User Tools

Site Tools


plugin:filter:3d_filters:start

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

plugin:filter:3d_filters:start [2019/01/23 04:53]
plugin:filter:3d_filters:start [2019/04/12 11:13] (current)
Line 1: Line 1:
 +
 +===== 3D Filters =====
 +3D filtering using ellipsoidal neighbourhood.
 +
 +===== Author =====
 +Thomas Boudier
 +
 +Matthias Labschütz contributed a fast version for isotropic kernels (for min, max and mean filtering)
 +
 +===== Description =====
 +
 +The plugin performs 3D filtering on image stacks. The kernel is ellipsoidal,​ you can then select three radii for X, Y, and Z. Note that the plugin uses parallel implementation,​ and a very fast version using //rolling ball// algorithm is used for isotropic kernel (all three radii equal). ​
 +
 +The 3D filters mean, median, variance, min and max are implemented in ImageJ since version 1.47.
 +
 +
 +Available filters :
 +
 +* Mean and variance filtering
 +
 +* Minimum and maximum filtering
 +
 +* Local maxima
 +
 +* TopHat transform (to detect spots-like objects)
 +
 +* Sobel (simple edge detection)
 +
 +* Adaptive Nagao-like ​
 +
 +{{:​plugin:​filter:​3d_filters:​3dvariance.png|}}
 +
 +3D variance
 +
 +
 +
 +
 +===== Download =====
 +For details go to the [[plugin:​stacks:​3d_ij_suite:​start|3D ImageJ Suite]].
 +
 +If you want fast version for non-isotropic kernels, you are invited to install the [[plugin:​filter:​3d_filters_with_jni:​start|JNI version]]. ​
 +
 +===== Citation =====
 +When using the //3D Filters// plugin 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]]).
 +
 +
 +===== Changelog =====
 +
 +  * 22/06/2011 : Parallelization updated
 +  * 22/10/2012 : bug fixed for filters3D with 32-bits images ​
 +  * 28/05/2013 : new filters Open and Close
 +  * 10/04/2017 : new timer for computing time
 +
 +===== Known Bugs =====
 +
 +  * ij1.47d : Bug in Color/​Split,​ the resulting stacks have incorrect bitdepth  ​