Abstract
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.
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Acknowledgements
We thank Akiya Watakabe for sharing his expertise in marmoset tracer injection studies, Masahide Maeda for his technical support in maintaining the server used in this work, and Carlos Enrique Guiterrez and Hiromichi Tsukada for their participation and contribution in previous tracer study activities.
Funding
This research was supported by the program for Brain Mapping by Integrated Neurotechnologies for Disease Studies (Brain/MINDS) from the Japan Agency for Medical Research and Development, AMED, Grants JP19dm0207001 and JP19dm0207088.
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All experimental procedures were approved by the Experimental Animal Committee of RIKEN, or by the Experimental Animal Committee of the National Center of Neurology and Psychiatry. The marmosets were handled in accordance with the “Guiding Principles of the Care and Use of Animals in the Field of Physiological Science” formulated by the Japanese Physiological Society.
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Woodward, A., Gong, R., Abe, H. et al. The NanoZoomer artificial intelligence connectomics pipeline for tracer injection studies of the marmoset brain. Brain Struct Funct 225, 1225–1243 (2020). https://doi.org/10.1007/s00429-020-02073-y
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DOI: https://doi.org/10.1007/s00429-020-02073-y