Connectome Analysis Unit, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
Laboratory for Molecular Analysis of Higher Brain Function, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
Brain Struct Funct. 2020 May;225(4):1225-1243. doi: 10.1007/s00429-020-02073-y. Epub 2020 May 4.
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.
我们描述了用于处理普通狨猴（Callithrix jacchus）大脑顺行示踪剂注射数据的连接组学管道。使用批量幻灯片扫描仪（NanoZoomer 2.0-HT）对脑切片进行成像，我们使用人工智能从荧光图像中的背景中精确地分割示踪剂信号。通过参考块面来重建每个大脑的形状，并且所有数据都被映射到具有图谱和 2D 皮质平面图的共同 3D 脑空间中。为了克服使用单个模板图谱来指定皮质边界的影响，对大脑进行细胞和髓鞘结构注释以创建个体 3D 图谱。在平面图谱空间中，在个体和常见大脑皮质边界之间进行配准，以吸收每个大脑的变化，并将所有示踪剂注射数据精确地映射到一个皮质脑空间中。我们描述了我们的管道的方法，并分析了我们的示踪剂分割和大脑注册方法的准确性。结果表明，我们的管道可以成功地将示踪剂注射实验处理和归一化为一个共同的空间，使其适用于以大脑皮层为重点的大规模连接组学研究。
