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plugin:analysis:3d_analysis:start [2019/01/23 04:54]
plugin:analysis:3d_analysis:start [2019/08/30 03:25] (current)
tboudier [Description]
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 +
 +===== 3D Analysis ​ =====
 +Various plugins for analysis of 3D images and objects.
 +
 +===== Author =====
 +Thomas Boudier
 +
 +===== Description =====
 +A plugin for 3D **Radial Distribution** of voxel values inside a sphere is available, select first a position with the point tool. If you compute the EVF (Eroded Volume Fraction = normalised Euclidean Distance Transform) you can use **EVF Distribution** to compute information in growing layers of equal volumes.
 +
 +You can compute **co-localisation** between labelled objects in two images using the [[plugin:​analysis:​details_about_multi-colocalisation_analysis:​start|MultiColoc]] plugin.  ​
 +
 +3D **segmentation** and labelling algorithms are available in [[plugin:​segmentation:​3d_spots_segmentation:​start|3D Segmentation]]. ​
 +
 +A plugin to **remove objects on borders** of the image (X, Y and Z) is available, and could be used before analysis. ​
 +
 +The following plugins work on 3D images of labelled objects (the value of voxel is the numbering of object as in count masks) :
 +
 +  * 3D **Geometrical** measurements (volume, surface, ...) for each labelled object.
 +  * 3D **Centroid**,​ to compute centroids of labelled objects.
 +  * 3D **Intensity** measurements (mean, integrated density, ...) in a opened image for each labelled object.
 +  * 3D **Shape** measurements (compactness,​ elongation, ...) for each labelled object. ​
 +  * 3D **Mesh** Measurements after triangulation (see [[http://​3dviewer.neurofly.de/​|3D Viewer]] for surface mesh computation).
 +  * 3D fitting by an **ellipsoid** and main direction computation ([[tutorial:​plugins:​3d_ellipsoid|details here]]).
 +  * 3D **convex hull** (see [[http://​rsbweb.nih.gov/​ij/​plugins/​3d-convex-hull/​index.html]]).
 +  * 3D Radial Distance Area Ratio ([[plugin:​analysis:​3d_radial_distance_area_ratio_rdar_:​|RDAR]])
 +  * 3D **Density**,​ to compute density of dots, based on closest distance analysis ([[plugin:​analysis:​density_2d_3d:​start|details here]]).
 +
 +
 +
 +
 +
 +
 +===== Download =====
 +For details go to the [[plugin:​stacks:​3d_ij_suite:​start|3D ImageJ Suite]].
 +
 +===== Citation =====
 +When using the //3D Analysis// plugins for publication,​ please refer to :
 +
 +J. Ollion, J. Cochennec, F. Loll, C. Escudé, T. Boudier. (**2013**) TANGO: A Generic Tool for High-throughput 3D Image Analysis for Studying Nuclear Organization. //​Bioinformatics//​ 2013 Jul 15;​29(14):​1840-1. [[http://​dx.doi.org/​10.1093/​bioinformatics/​btt276|doi]]
 +
 +===== License =====
 +GPL distribution (see [[http://​www.cecill.info/​index.en.html|license]]). Sources for plugins are available freely. Sources for core are available on request. ​
 +