Release notes from qupath

v0.7.0

2026-03-02T15:07:30Z

We're pleased to announce QuPath v0.7.0!

For more details, check out the the changelog - or the longer, auto-generated list of changes below.
For questions and discussions, please use the Scientific Community Image Forum.
For bug reports, please follow the template on GitHub issues.

Auto-generated changelog

Starting v0.7.0-SNAPSHOT by @petebankhead in #1949
Add map pin to iconfactory by @alanocallaghan in #1939
Ensure toolbar button heights are standardized by @petebankhead in #1950
Recover if opencv native libs unavailable by @petebankhead in #1951
Avoid empty tooltips in grid view by @petebankhead in #1952
Don't open servers to immediately close them by @petebankhead in #1959
Dependency & changelog updates by @petebankhead in #1962
Fix transform annotations with no main selection by @petebankhead in #1965
Fix RGB channel viewer defaults by @petebankhead in #1966
Update extension manager to 1.0.2 by @Rylern in #1968
Make moveToTrash public and improve documentation by @Rylern in #1969
Fixing tests where n might potentially be NULL by @zindy in #1967
Remove FormatException exceptions from public functions of TIFF writer by @Rylern in #1971
Sync mini/channel viewers with a main viewer in multiple ways by @petebankhead in #1970
Improve toggling between point and multipoint tools by @petebankhead in #1972
Log import objects error by @Rylern in #1977
Update to pom-scijava 42 by @petebankhead in #1979
Fix GeometryTools.union for non-polygonal geometry by @petebankhead in #1980
Fix SubtractOffsetAndScaleNormalizer by @petebankhead in #1981
Improve display histogram level choice by @petebankhead in #1982
Update to DJL 0.34.0 by @petebankhead in #1975
Fix forum link by @petebankhead in #1984
Add gradle update action by @alanocallaghan in #1944
Write perms for gradle update action by @alanocallaghan in #1985
Add PR perms to update gradle action by @alanocallaghan in #1986
Simplify update-gradle.yml by @alanocallaghan in #1988
Update to Groovy v5.0.0 by @petebankhead in #1983
Consider zarr images when trying to import images by @Rylern in #1989
Allow zarr images to be imported in project import images window by @Rylern in #1991
Update gradle via actions by @github-actions[bot] in #1992
Update macOS runners by @petebankhead in #1993
Update dependencies by @petebankhead in #1994
Remove misleading project merge error by @petebankhead in #1995
Fix memory reset bug by @petebankhead in #1996
Avoid garbage collecting grid view images too soon by @petebankhead in #1997
Create thresholder window height issue by @finglis in #2003
Use subscript for log10 by @petebankhead in #2002
Removal of separator within right click menu by @finglis in #2006
Remove bioformats2raw.layout in zarr attributes by @Rylern in #2008
Tentative move to Java 25 by @petebankhead in #2004
More relaxed javadocs by @petebankhead in #2011
Standardize createId(), use last modified time by @petebankhead in #2013
Pyramidal zarr writer by @Rylern in #1964
Dependency updates by @petebankhead in #2015
Show TMA measurements lowered in the Measure menu by @finglis in #2016
Update OpenCV/JavaCPP, reduce warnings by @petebankhead in #2017
Fix ZProjectedImageServer tile bug by @petebankhead in #2022
Update log-viewer to 0.3.0 by @Rylern in #2023
Clean up cell detection and fail fast on invalid input by @petebankhead in #2026
Add install headless extension and call it by @Rylern in #2027
Update Gradle license plugin by @petebankhead in #2029
Update gradle via actions by @github-actions[bot] in #2030
Fix thresholder selection by @petebankhead in #2031
Update dependencies by @petebankhead in #2032
Log at warn only if all supports failed by @alanocallaghan in #2036
Improve conversion of QuPath objects to/from ImageJ Rois by @petebankhead in #2034
Update DJL extension by @petebankhead in #2037
Reduce navigation speed using arrow keys in viewer by @petebankhead in #2038
Use length of Base64 binary array instead of bin data length by @Rylern in #2039
Create Histogram from edges and counts by @petebankhead in #2041
Add tooltips to image detail names as well as values by @alanocallaghan in #2042
Enable setting stage size from properties by @petebankhead in #2043
Update use of input display by @petebankhead in #2033
Change DEBUG to WARN log level when no primary selected object by @Rylern in #2044
Optionally use ICC profiles with OpenSlide images by @petebankhead in #2045
Turn off mnemonic parsing for 'Sort by' by @petebankhead in #2047
Ensure pending tile requests are cleared by @petebankhead in #2048
Update dependencies by @petebankhead in #2049
Optimize imports by @petebankhead in #2050
Warn when opacity is low by @petebankhead in #2051
Update dependencies by @petebankhead in #2059
Handle lines with shape simplifier by @petebankhead in #2054
Fix bug where threshold lines were added twice by @Rylern in #2062
Update extension manager to v1.1.1 by @Rylern in #2060
More efficient QP.mergeAnnotations() + tests by @Rylern in #2064
Change visibility of MiniViewers.MiniViewerManager.close() to public by @Rylern in #2066
Upgrade Bio-Formats, CommonMark by @petebankhead in #2067
Update CHANGELOG with housekeeping details by @alanocallaghan in #2068
Update preference node to 0.7 by @petebankhead in #2070
Improve project entry filtering by @petebankhead in #2071
Return reader only if pool not closed by @Rylern in #2074
More project browser enhancements by @petebankhead in #2072
Avoid bundling fonts with javadocs by @petebankhead in #2073
Update javadocviewer to 0.1.3 by @Rylern in #2076
Fix ICC profile bug by @petebankhead in #2077
Add a flip parameter on ProjectImportImagesCommand by @Rylern in #2075
Fix 'Remove TMA column' context menu command by @petebankhead in #2080
Set opacity of mini viewer tooltip to 0 if text empty by @Rylern in #2082
Don't sync TMA core selection if viewer sync off by @petebankhead in #2083
Remove pre-fetch step in measurement exporter by @alanocallaghan in #2069
Update javadoc viewer to v0.1.4 by @Rylern in #2084
Update JavaFX and Groovy by @petebankhead in #2086
Refactor measurement export code, externalise UI strings by @petebankhead in #2085
Further measurement export updates by @petebankhead in #2087
Add qupath-imglib2 as dependency by @petebankhead in #2019
Update for v0.7.0-rc1 by @petebankhead in #2088
Fix macOS installers by @petebankhead in #2089
Do not lowercase path when fixing by @alanocallaghan in #2090
Update libs.versions.toml by @petebankhead in #2091
Update links and funding period in README by @petebankhead in #2094
Add comment at start of auto-generated scripts by @petebankhead in #2092
Update version to 0.7 by @petebankhead in #2018
Update qupath-djl to 0.4.2 by @Rylern in #2095
Update qupath-imglib2 to v0.1.1 by @Rylern in #2096

New Contributors

@github-actions[bot] made their first contribution in #1992

Full Changelog: v0.6.0...v0.7.0

What to download

See the installation instructions - this explains what to do if security settings prevent QuPath being installed!

For Windows (two options, functionally the same)
- QuPath-v0.7.0-Windows.msi - if you want a standard Windows (local) installer
- QuPath-v0.7.0-Windows.zip - unzip it and double-click QuPath-v0.7.0.exe (no further installation needed)
For Mac (two options, depending upon processor)
- QuPath-v0.7.0-Mac-arm64.pkg - for Macs using Apple Silicon. This runs faster & is recommended for most users, but lacks support for a small number of file formats through Bio-Formats (particularly .czi with jpeg-xr compression & .ndpis).
- QuPath-v0.7.0-Mac-x64.pkg - for Macs with Intel Processors or Apple Silicon (M1/M2)
For Linux
- QuPath-v0.7.0-Linux.tar.xz - use chmod u+x /path/to/QuPath/bin/QuPath to make the launcher executable.

v0.7.0-rc1

2026-02-17T15:45:15Z

We're pleased to announce the first (hopefully only) release candidate for QuPath v0.7.0!

This is a preview version for testing. If no major issues are identified, v0.7.0 will be released very soon.

See the CHANGELOG for more details.

If you try it out and find problems, please let us know via GitHub or the user forum.

There may be bugs!
Please don't use v0.7.0-rc1 for important work, and make sure you back up any projects that you open with it.
It is not recommended to switch between v0.6.x and v0.7.0-rc1 for the same project.

What to download

See the installation instructions - this explains what to do if security settings prevent QuPath being installed!

For Windows (two options, functionally the same)
- QuPath-v0.7.0-rc1-Windows.msi - if you want a standard Windows (local) installer
- QuPath-v0.7.0-rc1-Windows.zip - unzip it and double-click QuPath-v0.7.0-rc1.exe (no further installation needed)
For Mac (two options, depending upon processor)
- QuPath-v0.7.0-rc1-Mac-arm64.pkg - for Macs using Apple Silicon. This runs faster & is recommended for most users, but lacks support for a small number of file formats through Bio-Formats (particularly .czi with jpeg-xr compression & .ndpis).
- QuPath-v0.7.0-rc1-Mac-x64.pkg - for Macs with Intel Processors or Apple Silicon (M1/M2)
For Linux
- QuPath-v0.7.0-rc1-Linux.tar.xz - use chmod u+x /path/to/QuPath/bin/QuPath to make the launcher executable.

v0.6.0

2025-06-27T11:44:10Z

We're pleased to announce QuPath v0.6.0 is now available!

For more details, check out the the release notes on image.sc
For questions and discussions, please use the Scientific Community Image Forum.
For bug reports, please follow the template on GitHub issues.

What to download

See the installation instructions for more details.

For Windows (two options, functionally the same)
- QuPath-v0.6.0-Windows.msi - if you want a standard Windows (local) installer
- QuPath-v0.6.0-Windows.zip - unzip it and double-click QuPath-v0.6.0.exe (no further installation needed)
For Mac (two options, depending upon processor)
- QuPath-v0.6.0-Mac-x64.pkg - for Macs with Intel Processors or Apple Silicon (e.g. M1/M2/M3/M4...)
- QuPath-v0.6.0-Mac-arm64.pkg - for Macs using Apple Silicon only.
  - The arm64 build runs faster & is recommended for most Mac users, but lacks support for a small number of file formats through Bio-Formats (particularly .czi with jpeg-xr compression).
For Linux
- QuPath-v0.6.0-Linux.tar.xz

v0.6.0-rc5

2025-05-11T12:44:56Z

We're pleased to announce the fifth release candidate for QuPath v0.6.0!

This is a preview version for testing.

We think it's the final preview version before v0.6.0 is released... although we've been wrong before.

If you try it out and find problems, please let us know via GitHub or the user forum.

There may be bugs!
Please don't use v0.6.0-rc5 for important work, and make sure you back up any projects that you open with it.
It is not recommended to switch between v0.5.x and v0.6.0-rcx for the same project.

Highlights

See v0.6.0-rc1, v0.6.0-rc2, v0.6.0-rc3 and v0.6.0-rc4 for information about the previous release candidates.

The main changes in v0.6.0-rc5 are:

Fixed a bug that could cause QuPath to use too much memory (#1864)
Update toolbar to important buttons are visible on smaller displays (#1841)
Save projects when running from command line with -s parameter (#1859)
Add a dock button to keep project descriptions open (#1856)
Use viewer gamma with RenderedImageServer (#1849)
Add support for OME-XML shapes (#1848)

Note: For users of macOS Sequoia
Recent security changes in macOS Sequoia may block QuPath's installer.
This can be overcome through Apple Menu > System Settings > Privacy & Security - see this page from apple.com for details.
(We know it's annoying, but we don't currently have the means to make QuPath a 'signed' app to avoid this)

What to download

See the installation instructions for more details.

For Windows (two options, functionally the same)
- QuPath-v0.6.0-rc5-Windows.msi - if you want a standard Windows (local) installer
- QuPath-v0.6.0-rc5-Windows.zip - unzip it and double-click QuPath-v0.6.0-rc5.exe (no further installation needed)
For Mac (two options, depending upon processor)
- QuPath-v0.6.0-rc5-Mac-x64.pkg - for Macs with Intel Processors or Apple Silicon (M1/M2)
- QuPath-v0.6.0-rc5-Mac-arm64.pkg - for Macs using Apple Silicon. This runs faster & is recommended for most users, but lacks support for a small number of file formats through Bio-Formats (particularly .czi with jpeg-xr compression).
  - To install: right-click and choose Open to install.
For Linux
- QuPath-v0.6.0-rc5-Linux.tar.xz - use chmod u+x /path/to/QuPath/bin/QuPath to make the launcher executable.

v0.6.0-rc4

2025-04-14T09:17:34Z

We're pleased to announce the fourth release candidate for QuPath v0.6.0!

This is a preview version for testing... a bit delayed, but with a lot of improvements since rc3 based on feedback and testing.

If you try it out and find problems, please let us know via GitHub or the user forum.

There may be bugs!
Please don't use v0.6.0-rc4 for important work, and make sure you back up any projects that you open with it.
It is not recommended to switch between v0.5.x and v0.6.0-rcx for the same project.

Highlights

See v0.6.0-rc1, v0.6.0-rc2 and v0.6.0-rc3 for information about the previous release candidates.

The main changes in v0.6.0-rc4 are:

All new Extension Manager
- Access via Extensions > Manage extensions
- Use this to install InstanSeg, P4J & the training extensions (these are no longer bundled, as in previous release candidates)
- Will enable us to fix bugs & add features to extensions more quickly - while better managing compatibility
- Extension developers can manage their own extension catalogs
More options to manage classifications & show/hide objects
New controls to navigate multidimensional images and calculate Z-projection overlays
Now possible to build QuPath + Fiji together
Much faster creation & rendering of complex ROIs
Many other bug fixes & performance improvements

Note: For users of macOS Sequoia
Recent security changes in macOS Sequoia may block QuPath's installer.
This can be overcome through Apple Menu > System Settings > Privacy & Security - see this page from apple.com for details.
(We know it's annoying, but we don't currently have the means to make QuPath a 'signed' app to avoid this)

What to download

For Windows (two options, functionally the same)
- QuPath-v0.6.0-rc4-Windows.msi - if you want a standard Windows (local) installer
- QuPath-v0.6.0-rc4-Windows.zip - unzip it and double-click QuPath-v0.6.0-rc4.exe (no further installation needed)
For Mac (two options, depending upon processor)
- QuPath-v0.6.0-rc4-Mac-x64.pkg - for Macs with Intel Processors or Apple Silicon (M1/M2)
- QuPath-v0.6.0-rc4-Mac-arm64.pkg - for Macs using Apple Silicon. This runs faster & is recommended for most users, but lacks support for a small number of file formats through Bio-Formats (particularly .czi with jpeg-xr compression).
  - To install: right-click and choose Open to install.
For Linux
- QuPath-v0.6.0-rc4-Linux.tar.xz - use chmod u+x /path/to/QuPath/bin/QuPath to make the launcher executable.

v0.6.0-rc3

2024-10-23T09:51:34Z

We're pleased to announce the third release candidate for QuPath v0.6.0!

This is a preview version for testing... released during the I2K workshops & just before the Virtual I2K event (28-30 October

We plan to have the final release in ~~October~~ November 2024.

If you try it out and find problems, please let us know via GitHub or the user forum.

There may be bugs!
Please don't use v0.6.0-rc3 for important work, and make sure you back up any projects that you open with it.
It is not recommended to switch between v0.5.x and v0.6.0-rcx for the same project.

Highlights

See v0.6.0-rc1and v0.6.0-rc2 for information about the previous release candidates.

The main changes in v0.6.0-rc3 are:

All new ImageJ script runner (replacing the old macro runner)
New extension to add a new Help → QuPath Tour command to learn the user interface
New extension to add support for Py4J

Note: Docs & other extensions (e.g. for StarDist) have not yet been updated for compatibility with this release candidate.
We plan to update them for the final release.

Note 2: For users of macOS Sequoia
Recent security changes in macOS Sequoia may block QuPath's installer.
This can be overcome through Apple Menu > System Settings > Privacy & Security - see this page from apple.com for details.
(We know it's annoying, but we don't currently have the means to make QuPath a 'signed' app to avoid this)

What to download

For Windows (two options, functionally the same)
- QuPath-v0.6.0-rc3-Windows.msi - if you want a standard Windows (local) installer
- QuPath-v0.6.0-rc3-Windows.zip - unzip it and double-click QuPath-v0.6.0-rc3.exe (no further installation needed)
For Mac (two options, depending upon processor)
- QuPath-v0.6.0-rc3-Mac-x64.pkg - for Macs with Intel Processors or Apple Silicon (M1/M2)
- QuPath-v0.6.0-rc3-Mac-arm64.pkg - for Macs using Apple Silicon. This runs faster & is recommended for most users, but lacks support for a small number of file formats through Bio-Formats (particularly .czi with jpeg-xr compression).
  - To install: right-click and choose Open to install.
For Linux
- QuPath-v0.6.0-rc3-Linux.tar.xz - use chmod u+x /path/to/QuPath/bin/QuPath to make the launcher executable.

v0.6.0-rc2

2024-09-20T16:06:12Z

We're pleased to announce the second release candidate for QuPath v0.6.0!

This is a preview version for testing. We plan to have the final release in October 2024.

If you try it out and find problems, please let us know via GitHub or the user forum.

There may be bugs!
Please don't use v0.6.0-rc2 for important work, and make sure you back up any projects that you open with it.
It is not recommended to switch between v0.5.x and v0.6.0-rcx for the same project.

Highlights

See v0.6.0-rc1 for information about the first release candidate.

The main changes in v0.6.0-rc2 are:

Much improved OME-Zarr support
- New File → Export images... → OME-Zarr command
- Convert images to ome.zarr from the command line via convert-ome
- Read and write metadata, such as pixel size and channel colors
- Read remote OME-Zarr images
The QuPath InstanSeg extension is now faster when detecting cells within large and complex regions of interest
QuPath now uses DeepJavaLibrary v0.30.0, which supports PyTorch 2.4.0 by default
- This is important if you want to add CUDA support on Windows or Linux - you'll need CUDA 12.4, or alternatively CUDA 12.1 with a launch script to request PyTorch 2.3.1

Note: Docs & other extensions (e.g. for StarDist) have not yet been updated for compatibility with this release candidate.
We plan to update them for the final release.

Note 2: For users of macOS Sequoia
Recent security changes in macOS Sequoia may block QuPath's installer.
This can be overcome through Apple Menu > System Settings > Privacy & Security - see this page from apple.com for details.
(We know it's annoying, but we don't currently have the means to make QuPath a 'signed' app to avoid this)

What to download

For Windows (two options, functionally the same)
- QuPath-v0.6.0-rc2-Windows.msi - if you want a standard Windows (local) installer
- QuPath-v0.6.0-rc2-Windows.zip - unzip it and double-click QuPath-v0.6.0-rc2.exe (no further installation needed)
For Mac (two options, depending upon processor)
- QuPath-v0.6.0-rc2-Mac-x64.pkg - for Macs with Intel Processors or Apple Silicon (M1/M2)
- QuPath-v0.6.0-rc2-Mac-arm64.pkg - for Macs using Apple Silicon. This runs faster & is recommended for most users, but lacks support for a small number of file formats through Bio-Formats (particularly .czi with jpeg-xr compression).
  - To install: right-click and choose Open to install.
For Linux
- QuPath-v0.6.0-rc2-Linux.tar.xz - use chmod u+x /path/to/QuPath/bin/QuPath to make the launcher executable.

v0.6.0-rc1

2024-09-13T16:07:25Z

We're pleased to announce the first release candidate for QuPath v0.6.0!

This is a preview version for testing. We plan to have the final release in October 2024.

If you try it out and find problems, please let us know via GitHub or the user forum.

There may be bugs!
Please don't use v0.6.0-rc1 for important work, and make sure you back up any projects that you open with it.
It is not recommended to switch between v0.5.x and v0.6.0-rc1 for the same project.

Highlights

There are lots of small and not-so-small changes listed in the Changelog.

But perhaps the biggest is that this release candidate introduces the QuPath InstanSeg extension to the world.

InstanSeg is a new, deep learning-based method for nucleus & cell segmentation that aims to be fast, accurate & easy to use.

We're working on more documentation, but for now see the extension repository for more info & links to two preprints that explain the method - both for brightfield and multiplexed images.

Note: Other extensions (e.g. for StarDist) have not been updated for compatibility with this release candidate.
We plan to update them for the final release.

What to download

For Windows (two options, functionally the same)
- QuPath-v0.6.0-rc1-Windows.msi - if you want a standard Windows (local) installer
- QuPath-v0.6.0-rc1-Windows.zip - unzip it and double-click QuPath-v0.6.0-rc1.exe (no further installation needed)
For Mac (two options, depending upon processor)
- QuPath-v0.6.0-rc1-Mac-x64.pkg - for Macs with Intel Processors or Apple Silicon (M1/M2)
- QuPath-v0.6.0-rc1-Mac-arm64.pkg - for Macs using Apple Silicon. This runs faster & is recommended for most users, but lacks support for a small number of file formats through Bio-Formats (particularly .czi with jpeg-xr compression).
  - To install: right-click and choose Open to install.
For Linux
- QuPath-v0.6.0-rc1-Linux.tar.xz - use chmod u+x /path/to/QuPath/bin/QuPath to make the launcher executable.

v0.5.1

2024-03-04T14:49:45Z

QuPath v0.5.1 is now available!

This is a minor update that is intended to be fully compatible with v0.5.0 while fixing bugs.

To see what it includes, check out the changelog here.

How to help

Please remember to cite the QuPath paper in any publications that use the software!

Please use the Scientific Community Image Forum for QuPath questions & discussions!

What to download

For Windows (two options, functionally the same)
- QuPath-v0.5.1-Windows.msi - if you want a standard Windows (local) installer
- QuPath-v0.5.1-Windows.zip - unzip it and double-click QuPath-v0.5.1.exe (no further installation needed)
For Mac (two options, depending upon processor)
- QuPath-v0.5.1-Mac-x64.pkg - for Macs with Intel Processors or Apple Silicon (M1/M2)
- QuPath-v0.5.1-Mac-arm64.pkg - for Macs using Apple Silicon. This runs faster, but lacks support for a small number of file formats through Bio-Formats (particularly .czi with jpeg-xr compression).
  - To install: right-click and choose Open to install.
For Linux
- QuPath-v0.5.1-Linux.tar.xz - use chmod u+x /path/to/QuPath/bin/QuPath to make the launcher executable.

v0.5.0

2023-12-01T16:35:54Z

QuPath v0.5.0 is now available!

This is a major update containing many improvements, new features and bug fixes. It is recommended that you do not mix projects between v0.5.0 and older versions.

To see what it includes, check out the changelog here.

How to help

Please remember to cite the QuPath paper in any publications that use the software!

Please use the Scientific Community Image Forum for QuPath questions & discussions!

What to download

For Windows (two options, functionally the same)
- QuPath-v0.5.0-Windows.msi - if you want a standard Windows (local) installer
- QuPath-v0.5.0-Windows.zip - unzip it and double-click QuPath-v0.5.0.exe (no further installation needed)
For Mac (two options, depending upon processor)
- QuPath-v0.5.0-Mac-x64.pkg - for Macs with Intel Processors or Apple Silicon (M1/M2)
- QuPath-v0.5.0-Mac-arm64.pkg - for Macs using Apple Silicon. This runs faster, but lacks support for a small number of file formats through Bio-Formats (particularly .czi with jpeg-xr compression).
  - To install: right-click and choose Open to install.
For Linux
- QuPath-v0.5.0-Linux.tar.xz - use chmod u+x /path/to/QuPath/bin/QuPath to make the launcher executable.