An Automated Pipeline to Create an Atlas of in Situ Hybridization Gene Expression Data in the Adult Marmoset Brain - IMT Mines Alès Access content directly
Conference Papers Year : 2023

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

Abstract

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.

Dates and versions

hal-04206980 , version 1 (14-09-2023)

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Cite

Charissa Poon, Muhammad Febrian Rachmadi, Michal Byra, Matthias Schlachter, Binbin Xu, et al.. 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, Apr 2023, Cartagena de Indias, Colombia. pp.1-5, ⟨10.1109/ISBI53787.2023.10230544⟩. ⟨hal-04206980⟩
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