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voluba – Interactive registration of high-resolution volumes to 3D reference atlases

A common problem in high-resolution brain atlasing is spatial anchoring of volumes of interest from imaging experiments into the anatomical context of an ultrahigh-resolution reference model like BigBrain. This process requires efficient 3D interaction with image volumes at the Terabyte scale. We developed the interactive volumetric alignment tool voluba, which is implemented as a web service and offers an intuitive interactive workflow:

Select reference space and input volume
Choose between BigBrain, Allen mouse or Waxholm rat reference volumes, and upload your own input image after authenticating via EBRAINS or ORCID.

Adjust the appearance of the input image
Customize contrast, brightness, colormaps, and intensity thresholds of the input image for optimal visualization.

Interactive Alignment
Manipulate position and orientation of the input volume using the mouse pointer and adjust global parameters including voxel scaling and axis orientations to obtain a 3D similarity transformation.

Refine With 3D Landmarks
Refine the alignment using interactive annotation of 3D landmark pairs to recalculate the transformation, with additional degrees of freedom including shearing.

    Use The Results
  • Save and reimport transformation and landmarks
  • Import the result in other tools, such as ANTs
  • Share a private URL to the anchored volume
  • Open the anchored volume in the 3D atlas viewer siibra-explorer

voluba was developed at the Institute of Neuroscience and Medicine (INM-1) at Forschungszentrum Jülich and is available under the Apache2 license and received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3).