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

Zakiewicz IM, Majka P, Wójcik DK, Bjaalie JG, Leergaard TB - PLoS ONE (2015)

Bottom Line: 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.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.The reconstructed image volumes are shared via the Rodent Brain Workbench (www.rbwb.org).

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Department of Neurophysiology, Nencki Institute of Experimental Biology, Warsaw, Poland.

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).

No MeSH data available.


Related in: MedlinePlus

3-D reconstruction workflow.Flowchart showing the processing steps for 3-D reconstruction of histological images. See text for details.
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pone.0137571.g001: 3-D reconstruction workflow.Flowchart showing the processing steps for 3-D reconstruction of histological images. See text for details.

Mentions: Complete series of images of BDA and neutral red sections (spaced at 100–200 μm) from four cases were downloaded in bulk, and 3-D reconstructed using a customized workflow (Fig 1). To streamline computations, images were downsampled to 15 μm per pixel. For each section image (Fig 1A), the best corresponding atlas plate (Fig 1B) was identified on basis of anatomical landmarks. Image masks (Fig 1C) were semi-automatically generated by smoothing the red channel of each slice image with a 5 × 5 pixel median filter, with a threshold at 95% of the maximum image intensity, before applying minor manual corrections to refine the masks and remove spatially inconsistent or displaced tissue elements. The spatially consistent regions were typically the striatum, brainstem, thalamus, superior colliculus and pons, while the cerebral cortex, parts of the hippocampus and cerebellum were often displaced during histological processing and excluded from the mask. The section image masks were used to create correspondingly masked atlas plates (Fig 1D) by use of the ITK-SNAP software application [30].


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

Zakiewicz IM, Majka P, Wójcik DK, Bjaalie JG, Leergaard TB - PLoS ONE (2015)

3-D reconstruction workflow.Flowchart showing the processing steps for 3-D reconstruction of histological images. See text for details.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4580429&req=5

pone.0137571.g001: 3-D reconstruction workflow.Flowchart showing the processing steps for 3-D reconstruction of histological images. See text for details.
Mentions: Complete series of images of BDA and neutral red sections (spaced at 100–200 μm) from four cases were downloaded in bulk, and 3-D reconstructed using a customized workflow (Fig 1). To streamline computations, images were downsampled to 15 μm per pixel. For each section image (Fig 1A), the best corresponding atlas plate (Fig 1B) was identified on basis of anatomical landmarks. Image masks (Fig 1C) were semi-automatically generated by smoothing the red channel of each slice image with a 5 × 5 pixel median filter, with a threshold at 95% of the maximum image intensity, before applying minor manual corrections to refine the masks and remove spatially inconsistent or displaced tissue elements. The spatially consistent regions were typically the striatum, brainstem, thalamus, superior colliculus and pons, while the cerebral cortex, parts of the hippocampus and cerebellum were often displaced during histological processing and excluded from the mask. The section image masks were used to create correspondingly masked atlas plates (Fig 1D) by use of the ITK-SNAP software application [30].

Bottom Line: 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.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.The reconstructed image volumes are shared via the Rodent Brain Workbench (www.rbwb.org).

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Department of Neurophysiology, Nencki Institute of Experimental Biology, Warsaw, Poland.

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).

No MeSH data available.


Related in: MedlinePlus