The Marmoset Brain Mapping and Marmoset Brain Connectome Projects: Understanding the Anatomical and Functional Organization of the Primate Brain

Date: Wednesday, February 16, 2022
Speaker: Afonso C. Silva, Ph.D.
Endowed Chair Professor of Translational Neuroimaging, Neurobiology, Department of Neurobiology, Center for Neuroscience at the University of Pittsburgh, University of Pittsburgh Brain Institute

Hosts: Dr. Robert Desimone and Dr. Mriganka Sur

Abstract: The common marmoset (Callithrix jacchus), a small non-human primate species endogenous to Brazil, has rapidly emerged as a promising animal model for biomedical and neuroscience research. The lissencephalic marmoset brain retains the stereotypical anatomical and functional organization of the primate brain, offering new opportunities to map neural circuits and functional connectome systemically and comprehensively. Developing appropriate analytical tools to study the marmoset brain anatomy and function in great detail is an essential enabling step to promote neuroimaging and connectome studies of marmosets. The Marmoset Brain Mapping project ( is a multi-atlas set of brain templates with labeled anatomical structures and highly accurate tissue-type segmentation maps that facilitate volumetric studies. The three main versions of the atlas (V1: Cortical Map; V2: White-Matter Pathways; V3: Population-Based Atlases) contain fully featured brain surfaces and cortical flat maps to facilitate 3D visualization and surface-based analyses, which are compatible with most surface analyzing tools, including FreeSurfer, AFNI/SUMA, and the Connectome Workbench. The anatomical Marmoset Brain Mapping Project includes multi-modal MRI and CT data of 27 marmosets, featuring the most comprehensive image modalities, accurate (manually corrected) tissue segmentation maps, multi-atlas labeled template space and fully featured brain surface and flat maps for surface-based analysis. To complement the Marmoset Brain Mapping Project, we also developed the Marmoset Brain Connectome Project ( consisting of over 70 hours of resting-state fMRI (RS-fMRI) data acquired at 500 µm isotropic resolution from 31 fully awake marmosets in a common stereotactic space. Three-dimensional functional connectivity (FC) maps for every cortical and subcortical gray matter voxel are stored in an online repository. Users can instantaneously view, manipulate, and download any whole-brain functional connectivity (FC) topology along with the raw datasets and preprocessing code. We expect that this resource will be of broad value, supporting novel hypotheses about the functional organization of the marmoset brain.


  1. Silva AC. Anatomical and functional neuroimaging in awake, behaving marmosets. Dev. Neurobiol. 2017 Mar;77(3):373-389.
  2. Liu C, Ye FQ, Yen CC, Newman JD, Glen D, Leopold DA, Silva AC. A digital 3D atlas of the marmoset brain based on multi-modal MRI. Neuroimage 2017 Dec 5;169:106-116.
  3. Yen CC, Papoti D, Silva AC. Investigating the spatiotemporal characteristics of the deoxyhemoglobin-related and deoxyhemoglobin-unrelated functional hemodynamic response across cortical layers in awake marmosets. Neuroimage 2018 Jan 1;164:121-130.
  4. Hirano Y, Yen CC, Liu JV, Mackel JB, Merkle H, Nascimento GC, Stefanovic B, Silva AC. Investigation of the BOLD and CBV fMRI responses to somatosensory stimulation in awake marmosets (Callithrix jacchus). NMR Biomed 2018 Mar;31(3). doi: 10.1002/nbm.3864. Epub 2017 Dec 29.
  5. Liu C, Yen CC, Szczupak D, Ye FQ, Leopold DA, Silva AC. Anatomical and functional investigation of the marmoset default mode network. Nat Commun. 2019 Apr 29;10(1):1975. doi: 10.1038/s41467-019-09813-7.
  6. Liu C, Ye FQ, Newman JD, Szczupak D, Tian X, Yen CCC, Majka P, Glen D, Rosa MGP, Leopold DA, Silva AC. A resource for detailed 3D mapping of white matter pathways in the marmoset brain. Nature Neurosci. 2020 Jan 13. doi:10.1038/s41593-019-0575-0.
  7. Majka P, Bednareka S, Chan JM, Jermakowa N, Liu C, Saworska G, Worthy K, Silva AC, Wójcik D, Rosa MGP. Histology-based average template of the marmoset cortex with probabilistic localization of cytoarchitectural areas. Neuroimage 2020 Dec 8:117625. doi: 10.1016/j.neuroimage.2020.117625.
  8. Liu C, Yen CCC, Szczupak D, Tian X, Glen D, Silva AC. Marmoset brain mapping v3: population multi-modal standard volumetric and surface-based templates. Neuroimage 2020 Dec 8:117620. doi: 10.1016/j.neuroimage.2020.117620.
  9. Szczupak D, Yen CCC, Liu C, Tian X, IRC5 Consortium, Lent R, Tovar-Moll FF, Silva AC. Dynamic Interhemispheric Desynchronization in Marmosets and Humans with Disorders of the Corpus Callosum. Frontiers Neural Circuits. 2020 Dec 8:612595. doi: 10.3389/fncir.2020.612595.
  10. Schaeffer DJ, Liu C, Silva AC, Everling S. Magnetic Resonance Imaging of Marmoset Monkeys. ILAR J. 2021 Feb 26:ilaa029. doi: 10.1093/ilar/ilaa029.
  11. Tian X, Silva AC, Liu C. The Brain Circuits and Dynamics of Curiosity-Driven Behavior in Naturally Curious Marmosets. Cereb Cortex 2021 Apr 12:bhab080. doi: 10.1093/cercor/bhab080.