VisuAlign

Fine-tune image registration using VisuAlign and the QUINT workflow

VisuAlign is one of several tools EBRAINS provides for brain atlas-based analysis and integration of experimental data and knowledge about the human and rodent brain. VisuAlign is a tool for applying user-guided nonlinear refinements (inplane) to an existing, affine 2D-to-3D registration, such as created using QuickNII.

While linear registration tools are vital in bringing experimental image data to standardised coordinate spaces, one has to address the residual anatomical variability among test subjects after registration for precise quantitative analysis. 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, 3, and 4 (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.

Use QuickNII and VisuAlign for:

• Identification of brain regions in histological brain section image series.
• Mapping the position of 3D reconstructed neurons.
• Cell count analysis using the QUINT workflow.

Outputs from these tools are customised atlas maps and image coordinates for each section, which enables quantitative spatial and atlas-based analyses, such as the QUINT workflow.