Data integration tools

Morphology Alignment Tool

QuickNII

Software for 2D image registration to 3D atlas.

VisuAlign

Software for 2D image registration to 3D atlas.

voluba – Alignment of high-resolution volumes of interest

Using voluba, you can upload an image file to a private storage space and register it interactively to a reference space in your web browser. Currently, voluba supports the BigBrain model, Waxholm rat template and Allen mouse template as reference spaces. voluba is compatible with siibra-explorer, so you can directly inspect your aligned data superimposed with brain region maps and other datasets. You can also submit your anchoring result to EBRAINS curation support for sharing.

voluba-mriwarp – Aligning human MRI volumes to atlas space

voluba-mriwarp enables you to integrate human whole-brain MRI scans into the detailed anatomical context of the Human Brain Atlas on your local computer. The tool automatically performs registration based on predefined parameters. The results can be used to assign anatomical locations to brain regions of the atlas. To perform a more detailed analysis, you can export assignments to a PDF report together with linked features like receptor densities or brain connectivity.

WebAlign

EBRAINS users can create their own workspace for analysing 2D histological section images.In this space, the data can be uploaded and registered to a common reference atlas using the webAlign service. Several other tools are available as well that can be combined in different workflows for further analysis.

WebWarp

WebWarp is an online tool for nonlinear refinement of spatial registration of histological section images from rodent brains to reference 3D atlases. Webwarp is compatible with registration performed with the WebAlign tool. Different experimental datasets registered to the same reference atlas allows you to spatially integrate, analyse and navigate these datasets within a standardised coordinate system. The output of Webwarp can be used for analysis in the online QUINT workflow.