Releases: qupath/qupath
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.
v0.5.0-rc2 (Release Candidate)
QuPath v0.5.0-rc2 is now available!
This is a release candidate, available for testing before the final v0.5.0 release.
This is a major update compared to v0.4.4. It is recommended that you do not mix projects between v0.4 and v0.5.
To see what it includes, check out the changelog here.
Important - v0.5.0-rc2 is not a final version!
It's available for early feedback, to help us find & fix any bugs before the final release.
Release candidates are not intended for final analysis.
The full v0.5.0 release is expected to follow within a few weeks.
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-rc2-Windows.msi- if you want a standard Windows (local) installerQuPath-v0.5.0-rc2-Windows.zip- unzip it and double-click QuPath-v0.5.0-rc2.exe (no further installation needed)
- For Mac (two options, depending upon processor)
QuPath-v0.5.0-rc2-Mac-x64.pkg- for Macs with Intel Processors or Apple Silicon (M1/M2)QuPath-v0.5.0-rc2-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-rc2-Linux.tar.xz- usechmod u+x /path/to/QuPath/bin/QuPathto make the launcher executable.
v0.5.0-rc1 (Release Candidate)
QuPath v0.5.0-rc1 is now available!
This is a release candidate, available for testing before the final v0.5.0 release.
This is a major update compared to v0.4.4. It is recommended not to mix projects between v0.4 and v0.5.
To see what it includes, check out the changelog here.
Important - v0.5.0-rc1 is not a final version!
It's available for early feedback and the QuPath workshop in San Diego, October 2023.
The full v0.5.0 release is expected to follow within a few weeks.
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-rc1-Windows.msi- if you want a standard Windows (local) installerQuPath-v0.5.0-rc1-Windows.zip- unzip it and double-click QuPath-v0.5.0-rc1.exe (no further installation needed)
- For Mac (two options, depending upon processor)
QuPath-v0.5.0-rc1-Mac-x64.pkg- for Macs with Intel Processors or Apple Silicon (M1/M2)QuPath-v0.5.0-rc1-Mac-arm64.pkg- for Macs using Apple Silicon. This runs faster, but lacks support for some 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-rc1-Linux.tar.xz- usechmod u+x /path/to/QuPath/bin/QuPathto make the launcher executable.
v0.4.4
QuPath v0.4.4 is now available!
This is a minor update, that aims to be compatible with earlier v0.4.x versions while fixing one bug.
To date, the bug has only been reported to affect a small number of people using the QuPath ABBA extension. But because it could impact analysis results in rare circumstances, it is recommended that users of QuPath v0.4.0 - v0.4.3 update to v0.4.4.
There is a full description at #1306
QuPath Course in San Diego - and v0.5.0
We're happy to announced there will be a QuPath Training Course in San Diego from October 9-11, 2023.
This will be followed by the Quantitative Bioimaging Society's workshop on Muliplex Image Analysis.
We are planning to release QuPath v0.5.0 shortly before these events, as the next major release of the software.
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-0.4.4-Windows.msi- if you want a standard Windows (local) installerQuPath-0.4.4-Windows.zip- unzip it and double-click QuPath-0.4.4.exe (no further installation needed)
- For Mac (two options, depending upon processor)
QuPath-0.4.4-Mac.pkg- for Macs with Intel Processors or Apple Silicon (M1/M2)QuPath-0.4.4-Mac-arm64.pkg- for Macs using Apple Silicon only (experimental). This runs much faster, but you'll need to install OpenSlide separately.- To install: right-click and choose Open to install. Note that this will try to install to /Applications/QuPath.app - if you have an older version at that location that you want to keep, you should rename it before installation.
- For Linux
QuPath-0.4.4-Linux.tar.xz- usechmod u+x /path/to/QuPath/bin/QuPathto make the launcher executable. If you suffer pixman problems, you might find the alternative bash script/path/to/QuPath/bin/QuPath.shbetter for launching the software.
v0.4.3
QuPath v0.4.3 is now available!
This is a minor update, that aims to be compatible with earlier v0.4.x versions while fixing bugs.
It also updates to Bio-Formats 6.12.0. This adds some additional fixes related to reading/writing images, and makes it possible for QuPath to support memoization again.
For more details about how memoization can speed up reading some images, and how to turn on the feature, see #1236
- See the v0.4.0 announcement for more details of the latest features and improvements
- See the changelog for a record of what extra fixes are in v0.4.3
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-0.4.3-Windows.msi- if you want a standard Windows (local) installerQuPath-0.4.3-Windows.zip- unzip it and double-click QuPath-0.4.3.exe (no further installation needed)
- For Mac (two options, depending upon processor)
QuPath-0.4.3-Mac.pkg- for Macs with Intel Processors or Apple Silicon (M1/M2)QuPath-0.4.3-Mac-arm64.pkg- for Macs using Apple Silicon only (experimental). This runs much faster, but you'll need to install OpenSlide separately.- To install: right-click and choose Open to install. Note that this will try to install to /Applications/QuPath.app - if you have an older version at that location that you want to keep, you should rename it before installation.
- For Linux
QuPath-0.4.3-Linux.tar.xz- usechmod u+x /path/to/QuPath/bin/QuPathto make the launcher executable. If you suffer pixman problems, you might find the alternative bash script/path/to/QuPath/bin/QuPath.shbetter for launching the software.
v0.4.2
QuPath v0.4.2 is now available!
This is a minor update, that aims to be compatible with v0.4.0 and v0.4.1 while fixing bugs.
- See the v0.4.0 announcement for more details of the latest features and improvements
- See the changelog for a record of what extra fixes are in v0.4.2
The main fix is in v0.4.2 to to point annotations, which couldn't have classifications assigned in v0.4.1 without throwing an error.
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-0.4.2-Windows.msi- if you want a standard Windows (local) installerQuPath-0.4.2-Windows.zip- unzip it and double-click QuPath-0.4.2.exe (no further installation needed)
- For Mac (two options, depending upon processor)
QuPath-0.4.2-Mac.pkg- for Macs with Intel Processors or Apple Silicon (M1/M2)QuPath-0.4.2-Mac-arm64.pkg- for Macs using Apple Silicon only (experimental). This runs much faster, but you'll need to install OpenSlide separately.- To install: right-click and choose Open to install. Note that this will try to install to /Applications/QuPath.app - if you have an older version at that location that you want to keep, you should rename it before installation.
- For Linux
QuPath-0.4.2-Linux.tar.xz- usechmod u+x /path/to/QuPath/bin/QuPathto make the launcher executable. If you suffer pixman problems, you might find the alternative bash script/path/to/QuPath/bin/QuPath.shbetter for launching the software.
v0.4.1
QuPath v0.4.1 is now available!
This is a minor update, that aims to be compatible with v0.4.0 while fixing bugs.
- See the v0.4.0 announcement for more details of the latest features and improvements.
- See the changelog for a record of what extra fixes are in v0.4.1
The most annoying bug by far is the one that broke the update message - so QuPath v0.4.0 sadly can't tell anyone that v0.4.1 is available. So ideally everyone on v0.4.0 would switch to v0.4.1 and we can put that little issue behind us.
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-0.4.1-Windows.msi- if you want a standard Windows (local) installerQuPath-0.4.1-Windows.zip- unzip it and double-click QuPath-0.4.1.exe (no further installation needed)
- For Mac (two options, depending upon processor)
QuPath-0.4.1-Mac.pkg- for Macs with Intel Processors or Apple Silicon (M1/M2)QuPath-0.4.1-Mac-arm64.pkg- for Macs using Apple Silicon only (experimental). This runs much faster, but you'll need to install OpenSlide separately.- To install: right-click and choose Open to install. Note that this will try to install to /Applications/QuPath.app - if you have an older version at that location that you want to keep, you should rename it before installation.
- For Linux
QuPath-0.4.1-Linux.tar.xz- usechmod u+x /path/to/QuPath/bin/QuPathto make the launcher executable. If you suffer pixman problems, you might find the alternative bash script/path/to/QuPath/bin/QuPath.shbetter for launching the software.