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J Comp Neurol. 2016 Aug 1;524(11):2161-81. doi: 10.1002/cne.24023.

Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template.

Majka P1,2,3,4, Chaplin TA1,2,4,5, Yu HH1,2,4,5, Tolpygo A6, Mitra PP4,6, Wójcik DK3, Rosa MG1,2,4,5.

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Neuroscience Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
Department of Physiology, Monash University, Clayton, VIC, Australia.
Nencki Institute of Experimental Biology, Warsaw, Poland.
Australian Research Council Centre of Excellence for Integrative Brain Function, Monash University Node, Clayton, VIC, Australia.
Monash Vision Group, Monash University, Clayton, VIC, Australia.
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.


The marmoset is an emerging animal model for large-scale attempts to understand primate brain connectivity, but achieving this aim requires the development and validation of procedures for normalization and integration of results from many neuroanatomical experiments. Here we describe a computational pipeline for coregistration of retrograde tracing data on connections of cortical areas into a 3D marmoset brain template, generated from Nissl-stained sections. The procedure results in a series of spatial transformations that are applied to the coordinates of labeled neurons in the different cases, bringing them into common stereotaxic space. We applied this procedure to 17 injections, placed in the frontal lobe of nine marmosets as part of earlier studies. Visualizations of cortical patterns of connections revealed by these injections are supplied as Supplementary Materials. Comparison between the results of the automated and human-based processing of these cases reveals that the centers of injection sites can be reconstructed, on average, to within 0.6 mm of coordinates estimated by an experienced neuroanatomist. Moreover, cell counts obtained in different areas by the automated approach are highly correlated (r = 0.83) with those obtained by an expert, who examined in detail histological sections for each individual. The present procedure enables comparison and visualization of large datasets, which in turn opens the way for integration and analysis of results from many animals. Its versatility, including applicability to archival materials, may reduce the number of additional experiments required to produce the first detailed cortical connectome of a primate brain. J. Comp. Neurol. 524:2161-2181, 2016.


Nissl staining; brain template; cerebral cortex; digital atlas; image registration; marmoset; neuroanatomical tracing

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