Stack Manipulation

Stack manipulation (ImageJ)
Author various (see below)
Maintainer Jean-Yves Tinevez (tinevez@mpi-cbg.de)
File Stack_Manipulation.jar
Source on GitHub
Latest version 27 December 2011
Development status stable, not active



Content and purpose

This package regroups various "small" plugins dedicated to the manipulation of stacks, allowing to sort them, combine them, etc... As they are more of a utility package, they all can be found in the Image  ▶ Stacks  ▶ Tools menu, next to the ones provided by bare ImageJ.


What they do is pretty much summarized by the following diagram, taken from the MBF ImageJ webpage.

Stack Manipulation.jpg


  • The Grouped ZProjector acts a bit like the Substack Maker, for it allows to reduce the number of frame within a stack. But rather than taking a slice every certain step, it combines a group of slices and project them on a single slice. The size of the groups is configurable, and must be a divisor of the total number of slice.


  • The Slice Keeper does the opposite that of Slice Remover. Instead of removing every nth slice in a stack, it creates a new stack by only keeping every nth slice from the original stack.



Author and licenses

We list here the authors for each part of this package, with corresponding licenses when relevant.

DeInterleave

By Tony Collins.


Stack Splitter

By Patrick Kelly, Greg Joss & Bob Cunningham. Last revision: 30 April 2003.


Stack Sorter

Taken from Bob Dougherty Stack_Sorter plugin (optinav website). Version 10: 11/18/2005.

License:

Copyright (c) 2002, 2005, 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 * 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.



Interleave

By Tony Collins.


Slice Remover

This command lets you remove multiple slices in one go. You can specify a start slice, and end slice and an increment (i.e. start=1, end=5, increment=2 will remove the slices 1, 3 and 5). Warning: The Slice Remover treats hyperstacks as if they were converted via Image  ▶ Hyperstacks  ▶ Hyperstack to Stack first.

Original code by Wayne Rasband.

Slice Keeper

By Tony Collins, initially part of his wonderful MBF Plugins Collection package. Tony mentioned credit should go to Wayne Rasband, for the initial code is his work.