1. | Poon Ch.♦, Rachmadi M.F.♦, Byra M., Schlachter M.♦, Xu B.♦, Shimogori T.♦, Skibbe H.♦, AN AUTOMATED PIPELINE TO CREATE AN ATLAS OF IN SITU HYBRIDIZATION GENE EXPRESSION DATA IN THE ADULT MARMOSET BRAIN, ISBI, 2023 IEEE 20th International Symposium on Biomedical Imaging, 2023-04-18/04-21, Cartagena (CO), DOI: 10.1109/ISBI53787.2023.10230544, pp.1-5, 2023Abstract: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 standard 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 expression patterns with minimal human bias. To reduce the number of labelled images required for training, 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 datasets, thereby facilitating a more holistic understanding of primate brain structure and function. Keywords:contrastive learning, gene atlas, segmen-tation, semi-supervised learning, registration Affiliations:Poon Ch. | - | other affiliation | Rachmadi M.F. | - | other affiliation | Byra M. | - | IPPT PAN | Schlachter M. | - | other affiliation | Xu B. | - | Tsinghua University (CN) | Shimogori T. | - | other affiliation | Skibbe H. | - | other affiliation |
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