Three-Dimensional Histology Volume Reconstruction of Axonal Tract Tracing Data: Exploring Topographical Organization in Subcortical Projections from Rat Barrel Cortex

Abstract

Topographical organization is a hallmark of the mammalian brain, and the spatial organization of axonal connections in different brain regions provides a structural framework accommodating specific patterns of neural activity. The presence, amount, and spatial distribution of axonal connections are typically studied in tract tracing experiments in which axons or neurons are labeled and examined in histological sections. Three-dimensional (3-D) reconstruction techniques are used to achieve more complete visualization and improved understanding of complex topographical relationships. 3-D reconstruction approaches based on manually or semi-automatically recorded spatial points representing axonal labeling have been successfully applied for investigation of smaller brain regions, but are not practically feasible for whole-brain analysis of multiple regions. We here reconstruct serial histological images from four whole brains (originally acquired for conventional microscopic analysis) into volumetric images that are spatially registered to a 3-D atlas template. The aims were firstly to evaluate the quality of the 3-D reconstructions and the usefulness of the approach, and secondly to investigate axonal projection patterns and topographical organization in rat corticostriatal and corticothalamic pathways. We demonstrate that even with the limitations of the original routine histological material, the 3-D reconstructed volumetric images allow efficient visualization of tracer injection sites and axonal labeling, facilitating detection of spatial distributions and across-case comparisons. Our results further show that clusters of S1 corticostriatal and corticothalamic projections are distributed within narrow, elongated or spherical subspaces extending across the entire striatum / thalamus. We conclude that histology volume reconstructions facilitate mapping of spatial distribution patterns and topographical organization. The reconstructed image volumes are shared via the Rodent Brain Workbench (www.rbwb.org).

Brain-Wide Mapping of Axonal Connections: Workflow for Automated Detection and Spatial Analysis of Labeling in Microscopic Sections

“…A range of other registration approaches and methods have been reported, including reconstruction of an image series to form a volume, followed by volume to volume registration ( Schormann and Zilles, 1998 ; for further references, see Osechinskiy and Kruggel, 2011 ). Automatic methods are available for 3D reconstruction and correction of shape distortions induced by histological processing ( Ju et al, 2006 ; Dauguet et al, 2007 ; Gaffling et al, 2015 ), as well as for volume to volume registration based on image intensity ( Johnson and Christensen, 2002 ; Kim and Fessler, 2004 ; Klein et al, 2010 ), mutual information ( Wells et al, 1996 ; Woo et al, 2015 ) or structural features ( Kasiri et al, 2014 ; Zakiewicz et al, 2015 ). These methods, however, work best on complete or nearly complete series of images acquired from sections showing high contrast between gray and white matter or other characteristic features.…”

Possum—A Framework for Three-Dimensional Reconstruction of Brain Images from Serial Sections

“…Another example might be processing legacy data by which we understand histological experimental material which has been collected without intention to reconstruct in it 3D but which may still constitute a valuable neuroscientific resource and therefore would benefit from integration with other digital atlasing resources, such as Zakiewicz et al ( 2015 ).…”

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

“…As the community moves towards analyzing brains in 3D, there has been a push towards collecting datasets that span the full brain, especially in the rodent [1, 2, 8–13]. While some laboratories have developed tools and workflows to reconstruct image series covering the whole brain back into 3D and register them to a canonical atlas [1, 11, 14–16]; the majority of investigators do not have access to these kinds of technical resources. Registering an individual 2D image to a 3D atlas is challenging and time-consuming, and registering a large series, especially when a number of slices lack anatomical information, is nearly impossible.…”