The NanoZoomer artificial intelligence 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

6 Citations (Scopus)


We describe our connectomics pipeline for processing anterograde 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 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 were 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, brains were cyto- and myelo-architectonically annotated to create individual 3D atlases. 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 the accuracy of our tracer segmentation and brain registration approaches. 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
Pages (from-to)1225-1243
Number of pages19
JournalBrain Structure and Function
Issue number4
Publication statusPublished - 2020 May 1
Externally publishedYes


  • Artificial intelligence
  • Atlas
  • Connectomics
  • Marmoset
  • Pipeline
  • Tracer injection

ASJC Scopus subject areas

  • Anatomy
  • General Neuroscience
  • Histology


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

Cite this