Data integration tools

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.

voluba-mriwarp is a desktop application that integrates whole brain T1-weighted MRI scans into the anatomical context of the Julich Brain Atlas. It incorporates all required components like skull stripping, registration to ICBM MNI152 2009c nonlinear asymmetric space, and detailed analysis with the siibra toolsuite. The corresponding functionalities are provided via open-source tools like HD-BET, ANTs and siibra-python. voluba-mriwarp is primarily designed for Windows 10 but can also be executed on Linux.

WebAlign is an online tool for spatial registration of histological section images from rodent brains to reference 3D atlases. 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 WebAlign can be used for analysis in the online QUINT workflow. WebAlign is available as an EBRAINS community app, accessible via the EBRAINS Collaboratory. For more information, see: https://wiki.ebrains.eu/bin/view/Collabs/image-registration-and-analysis-demo/

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.