Local Thickness
 
Author: Bob Dougherty (rpd@optinav.com)  Orderd by by Karl-Heinz Kunzelmann.
Installation: Download LocalThickness_.jar to the Plugins folder and restart ImageJ.
Description: ImageJ plugin to compute the local thickness of a 3D image stack.  The distance map is formed as an itermediate result.
References: "A new method for the model-independent assessment of thickness in three-dimensional images" T. Hildebrand and P. Rüesgsegger, J. of Microscopy, 185 (1996) 67-75.
"New algorithms for Euclidean distance transformation on an n-dimensional digitized picture with applications," T. Saito and J. Toriwaki, Pattern Recognition 27 (1994) 1551-1565.
Documentation: LocalThicknessEd.pdf "Computing Local Thickness of 3D Structures with ImageJ," R.P. Dougherty and K-H Kunzelmann, Microscopy & Microanalysis 2007 Meeting August 5-9, 2007, Ft. Lauderdale, Florida
Usage: The work is divided into 4 stages: computation of the distance map by the Euclidean distance tranformation, deletion of some redundant points to create a partially-formed distance ridge, conducting a search to find the local thickness, and cleaning up the local thickness to remove voxel effects from the surface.  These steps can be requested all at once by choosing Plugins/LocalThickness/Local Thickness (complete process).  Alternatively, they can be done one at time by running Plugins/LocalThickness/Geometry to Distance Map, Plugins/LocalThickness/Distance Map to Distance Ridge, Plugins/LocalThickness/Distance Ridge to Local Thickness, and finally Plugins/LocalThickness/Local Thickness to Cleaned-Up Local Thickness. In the "all at once" mode, be sure to wait until the status line says something like "Local Thickness (complete process): 2.166 seconds" and the title of the output image stack is changed to the title of the input stack followed by "_LocThk"   It might be possible to confuse the code by clicking on widows or doing other things in ImageJ while the plugins are running.
History: Aug. 2006 Grande Custom ImageJ Plugin ordered
Sept.-Oct. 2006 Various steps and versions released to Prof. Dr. Kunzelmann
July 2007 Multi-threaded version to take advantage of multi-processor computers
Aug. 2007 Presentation at the Microscopy & Microanalysis Conference and public release
May 2008 Paper selected for the 2008 Macres Award for the Best Instrumentation or Software Paper presented at Microscopy & Microanalysis 2007
License:

Copyright (c) 2006, 2007 OptiNav, Inc.
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  • Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
  • Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
  • Neither the name of OptiNav, Inc. nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

ImageJ: ImageJ can be freely downloaded from the ImageJ web site.