape to be a square.
Click and drag to draw an ellipse annotation. Hold down ‘Shift’ to constrain shape to be a circle.
Click and drag to draw a line annotation.
Create a closed polygon annotation, either by clicking individual points (with double-click to end) or clicking and dragging.
Create a polyline annotation, either by clicking individual points (with double-click to end) or clicking and dragging.
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.
Click and drag to draw with a wand tool. Adjust brightness/contrast or wand preferences to customize the sensitivity and behavior.
Click to add points to an annotation.
Turn on/off selection mode - this converts drawing tools into selection tools
Show analysis pane
Show/hide the analysis pane (the one on the left).
Show command list
Show the command list (much easier than navigating menus…).
Show recent commands
Show a list containing recently-used commands.
Show the brightness/contrast dialog. This enables changing how the image is displayed, but not the image data itself.
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.
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 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 the row containing the current viewer from the multi-view grid, if possible. The last row cannot be removed.
Remove the column containing the current viewer from the multi-view grid, if possible. The last column cannot be removed.
Reset grid size
Reset the multi-view grid so that all viewers have the same size
Close the image in the current viewer. This is needed before it’s possible to remove a viewer from the multi-view grid.
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.
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.
Set the zoom factor to 400% (downsample = 0.25).
Set the zoom factor to 100% (downsample = 1).
Set the zoom factor to 10% (downsample = 10).
Set the zoom factor to 1% (downsample = 100).
Zoom in for the current viewer.
Zoom out for the current viewer.
Zoom to fit
Adjust zoom for all images to fit the entire image in the viewer.
Rotate the image visually (this is only for display - the coordinate system remains unchanged).
Cell boundaries only
Show cells by drawing the outer boundary ROI only.
Show cells by drawing the nucleus ROI only (if available).
Nuclei & cell boundaries
Show cells by drawing both the outer boundary and nucleus ROIs (if available).
Show cells by drawing the centroids only.
Toggle showing all annotations in the viewer.
Toggle showing annotation ROIs as filled shapes in the viewer.
Toggle showing all annotation names in the viewer.
Show TMA grid
Toggle showing any TMA grid in the viewer.
Show TMA grid labels
Toggle showing any TMA core labels in the viewer.
Toggle showing all detections in the viewer.
Toggle showing detection ROIs as filled shapes in the viewer.
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
Toggle pixel classification overlays in the viewer. This only has an effect if there is actually a pixel classification available.
Show slide overview
Toggle showing the image overview in the viewer. This is a clickable thumbnail used for navigation.
Show cursor location
Toggle showing the cursor location in the viewer.
Toggle showing the scalebar in the viewer.
Toggle showing the counting grid in the viewer.
Set grid spacing
Adjust the counting grid spacing for the viewers.
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 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.
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 the selected objects for the current image.
Select TMA cores
Select all TMA cores for the current image.
Select all annotation objects for the current image.
Select all detections
Select all detection objects for the current image (this includes cells and tiles).
Select all cell objects for the current image.
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 visiible in the viewer.
Lock selected objects
Lock all currently selected objects.
Unlock selected objects
Unlock all currently selected objects.
Toggle selected objects locked
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).
Create a rectangle or ellipse annotation with the specified properties.
Create full image annotation
Create an annotation representing the full width and height of the current image.
Insert into hierarchy
Insert the selected objects in the object hierarchy. This involves resolving parent/child relationships based upon regions of interest.
Resolve the object hierarchy by setting parent/child relationships between objects based upon regions of interest.
Interactively translate and/or rotate the current selected annotation.
Duplicate selected annotations
Duplicate the selected annotations.
Copy annotations to current plane
Duplicate the selected objects and paste them on the current plane (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
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 (or contract) the selected annotations, optionally removing the interior.
Split complex annotations that contain disconnected pieces into separate annotations.
Remove fragments & holes
Remove small fragments of annotations that contain disconnected pieces.
Fill holes occurring inside annotations.
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 the selected annotations to become one, single annotation.
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.
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 before
Add a row to the TMA grid before (above) the row containing the current selected object.
Add TMA row after
Add a row to the TMA grid after (below) the row containing the current selected object.
Add TMA column before
Add a column to the TMA grid before (to the left of) the column containing the current selected object.
Add TMA column after
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 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.
Show measurement maps
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 cores.
Show annotation measurements
Show a measurement table for annotation objects.
Show detection measurements
Show a measurement table for detection objects.
Annotation grid summary view
Show all the annotations in the current image in a grid view, which can be ranked by measurements.
TMA grid summary view
Show all the TMA cores in the current image in a grid view, which can be ranked by measurements.
Export summary measurements for multiple images within a project.
Show script editor
Open the script editor.
Open a script interpreter. This makes it possible to run scripts interactively, line by line. However, in general the Script Editor is more useful.
Show workflow command history
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.
No scripts found
No scripts found
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. 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.
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
Add new shape-based features to objects.
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).
Detect 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.
Positive pixel count (deprecated)
Area-based quantification of positive pixels with DAB staining. This command does not handle large regions well; if possible, pixel classification should usually be used instead.
Simple tissue detection (deprecated)
Detect large regions using a simple thresholding method. This command is not very flexible and lacks any preview of the results; if possible, pixel classification should usually be used instead.
Cell + membrane detection (deprecated)
Cell detection that uses membrane information to constrain cell boundary expansion.
This was designed specifically for hematoxylin and DAB staining, and works only where membrane staining is either very clear or absent. It is not recommended in general.
Create density map
Load density map
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
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
Train a pixel classifier. This can be used to quantify areas, or to generate or classify objects.
Create a simple pixel classifier that applies a 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.
View a 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.
Show welcome message
Show the welcome message that appears when QuPath is first launched
Open the main QuPath documentation website.
YouTube channel (web)
Open the QuPath demo videos and tutorials.
Check for updates (web)
Check online for an updated QuPath release.
Cite QuPath (web)
Please cite the QuPath publication if you use the software! This command opens a web page to show how.
Report bug (web)
Report a bug. Please follow the template and do not use this for general questions!
View user forum (web)
Visit the user forum. This is the place to ask questions (and give answers).
View source code (web)
View the QuPath source code online.
View license information for QuPath and its third-party dependencies.
View system information.