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added base ROI3DZShape / ROI3DBoxShape abstract classes for easier 3D ROI implementation added ROI2DShape getMinZ()/getMaxZ() methods for easier display evolution ROI3DStackEllipse, ROI3DStackRectangle and ROI3DStackPolygon are now deprecated added new 3D ROIs ROI3DRectangle, ROI3DCylinder and ROI3DFlatPolygon ROIs classes * fixed links to LICENSE, CHANGELOG and README + tweaked About to redirect to the README. * allow illegal-access with Java 16 or above * fixed possible death locks on starting (happen only with certain OpenJDK and on Linux) upgraded JOAMP / JOGL library to vrsion 2.4.0-rc (fix osx crash with VTK) upgraded VTK / 3D visualization library to version 8.0.1 added new 3D ROIs Rectangle3D, Cylinder3D and FlatPolygon3D which are Z extended version of ROI2DRectangle, ROI2DEllipse and ROI2DPolygon fixed images grouping (could group image of different type or dimension) * bit of refactoring / cleanup in project structure (moved all package.html file to 'javadoc' folder) * deprecated all illegal reflective access methods added new VtkArrow/Cylinder/PlaneObject classes for easy drawing of these primitives.

Still need some work to allow the image cache engine to work with Java 17 * improved Java 17 compatibility (replacing illegal reflective access where possible) * fixed ImageJ / Icy image conversion switch * switch dataset to 'virtual' state asynchronously (as it can takes age to do so) small optimization on 'Erosion' / 'Watershed' process time improved histogram info display to remain visible even when moving bounds fixed histogram log/linear display state restoration fixed a minor viewer toolbar refresh bug when switching rendering mode fixed loading non image files from Open command with 'All files' filter selected improved 'InterruptedException' throw / propagation and handling removed IcySecurityManager (deprecated with Java 14 or >) added ClassPatcher.getField(.) and tFieldPublic(.) methods fixed a small bug with puteWatershedSeparation(.) added Cache.clean() and Cache.isEmpty() methods removed Cache.isEnabled() method (higher level now) better handling of volatile image on loading process reworked image cache so it does not anymore require usage of illegal reflection implemented proper ColorSpace sharing on Ic圜olorModel (not anymore using illegal reflection) fixed exe launcher to accept Java 12 or above added general 'interruptible' background process actions re-introduced library path patching for Java version supporting it (still marked as deprecated but better to keep it when supported) fixed and improved automatic bug report plugin detection OSX: removed automatic native library signature image cache can now be initialized and shutdown at runtime (better performance and better memory usage) added current image name in viewer title Plugin citation: see plugin documentation on the Icy website and/or contact the authors. (2012) Icy: an open bioimage informatics platform for extended reproducible research, (), 9, pp. Please cite Icy and the Icy plugins you used in your scientific publications.

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Have a look at our training material page, our contributing guide and code of conduct, and at our blog posts to get started with the Icy software. Source code of Icy plugins developed by the Bioimage Analysist Unit: Documentation Icy is coded in Java and uses a Maven project environment. Users can process images via its rich graphical user interface, or via scripting (in Javascript), graphical programming using the Protocols tool and development of Java plugins. Icy contains state-of-the-art as well as cutting edge image processing tools.

Its kernel and main plugins are developed by the Biological Image Analysis unit at Institut Pasteur.

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It is a modular software composed of a kernel and plugins.

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Icy is free and open source ( license GPLv3). Icy is a software to do image analysis, and is mainly oriented toward the analysis of biological images.

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