The three image series (hAPP, pan-Aβ and pE-Aβ) were aligned to reference atlas space with the QuickNII atlasing tool (Figure 2 ; Puchades et al., 2019 (link)). This open access software allows assignment of spatial location to serial brain section images. The reference atlases available in the tool are the Waxholm Space Rat Atlas for rat data (Papp et al., 2014 (link); Kjonigsen et al., 2015 (link)) and the Allen Mouse Brain Atlas for mouse data (© 2004 Allen Institute for Brain Science. Allen Mouse Brain Atlas. Available from: http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2015/ ) (Lein et al., 2007 (link); Oh et al., 2014 (link)).
Within QuickNII, the volumetric brain reference atlases are used to generate customised atlas maps that match the spatial orientation and proportions of the experimental sections. In the software, the location is defined by superimposing the reference atlas onto the section images in a process termed “anchoring.” In “anchoring” the cutting angle of the reference atlas is adjusted to match the plane of the sections, with the position of each section identified prior to a manual adaptation of each atlas image to match the section images using affine transformations. Anchoring of a series of, e.g., 100 sections from an animal, typically takes 2–6 h, depending on the quality of the sections in the series (distorted sections are more difficult to anchor).
The QuickNII software is available at NITRC4 through the HBP1.
Within QuickNII, the volumetric brain reference atlases are used to generate customised atlas maps that match the spatial orientation and proportions of the experimental sections. In the software, the location is defined by superimposing the reference atlas onto the section images in a process termed “anchoring.” In “anchoring” the cutting angle of the reference atlas is adjusted to match the plane of the sections, with the position of each section identified prior to a manual adaptation of each atlas image to match the section images using affine transformations. Anchoring of a series of, e.g., 100 sections from an animal, typically takes 2–6 h, depending on the quality of the sections in the series (distorted sections are more difficult to anchor).
The QuickNII software is available at NITRC
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