MultiStackRegistration

Modified version of MultiStackRegistration, for use from scripts.

Authors

• Brad Busse (Designer, Developer, - v 1.45)
  • [email protected]
• Kota Miura (Minor upgrades, v1.46)
  • Mavenized, Scripting enabled, bug fixing.
  • [email protected]

Installation

Please add the plugin "MultistackReg" using Update Sites function in Fiji.

• briefly, [help > Update...], then in the Updater window, click "Manage Update Site", and tick "MultiStackReg" (also tick "BIG_EPFL" for the dependency) - close the window, click "Apply Changes". When downloading is done, please restart Fiji.

Dependencies

• ImageJ
  • http://imagej.org
• TurboReg
  • http://bigwww.epfl.ch/thevenaz/turboreg/
  • TurboReg is included in the UpdateSite package from "BIG_EPFL", so please simply add the site to your Fiji installation.

Usage

Welcome to MultiStackReg v1.5!

This plugin has three modes of use:

1. Align a single stack of images
2. Align a stack to another stack
3. Load a previously created transformation file

To align a single stack:

Choose the image to be aligned in the Stack 1 dropdown box. Leave 'Align' in the Action 1 box.

To align two stacks:

Place the reference stack in Stack 1's box, and the stack to be aligned in Stack 2's box. Select 'Use as Reference' as Action 1 and 'Align to First Stack' as Action 2.

To load a transformation file:

Place the stack to be aligned in either stack box, choose 'Load Transformation File' in its Action dropdown box. The File field can be used as a shortcut to avoid having to select the matrix manually.

Javadoc

http://wiki.cmci.info/javaapi/multiStackReg_/

Forum

See the thread below in the Forum for discussions, macro usages, and Q&As.

https://forum.image.sc/t/multistackreg-macro/174

Credits:

This work is based on the following paper:

P. Thévenaz, U.E. Ruttimann, M. Unser
A Pyramid Approach to Subpixel Registration Based on Intensity
IEEE Transactions on Image Processing
vol. 7, no. 1, pp. 27-41, January 1998.

This paper is available on-line at

• http://bigwww.epfl.ch/publications/thevenaz9801.html

Other relevant on-line publications are available at

• http://bigwww.epfl.ch/publications/

Additional help available at

• http://bigwww.epfl.ch/thevenaz/stackreg/

Ancillary TurboReg_ plugin available at

• http://bigwww.epfl.ch/thevenaz/turboreg/

You'll be free to use this software for research purposes, but you should not redistribute it without our consent. In addition, we expect you to include a citation or acknowledgment whenever you present or publish results that are based on it.

A few changes (loadTransform, appendTransform, multi stack support) to support load/save functionality and multiple stacks were added by Brad Busse ( [email protected] ) and released into the public domain, so go by their ^^ guidelines for distribution, etc.