Contributors: Institut de biologie de l'ENS Paris (IBENS); Département de Biologie - ENS-PSL (IBENS); École normale supérieure - Paris (ENS-PSL); Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL); Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS); University of Zagreb; King‘s College London; Karolinska Institutet = Karolinska Institute Stockholm; University of Oxford; Analyse d'images biologiques - Biological Image Analysis (BIA); Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité); University of Cambridge Cambridge, UK (CAM); D.H. research is supported by a grant ANR AstroXite-22-CE16-0027, ANR 10LabX54 Memolife, ANR AnalysisSpectralEEG and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 882673). D.A.M. was supported by a Springboard grant funded by the British Council (grant agreement No 1170803491), and T.L.’s research is partially supported by grants from France-BioImaging infrastructure (ANR-10-INBS-04) and the Labex IBEID (ANR-10-LABX-62-IBEID). Experimental work was supported by K.L., who is supported by a Medical Research Council career development award (MR/S025065/1) at the MRC Center for Neurodevelopmental Disorders, KCL, London, UK, and the Croatian Institute for Brain Research and the Zagreb brain collection. Z.K. was supported by a Croatian Science Foundation Grant (HRZZ-IP-2022-10-5975). We would like to acknowledge Dr Ahmed Osman at the Karolinska Institute, and Dr Jenny Dewing-Burton at the University of Southampton. We acknowledge the Oxford Brain Bank, supported by the Brains for Dementia Research (BDR) (Alzheimer Society and Alzheimer Research UK), and the NIHR Oxford Biomedical Research Center.; ANR-22-CE16-0027,AstroXcite,Activité électrique des astrocytes et rôle dans la neurotransmission chez la souris et l'homme(2022); ANR-10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010); ANR-23-CE46-0016,AnalysisSpectralEEG,Modelisation et analyse spectral temps reel de l'EEG(2023); ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010); ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010); European Project: 882673,ERC-2019-ADG,ERC-2019-ADG,OrganellenanoComp(2021)
نبذة مختصرة : International audience ; Mapping cellular organization in the developing brain presents significant challenges due to the multidimensional nature of the data, characterized by complex spatial patterns that are difficult to interpret without high-throughput tools. Here, we present DeepCellMap, a deep-learning-assisted tool that integrates multi-scale image processing with advanced spatial and clustering statistics. This pipeline is designed to map microglial organization during normal and pathological brain development and has the potential to be adapted to any cell type. Using DeepCellMap, we capture the morphological diversity of microglia, identify strong coupling between proliferative and phagocytic phenotypes, and show that distinct spatial clusters rarely overlap as human brain development progresses. Additionally, we uncover an association between microglia and blood vessels in fetal brains exposed to maternal SARS-CoV-2. These findings offer insights into whether various microglial phenotypes form networks in the developing brain to occupy space, and in conditions involving haemorrhages, whether microglia respond to, or influence changes in blood vessel integrity. DeepCellMap is available as an open-source software and is a powerful tool for extracting spatial statistics and analyzing cellular organization in large tissue sections, accommodating various imaging modalities. This platform opens new avenues for studying brain development and related pathologies.
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