An Automated Pipeline to Create An Atlas of In Situ Hybridization Gene Expression Data In the Adult Marmoset Brain

We present the first automated pipeline to create an atlas of in situ hybridization gene expression in the adult marmoset brain in the same stereotaxic space. The pipeline consists of segmentation of gene expression from microscopy images, and registration of images to a common brain template space. Automation of this pipeline is necessary to analyze the large volume of data in the genome-wide whole brain dataset, and to process images that have varying intensity profiles and gene expression patterns with minimal human bias. To reduce the number of labelled images required for segmentation, we develop a semi-supervised segmentation model. We further develop an iterative algorithm to register images to a standard space, enabling comparative analysis between genes and concurrent visualization with other imaging data, thereby facilitating a more holistic understanding of primate brain development, structure, and function.