VisuAlign is a tool for applying user-guided nonlinear refinements (inplane) to an existing, affine 2D-to-3D registration (a compatible registration tool is offered at
While linear registration tools are vital in bringing experimental image data to standardized coordinate spaces, for precise quantitative analysis one has to address the residual anatomical variability among test subjects after registration. VisuAlign is a tool designed for this task.

Rodent atlas delineations provided with VisuAlign:
- Waxholm Space Atlas of the Sprague Dawley rat brain, versions 2 and 3 (at 39 μm resolution)
- Allen Mouse Brain Atlas reference atlas, CCFv3 (delineations from 2015 and 2017 at 25 μm resolution)

Output of VisuAlign can be directly used for numerical quantification with Nutil (
VisuAlign is available on GitHub under MIT license:

Download Now Download

OR   See All Files