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Atlas Toolkit

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The Atlas Toolkit plugin is a collection of tools developed to achieve group-wise elastic registration of 3D objects by decomposing the alignment problem into a sequence of orthogonal 2D elastic registrations, for which each object is registered to every other. These 2D elastic registrations are powered by the BUnwarpJ plugin, and registration is guided by the gross morphology of the corresponding 3D objects, which can be defined using the Segmentation Editor plugin.

Installation of the plugin

The plugin can be quickly installed via the project’s update site. Please refer to the tutorial on how to add our update site to your Fiji installation. Our update site has the following URL:

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What’s in the toolkit?

Atlas Toolkit includes a number of different tools to help building atlases. Many of these will be of limited use/interest.

For those interested in 3D image registration, the most important tools will be Label Registration 3D and Apply Label Registration.

The complete list of tools is as follows:

  • Extract Nuclear Signal
  • Project to Segment Label
  • Merge Registered Volumes
  • Sample Volumes for Clustering
  • Cluster Viewer

Label Registration 3D

Video demonstration

The following screencast demonstrates Label Registration 3D in use.


Please cite the following original research article in which the Atlas Toolkit is described:



This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation (

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.