Three-Dimensional Histology Volume Reconstruction of Axonal Tract Tracing Data: Exploring Topographical Organization in Subcortical Projections from Rat Barrel Cortex
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{"title"=>"Three-dimensional histology volume reconstruction of axonal tract tracing data: Exploring topographical organization in subcortical projections from rat barrel cortex", "type"=>"journal", "authors"=>[{"first_name"=>"Izabela M.", "last_name"=>"Zakiewicz", "scopus_author_id"=>"44961599600"}, {"first_name"=>"Piotr", "last_name"=>"Majka", "scopus_author_id"=>"54882418300"}, {"first_name"=>"Daniel K.", "last_name"=>"W�jcik", "scopus_author_id"=>"57201045494"}, {"first_name"=>"Jan G.", "last_name"=>"Bjaalie", "scopus_author_id"=>"7004240123"}, {"first_name"=>"Trygve B.", "last_name"=>"Leergaard", "scopus_author_id"=>"6602312453"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0137571", "sgr"=>"84946935125", "scopus"=>"2-s2.0-84946935125", "issn"=>"19326203", "pui"=>"606828457"}, "id"=>"7fbb6808-4772-3465-b7be-d563186564cb", "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)", "link"=>"http://www.mendeley.com/research/threedimensional-histology-volume-reconstruction-axonal-tract-tracing-data-exploring-topographical-o", "reader_count"=>21, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>7, "Student > Ph. D. Student"=>5, "Student > Master"=>2, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>7, "Student > Ph. D. Student"=>5, "Student > Master"=>2, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>4, "Medicine and Dentistry"=>2, "Neuroscience"=>6, "Computer Science"=>6}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Neuroscience"=>{"Neuroscience"=>6}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Computer Science"=>{"Computer Science"=>6}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Germany"=>2}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2285214"], "description"=>"<p>3-D visualization of topographical organization in corticostriatal and corticothalamic pathways. (A-D) Stereo-image pairs showing color coded 3-D surface models of the delineated axonal clusters in the striatum (A,B) and thalamus (C,D), in slightly offset views from anterior (A), medial (B,D), and posterior (C), as indicated in the inset figures (right column). To perceive the 3-D images the viewer must cross the eye axis to let the image pairs merge. (A,B) Clusters representing corticostriatal axons are distributed within a narrow, laminar subspace, extending in an anteroposterior direction through the dorsolateral striatum. (C,D) Clusters representing corticothalamic axons are distributed within a narrow, spherical shell-like subspace in the thalamus. A, anterior; D, dorsal; M, medial; P, posterior.</p>", "links"=>[], "tags"=>["Rat Barrel Cortex Topographical organization", "visualization", "histological", "axonal connections", "Rodent Brain Workbench", "brain regions", "topographical organization", "approach", "image", "Exploring Topographical Organization", "tracer injection sites", "S 1 corticostriatal", "corticothalamic", "histology volume reconstructions", "analysis", "axonal projection patterns"], "article_id"=>1553637, "categories"=>["Biological Sciences"], "users"=>["Izabela M. Zakiewicz", "Piotr Majka", "Daniel K. Wójcik", "Jan G. Bjaalie", "Trygve B. Leergaard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0137571.g005", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_3_D_surface_models_of_corticostriatal_and_corticothalamic_projections_/1553637", "title"=>"3-D surface models of corticostriatal and corticothalamic projections.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-23 03:01:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/2285204"], "description"=>"<p>Analysis of the spatial location of tracer injection sites in the four cases investigated. (A) Coronal, sagittal, and horizontal slices through the injection site centers at the level of cortical layer V, facilitating comparison of the spatial location and extent of the four tracer injections. Dashed lines indicate slice locations in corresponding images. (B) Cartoon representations of the primary somatosensory cortex (redrawn and modified from [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137571#pone.0137571.ref034\" target=\"_blank\">34</a>] with permission) showing the estimated locations of the tracer injection sites. (C) Horizontal slice through the 3-D reconstructed atlas (at level of layer V) showing the relative location and extent of the co-registered delineations of the four injection sites. (D) Estimated stereotaxic positions of injection sites projected onto a composite map of M1 and S1 based on several earlier electrophysiological studies (redrawn and modified from [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137571#pone.0137571.ref059\" target=\"_blank\">59</a>] with permission). This map indicates that the stereotaxic location of the tracer injection in case R601 to a larger degree involves the forelimb representation in M1, rather than S1. C, cingulate cortex; FBP, furry buccal pad; FL, forelimb; HL, hindlimb; LJ, lower jaw; M, motor cortex; N, nose; P, parietal cortex; PO, perioral; R, retrosplenical cortex; S, somatosensory cortex; TR, trunk; UZ, unresponsive zone; V, visual cortex; W, whisker; Scale bar, 1 mm.</p>", "links"=>[], "tags"=>["Rat Barrel Cortex Topographical organization", "visualization", "histological", "axonal connections", "Rodent Brain Workbench", "brain regions", "topographical organization", "approach", "image", "Exploring Topographical Organization", "tracer injection sites", "S 1 corticostriatal", "corticothalamic", "histology volume reconstructions", "analysis", "axonal projection patterns"], "article_id"=>1553630, "categories"=>["Biological Sciences"], "users"=>["Izabela M. Zakiewicz", "Piotr Majka", "Daniel K. Wójcik", "Jan G. Bjaalie", "Trygve B. Leergaard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0137571.g002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_3_D_reconstructed_injections_combined_in_atlas_template_/1553630", "title"=>"3-D reconstructed injections combined in atlas template.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-23 03:01:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/2285209"], "description"=>"<p>Visualization of axonal labeling in three-plane slices centered on clusters with highest labeling density in the thalamus of the four cases investigated (A-L). Insets (left) indicate the location of tracer injections in the primary somatosensory cortex (presentation as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137571#pone.0137571.g002\" target=\"_blank\">Fig 2</a>). Dashed lines indicate slice locations in corresponding images. ic, internal capsule. (M) Oblique horizontal slice through a volumetric rat brain atlas [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137571#pone.0137571.ref057\" target=\"_blank\">57</a>] indicating the orientation of an arbitrary slice through an image volume (N), showing an almost continuous ring of axonal labeling in the thalamus (case R602). Scale bars, 0.5 mm.</p>", "links"=>[], "tags"=>["Rat Barrel Cortex Topographical organization", "visualization", "histological", "axonal connections", "Rodent Brain Workbench", "brain regions", "topographical organization", "approach", "image", "Exploring Topographical Organization", "tracer injection sites", "S 1 corticostriatal", "corticothalamic", "histology volume reconstructions", "analysis", "axonal projection patterns"], "article_id"=>1553635, "categories"=>["Biological Sciences"], "users"=>["Izabela M. Zakiewicz", "Piotr Majka", "Daniel K. Wójcik", "Jan G. Bjaalie", "Trygve B. Leergaard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0137571.g004", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_3_D_shape_and_distribution_of_corticothalamic_projections_/1553635", "title"=>"3-D shape and distribution of corticothalamic projections.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-23 03:01:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/2285208"], "description"=>"<p>Visualization of axonal labeling in three-plane slices centered on clusters with highest labeling density in the striatum of the four cases investigated. Insets (left) indicate the location of tracer injections in S1 (presentation as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137571#pone.0137571.g002\" target=\"_blank\">Fig 2</a>). Dashed lines indicate slice locations in corresponding images. ac, anterior commissure; cc, corpus callosum; ec, external capsule; ic, internal capsule; Cpu, caudate-putamen complex (striatum). Scale bar, 0.5 mm.</p>", "links"=>[], "tags"=>["Rat Barrel Cortex Topographical organization", "visualization", "histological", "axonal connections", "Rodent Brain Workbench", "brain regions", "topographical organization", "approach", "image", "Exploring Topographical Organization", "tracer injection sites", "S 1 corticostriatal", "corticothalamic", "histology volume reconstructions", "analysis", "axonal projection patterns"], "article_id"=>1553634, "categories"=>["Biological Sciences"], "users"=>["Izabela M. Zakiewicz", "Piotr Majka", "Daniel K. Wójcik", "Jan G. Bjaalie", "Trygve B. Leergaard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0137571.g003", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_3_D_shape_and_distribution_of_corticostriatal_projections_/1553634", "title"=>"3-D shape and distribution of corticostriatal projections.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-23 03:01:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/2285197"], "description"=>"<p>Flowchart showing the processing steps for 3-D reconstruction of histological images. See text for details.</p>", "links"=>[], "tags"=>["Rat Barrel Cortex Topographical organization", "visualization", "histological", "axonal connections", "Rodent Brain Workbench", "brain regions", "topographical organization", "approach", "image", "Exploring Topographical Organization", "tracer injection sites", "S 1 corticostriatal", "corticothalamic", "histology volume reconstructions", "analysis", "axonal projection patterns"], "article_id"=>1553623, "categories"=>["Biological Sciences"], "users"=>["Izabela M. Zakiewicz", "Piotr Majka", "Daniel K. Wójcik", "Jan G. Bjaalie", "Trygve B. Leergaard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0137571.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_3_D_reconstruction_workflow_/1553623", "title"=>"3-D reconstruction workflow.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-23 03:01:45"}

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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