The nanozoomer connectomics pipeline for tracer injection studies of the marmoset brain

Alexander Woodward, Rui Gong, Hiroshi Abe, Ken Nakae, Junichi Hata, Henrik Skibbe, Yoko Yamaguchi, Shin Ishii, Hideyuki Okano, Tetsuo Yamamori, Noritaka Ichinohe

Research output: Contribution to journalArticlepeer-review


We describe our connectomics pipeline for processing tracer injection data for the brain of the common marmoset (Callithrix jacchus). Brain sections were imaged using a batch slide scanner (NanoZoomer 2.0-HT) and we used artificial intelligence to precisely segment the anterograde tracer signal from the background in the fluorescence images. The shape of each brain was reconstructed by reference to a block-face and all data was mapped into a common 3D brain space with atlas and 2D cortical flat map. To overcome the effect of using a single template atlas to specify cortical boundaries, each brain was cytoarchitectonically annotated and used for making an individual 3D atlas. Registration between the individual and common brain cortical boundaries in the flat map space was done to absorb the variation of each brain and precisely map all tracer injection data into one cortical brain space. We describe the methodology of our pipeline and analyze tracer segmentation and brain registration accuracy. Results show our pipeline can successfully process and normalize tracer injection experiments into a common space, making it suitable for large-scale connectomics studies with a focus on the cerebral cortex.

Original languageEnglish
JournalUnknown Journal
Publication statusPublished - 2019 Aug 28


  • Artificial Intelligence
  • Atlas
  • Connectomics
  • Marmoset
  • Pipeline
  • Tracer Injection

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Immunology and Microbiology(all)
  • Neuroscience(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

Fingerprint Dive into the research topics of 'The nanozoomer connectomics pipeline for tracer injection studies of the marmoset brain'. Together they form a unique fingerprint.

Cite this