Marmoset Brain Connectivity Atlas

Supplementary material

The web page http://www.marmosetbrain.org/nencki_monash_template contains the most recent versions of the supplementary materials for the article:

Histology-Based Average Template of the Marmoset Cortex
With Probabilistic Localization of Cytoarchitectural Areas

Abstract

The rapid adoption of marmosets in neuroscience has created a demand for three dimensional (3D) atlases of the brain of this species to facilitate data integration in a common reference space. We report on a new open access template of the marmoset cortex (the Nencki–Monash, or NM template), representing a morphological average of 20 brains of young adult individuals, obtained by 3D reconstructions generated from Nissl-stained serial sections. The method used to generate the template takes into account morphological features of the individual brains, as well as the borders of clearly defined cytoarchitectural areas. This has resulted in a resource which allows direct estimates of the most likely coordinates of each cortical area, as well as quantification of the margins of error involved in assigning voxels to areas, and preserves quantitative information about the laminar structure of the cortex. We provide spatial transformations between the NM and other available marmoset brain templates, thus enabling integration with magnetic resonance imaging (MRI) and tracer-based connectivity data. The NM template combines some of the main advantages of histology-based atlases (e.g. information about the cytoarchitectural structure) with features more commonly associated with MRI-based templates (isotropic nature of the dataset, and probabilistic analyses). The underlying workflow may be found useful in the future development of brain atlases that incorporate information about the variability of areas in species for which it may be impractical to ensure homogeneity of the sample in terms of age, sex and genetic background.

The following datasets are available for download:

1. The main data layers of the Nencki-Monash template.
   All 3D images are provided as NIfTI files, represented at 50 µm isotropic resolution.
   • Nissl-stained histology image,
   • Maximum-probability segmentation,
   • Segmentation confidence map,
   • Cortical thickness map,
   • Normalized thickness map,
   • Depth below the pial surface.
   And:
   • Liu et al. (2020) Fractional Anisotropy map,
   • Liu et al. (2020) Mean Diffusivity map,
   • Liu et al. (2020) Color-encoded Fiber Orientation Distribution map,
   registered to the Nencki-Monash template space.
2. Probability maps for 116 cytoarchitectural areas.
3. Surface models in GIFTI format (midthickness surface and flatmap).
4. Cytoarchitectonic profiles of individual cortical areas.
5. Histograms of cortical thickness.
6. Spatial transformations between the Nencki-Monash template and other atlases of the marmoset brain.
   • Paxinos et al. (2012),
   • Woodward et al. (2018),
   • Liu et al. (2020).

Licensing

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