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