{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/an-automated-pipeline-to-create-an-atlas-of","title":"An automated pipeline to create an atlas of in situ hybridization gene expression data in the adult marmoset brain","arxiv_id":"2303.06857","date":"2023-03-13","proceeding":null,"authors":["Charissa Poon","Muhammad Febrian Rachmadi","Michal Byra","Matthias Schlachter","Binbin Xu","Tomomi Shimogori","Henrik Skibbe"],"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.","url_abs":"https://arxiv.org/abs/2303.06857v1","url_pdf":"https://arxiv.org/pdf/2303.06857v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"an-automated-pipeline-to-create-an-atlas-of","repo_url":"https://github.com/brainimageanalysis/marmosetgeneatlas_adult","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":{"status":"ok","spdx":"Apache-2.0"}}],"tasks":[{"task_slug":"segmentation","task_name":"Segmentation"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}