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.


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QuickNII and VisuAlign are part of the QUINT workflow

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QuickNII is a stand-alone application for user-guided affine spatial registration (anchoring) of section images, typically high resolution histological images, to 3D reference atlas space. A key feature of the tool is its ability to generate user-defined cut planes through the atlas templates that match the orientation of the cutting plane of the 2D experimental images (atlas maps). The reference atlas is transformed to match anatomical landmarks in the corresponding experimental images. In this way, the spatial relationship between the experimental image and the 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. These propagations must be validated and saved by the user for each section, with application of fine positional adjustments as required. We recommend the use of VisuAlign to perform nonlinear adjustments after the QuickNII registration for an optimal fit.

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Figure from Bjerke et al. 2018. Front Neuroanat.