Skip to content


Folders and files

Last commit message
Last commit date

Latest commit



42 Commits

Repository files navigation


Modified version of MultiStackRegistration, for use from scripts.



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.



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.



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


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

Other relevant on-line publications are available at

Additional help available at

Ancillary TurboReg_ plugin available at

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 ( ) and released into the public domain, so go by their ^^ guidelines for distribution, etc.


Modified version of MultiStackRegistration, for use from scripts.






No packages published