![]() V2.6 : bug fixes and improvements, new filters openGray and closeGray.V2.7 : new segmentation Iterative thresholding check for required libraries at startup 32-bits segmentation and labelling.V2.9 : new Results Tables for 3DManager.Macros functions to save results for 3D Manager. V3.0 : closest object in selection for 3D Manager.V3.1 : bug in colocalisation (rare objects configuration) + improved split + poles in ellipsoid fitting.V3.2 : improved watershed (especially for flat regions).V3.3 : new function closeResults saveResults 3DManager + exclude on edges.V3.4 : redesigned Watershed, Record Iterative Thresholding, Quantification in 32-bits images with NaN values.V3.5 : compatibility with ImageScience 3.0.V3.6 : bug fixes, new edge and symmetry filters, sync between 3D Viewer select object and 3DManager.V3.7 : bug fixes, new plugin exclude objects on borders.V3.82: compatibility with new version of 3D viewer, improvements and bug fixes.V3.83: New plugin Radial Distance Area Ratio (RDAR), Watershed improved.V3.9 : Display computing time and ETC for filters, new LooknFeel for Manager.New plugins MultiColoc, EVF radial analysis and density. V4.01: Redesigned code for 3D Objects and measurements new plugins and organisation.V4.01: Changed Value to Label for segmented objects.New method FillHoles in Binar圜loseLabels. V4.1.5: Bug fixes, seeds option for segmentation. ![]() Gilles and the developers of the following plugins : Sources available on Framagit (see Download). ![]() ( 2013) TANGO: A Generic Tool for High-throughput 3D Image Analysis for Studying Nuclear Organization. If you use the 3D suite for your publication, please cite : Sources are available on Framagit for core and plugins. For versions 2 and 3, the imagescience library is required : download here.ĭownload plugins : mcib3d_plugins-4.1.5.jar Java3D is also required, check that 3D Viewer is working.įrom version 3.83 and later, for ImageJ users the new version 4.0.1 of 3D Viewer is required (please remove the 3D Viewer plugin provided by ImageJ and replace it by this version, just unzip the file in the plugins directory). The various plugins will appear in the menu 3D of the plugins list.įor versions 2 and 3, you have also to manually download and copy into your plugins directory the imagescience.jar library from here. You can also install 3D ImageJ Suite manually (see download section) and unzip it in your plugins folder. For versions 2 and 3, the ImageScience update site must also be activated in Fiji. The Java8 update site must be activated in Fiji. Various tools are also available, especially to create 3D Shapes or Draw 3D contours as Rois.įrom version 2.7, 3D ImageJ Suite is available in Fiji as an update site. The 3D Manager interface acts a a manager for 3D objects, to perform measurements. Finally 3D spatial organisation can be assessed with plugins such as EVF Analysis or Spatial Statistics. Relationships between objects can also be studied with plugins such as distances or co-localisation. Custom segmentation plugins are also available for spots or nuclei (in culture cells images).Īnalysis to perform various 3D measurements of the objects, such as geometry, shape, or -intensity. For seeds-based detection watershed segmentation can be used. Labelling will detect the different objects in a binary image (see simple, hysteresis or iterative segmentation plugins). Thresholding will create a binary image and can be performed using Adjust/Threshold. Maps can also be created such as distance map to compute distance from all pixels to the border of the labelled objects. For labelled image close labels can help make objects shape more compact. Some filters (edge and symmetry or maxima finder) can help detect seeds for further segmentation (such as spot segmentation or watershed)īinary filters will improve thresholding or segmentation results such as fill holes or exclude objects on edges. Filters can be used to reduce noise (see median filter in 3D Fast Filters). This suite is composed of plugins to perform different tasks on image stacks :įilters for pre- and post-filtering. Ollion, Laboratoire Jean Perrin, Paris, France. You can contact me on image.sc many contributions from J. ![]() Thomas Boudier, Centrale Méditerranée, Nice Campus, France. The associated project for automation is available in TAPAS. ![]() The QAs are available on the image.sc forum. The associated video is available on YouTube. The pdf of the NEUBIAS academy presentation " Introduction to 3D Analysis with 3D ImageJ suite" is available : ( pdf). Updated contents from 3D Suite on ImageJ Documentation Website. This suite provides plugins to enhance 3D capabilities of ImageJ. ![]()
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