A Deep Learning-Based Pipeline for Segmenting the Cerebral Cortex Laminar Structure in Histology Images

A Deep Learning-Based Pipeline for Segmenting the Cerebral Cortex Laminar Structure in Histology Images | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article A Deep Learning-Based Pipeline for Segmenting the Cerebral Cortex Laminar Structure in Histology Images Jiaxuan Wang, Rui Gong, Shahrokh Heidari, Mitchell Rogers, Toshiki Tani, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4647115/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 17 Oct, 2024 Read the published version in Neuroinformatics → Version 1 posted 15 You are reading this latest preprint version Abstract Characterizing the anatomical structure and connectivity between cortical regions is a critical step towards understanding the information processing properties of the brain and will help provide insight into the nature of neurological disorders. A key feature of the mammalian cerebral cortex is its laminar structure, with the neocortex differentiated into up to six layers. Identifying these layers in neuroimaging data is important for providing a foundation for understanding the axonal projection patterns of neurons in the brain. These patterns can be seen in experiments using anterograde tracer or are reflected in the brain activity seen in layer-fMRI, etc. We studied Nissl-stained histological slice images of the brain of the common marmoset (Callithrix jacchus), which is a new world monkey that is becoming increasingly popular in the neuroscience community as an object of study. We present a novel computational framework that first acquired the cortical labels using AI-based tools followed by a trained deep learning model to segment cerebral cortical layers. We cross-tested and compared our pipeline with the existing advanced pipeline. Cerebral Cortex Laminar Structure Image Segmentation Deep Learning Artificial Intelligence Computer Vision Neuroscience Neuroanatomy Histological Data Cell Microscopy Full Text Additional Declarations No competing interests reported. Supplementary Files SupplementaryInformation.pdf Cite Share Download PDF Status: Published Journal Publication published 17 Oct, 2024 Read the published version in Neuroinformatics → Version 1 posted Editorial decision: Revision requested 16 Jul, 2024 Reviews received at journal 14 Jul, 2024 Reviews received at journal 08 Jul, 2024 Reviews received at journal 08 Jul, 2024 Reviews received at journal 01 Jul, 2024 Reviewers agreed at journal 01 Jul, 2024 Reviewers agreed at journal 01 Jul, 2024 Reviewers agreed at journal 01 Jul, 2024 Reviewers agreed at journal 30 Jun, 2024 Reviewers agreed at journal 30 Jun, 2024 Reviewers agreed at journal 30 Jun, 2024 Reviewers invited by journal 30 Jun, 2024 Editor assigned by journal 27 Jun, 2024 Submission checks completed at journal 27 Jun, 2024 First submitted to journal 27 Jun, 2024 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4647115","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":327678569,"identity":"870f3f75-544b-43b9-9ca1-b88a6d5ba347","order_by":0,"name":"Jiaxuan Wang","email":"","orcid":"","institution":"University of Auckland","correspondingAuthor":false,"prefix":"","firstName":"Jiaxuan","middleName":"","lastName":"Wang","suffix":""},{"id":327678570,"identity":"8fb78fa9-7aa9-4f9d-a705-21a71fb3d874","order_by":1,"name":"Rui Gong","email":"","orcid":"","institution":"National Institutes of Natural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Rui","middleName":"","lastName":"Gong","suffix":""},{"id":327678571,"identity":"69226f4d-8627-4022-9edc-268cf5dbbf65","order_by":2,"name":"Shahrokh Heidari","email":"","orcid":"","institution":"University of Auckland","correspondingAuthor":false,"prefix":"","firstName":"Shahrokh","middleName":"","lastName":"Heidari","suffix":""},{"id":327678572,"identity":"38a91794-0891-473a-b7f8-6a5ee6f5b889","order_by":3,"name":"Mitchell Rogers","email":"","orcid":"","institution":"University of Auckland","correspondingAuthor":false,"prefix":"","firstName":"Mitchell","middleName":"","lastName":"Rogers","suffix":""},{"id":327678573,"identity":"2ab73e25-12b3-4eea-a200-f5b342ec9e45","order_by":4,"name":"Toshiki Tani","email":"","orcid":"","institution":"RIKEN Center for Brain Science","correspondingAuthor":false,"prefix":"","firstName":"Toshiki","middleName":"","lastName":"Tani","suffix":""},{"id":327678574,"identity":"34c8b8a0-1153-4102-ae20-90dd8cc1d58e","order_by":5,"name":"Hiroshi Abe","email":"","orcid":"","institution":"RIKEN Center for Brain Science","correspondingAuthor":false,"prefix":"","firstName":"Hiroshi","middleName":"","lastName":"Abe","suffix":""},{"id":327678575,"identity":"02fc8b3c-eee7-4a79-9664-cbf49ab08566","order_by":6,"name":"Noritaka Ichinohe","email":"","orcid":"","institution":"National Center of Neurology and Psychiatry","correspondingAuthor":false,"prefix":"","firstName":"Noritaka","middleName":"","lastName":"Ichinohe","suffix":""},{"id":327678576,"identity":"58f8eea3-784e-4124-b0ea-01031a8f373e","order_by":7,"name":"Alexander Woodward","email":"","orcid":"","institution":"University of Auckland","correspondingAuthor":false,"prefix":"","firstName":"Alexander","middleName":"","lastName":"Woodward","suffix":""},{"id":327678577,"identity":"03cd24dd-e85e-46ce-8ca5-50ea4e6016b9","order_by":8,"name":"Patrice J. 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