Releases: qupath/qupath
v0.7.0
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 https://github.com/qup...
Contributors
Assets 7
v0.7.0-rc1
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) installerQuPath-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- usechmod u+x /path/to/QuPath/bin/QuPathto make the launcher executable.
v0.6.0
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) installerQuPath-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
v0.6.0-rc5
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
-sparameter (#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) installerQuPath-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- usechmod u+x /path/to/QuPath/bin/QuPathto make the launcher executable.
v0.6.0-rc4
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) installerQuPath-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- usechmod u+x /path/to/QuPath/bin/QuPathto make the launcher executable.
v0.6.0-rc3
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) installerQuPath-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- usechmod u+x /path/to/QuPath/bin/QuPathto make the launcher executable.
v0.6.0-rc2
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) installerQuPath-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- usechmod u+x /path/to/QuPath/bin/QuPathto make the launcher executable.
v0.6.0-rc1
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) installerQuPath-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- usechmod u+x /path/to/QuPath/bin/QuPathto make the launcher executable.
v0.5.1
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) installerQuPath-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- usechmod u+x /path/to/QuPath/bin/QuPathto make the launcher executable.
v0.5.0
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) installerQuPath-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- usechmod u+x /path/to/QuPath/bin/QuPathto make the launcher executable.