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

Piotr Majka, Tristan A. Chaplin, Hsin-Hao Yu, Alexander Tolpygo, Partha P. Mitra, Daniel K. Wojcik, Marcello G.P. Rosa

Research output: Contribution to journalArticleResearchpeer-review

Abstract

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.
Original languageEnglish
Pages (from-to)2161-2181
Number of pages21
JournalJournal of Comparative Neurology
Volume524
Issue number11
DOIs
Publication statusPublished - 1 Aug 2016

Keywords

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

Cite this

@article{5703f8978f6746ba9b9c194451156462,
title = "Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template",
abstract = "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.",
keywords = "digital atlas, marmoset, cerebral cortex, neuroanatomical tracing, image registration, Nissl staining, brain template",
author = "Piotr Majka and Chaplin, {Tristan A.} and Hsin-Hao Yu and Alexander Tolpygo and Mitra, {Partha P.} and Wojcik, {Daniel K.} and Rosa, {Marcello G.P.}",
year = "2016",
month = "8",
day = "1",
doi = "10.1002/cne.24023",
language = "English",
volume = "524",
pages = "2161--2181",
journal = "Journal of Comparative Neurology",
issn = "0021-9967",
publisher = "Wiley-Blackwell",
number = "11",

}

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, Piotr; Chaplin, Tristan A.; Yu, Hsin-Hao; Tolpygo, Alexander; Mitra, Partha P.; Wojcik, Daniel K.; Rosa, Marcello G.P.

In: Journal of Comparative Neurology, Vol. 524, No. 11, 01.08.2016, p. 2161-2181.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Towards a comprehensive atlas of cortical connections in a primate brain

T2 - Mapping tracer injection studies of the common marmoset into a reference digital template

AU - Majka, Piotr

AU - Chaplin, Tristan A.

AU - Yu, Hsin-Hao

AU - Tolpygo, Alexander

AU - Mitra, Partha P.

AU - Wojcik, Daniel K.

AU - Rosa, Marcello G.P.

PY - 2016/8/1

Y1 - 2016/8/1

N2 - 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.

AB - 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.

KW - digital atlas

KW - marmoset

KW - cerebral cortex

KW - neuroanatomical tracing

KW - image registration

KW - Nissl staining

KW - brain template

UR - http://www.ncbi.nlm.nih.gov/pubmed/27099164

U2 - 10.1002/cne.24023

DO - 10.1002/cne.24023

M3 - Article

VL - 524

SP - 2161

EP - 2181

JO - Journal of Comparative Neurology

JF - Journal of Comparative Neurology

SN - 0021-9967

IS - 11

ER -