Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool

Abstract

Modern high throughput brain wide profiling techniques for cells and their morphology, connectivity, and other properties, make the use of reference atlases with 3D coordinate frameworks essential. However, anatomical location of observations made in microscopic sectional images from rodent brains is typically determined by comparison with 2D anatomical reference atlases. A major challenge in this regard is that microscopic sections often are cut with orientations deviating from the standard planes used in the reference atlases, resulting in inaccuracies and a need for tedious correction steps. Overall, efficient tools for registration of large series of section images to reference atlases are currently not widely available. Here we present QuickNII, a stand-alone software tool for semi-automated affine spatial registration of sectional image data to a 3D reference atlas coordinate framework. A key feature in the tool is the capability to generate user defined cut planes through the reference atlas, matching the orientation of the cut plane of the sectional 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 distortions in the original experimental images. Following anchoring of a limited number of sections containing key landmarks, transformations are propagated across the entire series of sectional images to reduce the amount of manual steps required. By having coordinates assigned to the experimental images, further analysis of the distribution of features extracted from the images is greatly facilitated.

Defined astrocytic expression of human amyloid precursor protein in Tg2576 mouse brain

“…This link to the virtual microscopy viewer Navigator3 allows interactive zooming and panning of high‐resolution images. The series has been registered to the Allen brain mouse atlas available from: http://connectivity.brain-map.org/) using the QuickNII software tool (Puchades, Csucs, Ledergerber, Leergaard, & Bjaalie, ). This link shows the same sections with their custom atlas overlay, adjusted for angle deviations.…”

Experimental and computational study on motor control and recovery after stroke: towards a constructive loop between experimental and virtual embodied neuroscience

“…3, panel B) was spatially translated to the Allen Common Coordinate Framework (CCF, v3, 2015; (Oh et al, 2014)). Since the CCF lacks stereotactic skull landmarks, these were introduced by spatially co-registering all diagrams from a standard stereotaxic mouse brain atlas (Franklin et al, 2008) to the CCF coordinate space with affine transformations defined using the QuickNii tool (Puchades et al, 2019). Using bregma and the sagittal suture as a reference, the four corners of the downsampled 128×128 pixels field-of-view of the recorded images were positioned in CCF, taking the 5 degree lateral tilt of the camera view into account.…”

Navigating the Murine Brain: Toward Best Practices for Determining and Documenting Neuroanatomical Locations in Experimental Studies

“…We used the Human Brain Project software tool QuickNII ( Puchades et al, 2017 ) to register single or serial section images to a 3-D reference atlas template by positioning and slicing the atlas in user-defined planes of sectioning. The QuickNII tool is bundled either with the Waxholm Space atlas of the Sprague-Dawley rat brain (version 2, Papp et al, 2014 ; Kjonigsen et al, 2015 ) 1 or the Allen Mouse Common Coordinate Framework (version 3, downloaded June 17, 2016; Oh et al, 2014 ) 2 .…”

“…Electron microscopy data showing parvalbumin positive neurons in the rat medial entorhinal cortex ( Berggaard et al, 2018 ), was generously made available to the present study by Nina Berggaard (Norwegian University of Science and Technology, Norway). In vivo electrophysiology recording data from the rat hippocampal region were produced by Debora Ledergerber (Norwegian Institute of Science and Technology, Norway; Puchades et al, 2017 ). Immunohistological material showing parvalbumin positive neurons across a horizontally cut hemisphere ( Boccara et al, 2015 ) was shared through the Human Brain Project by Menno P. Witter (Norwegian University of Science and Technology, Norway).…”

“…Building upon a new generation of 3-D brain atlases, the EU Human Brain Project develops tools and workflows for integrating, sharing and analyzing brain data that have been defined within a common anatomical framework. The project has established workflows for mapping diverse types of murine and human image data to common spatial reference atlas frameworks, building on tools for spatial registration of two-dimensional (2-D) histological image data to a 3-D reference volume ( Papp et al, 2016 ; Puchades et al, 2017 ), and use of organized collections of metadata describing basic features of data, including descriptions of the anatomical location from which the data originate. These tools and workflows are currently routinely used in the Human Brain Project, but their wider adoption outside the project requires a better understanding of the presently used approaches for describing and documenting neuroanatomical location in experimental studies of murine brains.…”