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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 seg-
mentation 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 algo-
rithm to register images to a standard space, enabling com-
parative analysis between genes and concurrent visualization
with other datasets, thereby facilitating a more holistic under-
standing 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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