biostudies-literatureMegjhani MNIBIB NIH HHS2190-8https://www.ebi.ac.uk/biostudies/studies/S-EPMC4481841biostudies-literatureUnknown31(13)<h4>Motivation</h4>The arbor morphologies of brain microglia are important indicators of cell activation. This article fills the need for accurate, robust, adaptive and scalable methods for reconstructing 3-D microglial arbors and quantitatively mapping microglia activation states over extended brain tissue regions.<h4>Results</h4>Thick rat brain sections (100-300 µm) were multiplex immunolabeled for IBA1 and Hoechst, and imaged by step-and-image confocal microscopy with automated 3-D image mosaicing, producing seamless images of extended brain regions (e.g. 5903 × 9874 × 229 voxels). An over-complete dictionary-based model was learned for the image-specific local structure of microglial processes. The microglial arbors were reconstructed seamlessly using an automated and scalable algorithBioinformatics (Oxford, England)Population-scale three-dimensional reconstruction and quantitative profiling of microglia arbors.PMC4481841R01 EB014955R01EB014955Rey-Villamizar NRoysam BLu YHarris CMerouane AMegjhani MChong PMukherjee ATrett KShain WfalsePopulation-scale three-dimensional reconstruction and quantitative profiling of microglia arbors.<h4>Motivation</h4>The arbor morphologies of brain microglia are important indicators of cell activation. This article fills the need for accurate, robust, adaptive and scalable methods for reconstructing 3-D microglial arbors and quantitatively mapping microglia activation states over extended brain tissue regions.<h4>Results</h4>Thick rat brain sections (100-300 µm) were multiplex immunolabeled for IBA1 and Hoechst, and imaged by step-and-image confocal microscopy with automated 3-D image mosaicing, producing seamless images of extended brain regions (e.g. 5903 × 9874 × 229 voxels). An over-complete dictionary-based model was learned for the image-specific local structure of microglial processes. The microglial arbors were reconstructed seamlessly using an automated and scalable algorith2015-01-01T00:00:00Z2015 Jul2025-04-05T10:12:19.288Z2019-03-27T01:54:08ZS-EPMC44818412570157010.1093/bioinformatics/btv109