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University of Pittsburgh Marmoset Invivo Images

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This repository provides curated, research-ready derivatives and documentation derived from the Marmoset Brain Connectivity Atlas (adult Callithrix jacchus), with emphasis on transparent provenance, standardized organization, and reproducible usage in connectivity analysis.

Scope. Fluorescent retrograde tracer injection cases registered to a marmoset cortical template (Paxinos et al., 2012), with section images, cell-label coordinates, and per-case metadata suitable for quantitative analyses and atlas overlays.

Provenance (Original Project)

The original atlas collates two decades of tracer experiments using fluorescent retrograde tracers in adult marmosets to map cortico-cortical and subcortical inputs to defined sites. Data were digitized and registered to a Paxinos et al. (2012) template, viewable as 3D mid-thickness cortex or unfolded cortical maps.

Key references stemming from the source material include (non-exhaustive):
Rosa 2009; Burman 2011, 2014, 2015; Reser 2013; Majka 2016, 2018; Woodward 2018.

Methods (Brief)

Tracer types (retrograde):

  • Fluororuby (FR), Fluoroemerald (FE), Fast Blue (FB), Diamidino Yellow (DY), and CTB (Alexa 488 = CTBgr; Alexa 594 = CTBr).
  • Typical injections: 0.02 µL deposits over 15–20 min at multiple depths; up to four tracers per animal.

Sectioning & imaging:

  • 40 µm frozen sections (mostly coronal); 1-in-5 series for fluorescence mapping.
  • Histology (Nissl/NeuN, myelin, cytochrome oxidase) on adjacent series.
  • Scanned at ~0.50 µm/pixel (×20). Left-hemisphere injections horizontally flipped for consistency.

Preprocessing & registration:

  • Downsampled section series assembled in rostro-caudal order; artefact padding as needed.
  • Cell-label SVG overlays aligned to histology (translation/rotation/scale).
  • 3D reconstruction with iterative in-plane alignments + deformable corrections.
  • Atlas registration (affine + SyN deformable) using ANTs; QC included.

Template:

  • Cortical parcellation from Paxinos et al. (2012); stereotaxic coordinate system.
  • 3D Brain Atlas Reconstructor / custom scripts for volume/surface generation.

Software (source project):

  • ANTs, Convert3D, ImageMagick, VTK/ITK; pipelines via poSSum framework.
  • Original web viewer: OpenLayers-based tiled imagery with vector overlays.

Data Organization

  • Per-case folder: sections/CASE_ID/ (tiles) · cells/CASE_ID.csv (label points) · registration/CASE_ID/ (affine, warp fields, QC) · metadata/CASE_ID.json
  • Coordinates:
    • *_section: pixel coordinates in section space
    • *_template: coordinates in template space (after warp)
  • Template surfaces: mid-thickness mesh (template/surface/) and unfolded maps (template/unfolded/)

How to Use

  1. Visualize sections + labels
    Use examples/01_view_sections.ipynb to load a section tile and overlay cell points.
  2. Map to cortical areas
    Apply registration/CASE_ID transforms to bring cell points into template space, then intersect with area labels.
  3. Quantify connectivity
    Aggregate counts by parcel (optionally normalize by parcel area / section sampling), export CSV for stats.

License & Citation

  • License: Images and figures from the source project are distributed under CC BY 4.0; see LICENSE and the original Licensing and Citation Policy. Derived metadata and code in this repository follow the license declared in LICENSE.
  • Acknowledge (example):
    “Data derived from the Marmoset Brain Connectivity Atlas. Please see the original project and licensing page for details.”
  • Suggested citation (source project):
    Cite the Marmoset Brain Connectivity Atlas and relevant methods papers (e.g., Majka et al., 2016/2018; Paxinos et al., 2012), plus this repository (Pittsburgh team) for derivatives.

Funding acknowledgements (source project): Support from ARC and NHMRC projects; ARC Centre of Excellence for Integrative Brain Function; INCF seed grant; and related institutional support (Monash University, CSHL). See original project pages for full details.

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