Integrate data into a brain atlas

QuickNII is a stand-alone tool for user guided affine spatial registration (anchoring) of sectional image data, typically high resolution microscopic images, to a 3D reference atlas space. QuickNII is one of several tools developed by the Human Brain Project (HBP) with the aim of facilitating brain atlas based analysis and integration of experimental data and knowledge about the human and rodent brain. A key feature in the tool is the capability to generate user defined cut planes through the atlas templates, matching the orientation of the cut plane of the 2D experimental image data. The reference atlas is transformed to match anatomical landmarks in the corresponding experimental images. In this way, the spatial relationship between experimental image and atlas is defined, without introducing transformations in the original experimental images. Following anchoring of a limited number of sections containing key landmarks, transformations are propagated across the entire series of images to reduce the amount of manual steps required.

VisuAlign is one of several tools developed by the Human Brain Project (HBP) with the aim of facilitating 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.

voluba is an interactive web application which allows anchoring of volumetric image data to large reference image volumes at microscopic resolutions. The application is implemented around a 3D image viewer, and provides multiple reference brain templates as anchoring targets. Users can upload data from their own imaging experiments to a private working space to perform the alignment. The anchoring process includes interactive manipulation of image position, scale, and orientation, flipping of coordinate axes, as well as entering of anatomical point landmark pairs in 3D. From given landmarks, voluba calculates a 4x4 transformation matrix between the source and target image volumes. The transformation can be chosen with different degrees of freedom, including rigid, similarity and affine types. The result can be downloaded in a predefined json format which includes unique coordinate space identifiers. Furthermore, the aligned volume can be opened in the interactive atlas viewer siibra-explorer to link it to brain regions and related informations of the EBRAINS reference atlases.