v0.1.2
Do you want to try out the latest features?
Click here for the latest milestone release.
Before you download QuPath from the links below...
- Don't forget to reference the Scientific Reports publication if you use QuPath in your research, see Citing QuPath
- For specific questions about using the software, see Google Groups
- For tips to get started, see the Step-by-step guides and tutorials on YouTube
- For the latest news, developments & future plans, see Pete's blog
- If you have trouble opening your whole slide images, see Supported image formats
This release contains many small-but-important fixes and updates requested over the past month.
Most noticeably, it is now possible to export annotation and detection measurements more easily from within scripts.
Additionally, this release adds a new command for detecting subcellular spots and clusters. This has been written in a particularly general way, so that it can be applied to up to 2 chromogenic stains (brightfield) or any number of fluorescence stains that QuPath can handle. Further testing is required and the command still subject to change... therefore feedback would be welcome if you find it useful.
Installation instructions for QuPath are here.
- Windows users download
QuPath-0.1.2.exeto install with administrator privileges - Windows users download
QuPath-0.1.2.zipto run without installation (just extract the zip files) - Mac users download
QuPath-0.1.2.dmg - Linux users download
QuPath-0.1.2.tar.gz
Finally, for anyone who writes code, there are several new methods available for scripting, and the ImageJ macro runner now has an experimental option for parallel processing.
For anyone interested in the broader principles of image analysis - especially (but not exclusively) when working with fluorescence data - I have also updated my free introduction to image analysis, in addition to making it open source and turning into a website. You can find it online here.
Changelog
- Saving measurement tables is now logged, and can be called from scripts
- New 'View -> Show slide label' option added to make labels easier to find
- Added 'Analyze -> Cell analysis -> Subcellular detection' command (still experimental, for early testing & feedback)
- Minor changes to display names of detection classifiers to match with OpenCV's names (functionality unaffected)
- Fixed bug that prevented images being opened if OpenSlide native libraries could not be found
- Fixed estimate of image size used when opening non-pyramidal images
- Fixed bug that prevented 3rd stain vector being set through the GUI if it was previously set to be the 'residual' stain, when image type is 'Brightfield (Other)'
- New scripting methods (e.g. setIntensityClassifications) to simplify (sub-)classifying cells according to staining intensity
- New 'getCellObjects' scripting method
- New, non-default PathClasses are now assigned a random color (rather than black)
- Modified default color for 'Stroma' classifications, to improve contrast
- Using PROJECT_BASE_DIR in a script now fails with an appropriate error when called without a corresponding project
- Added experimental guiscript option for running short GUI-oriented scripts in the JavaFX Platform thread (example)
- DialogHelperFX methods can now be called from any thread (not only the Platform thread)
- Improved number formatting within numeric fields
- ImageJ macro runner supports parallel processing (experimental)
- ImageJ macro runner now prompts to select all TMA cores if none are selected