ArticleBrain structure & function2017
Quantification of neuronal density across cortical depth using automated 3D analysis of confocal image stacks.
Article in Brain structure & function, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Article
- Spindle neurons in human cortex possess distinctive firing properties and transcriptomic signatures.Nature communications · 2026Article
- Thermal Stress-Induced Alterations to Oxylipin Signal Receptors in the Cnidarian-Dinoflagellate Symbiosis.Environmental microbiology · 2026Article
- High-Resolution Laminar Identification in Macaque Primary Visual Cortex Using Neuropixels Probes.bioRxiv : the preprint server for biology · 2024Article
- Neuronal composition of processing modules in human V1: laminar density for neuronal and non-neuronal populations and a comparison with macaque.Cerebral cortex (New York, N.Y. : 1991) · 2024Article
- Strain in the Midbrain: Impact of Traumatic Brain Injury on the Central Serotonin System.Brain sciences · 2024Review
- Multi-Scale Label-Free Human Brain Imaging with Integrated Serial Sectioning Polarization Sensitive Optical Coherence Tomography and Two-Photon Microscopy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Data-driven multiscale model of macaque auditory thalamocortical circuits reproduces in vivo dynamics.Cell reports · 2023Article
- Drebrin Regulates Collateral Axon Branching in Cortical Layer II/III Somatosensory Neurons.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2023Article
- Immunolocalization of Metabolite Transporter Proteins in a Model Cnidarian-Dinoflagellate Symbiosis.Applied and environmental microbiology · 2022Article
- Automated bone cell classification for confocal laser scanning microscopy volumes.Optics continuum · 2022Article
- Similar neural and perceptual masking effects of low-power optogenetic stimulation in primate V1.eLife · 2022Article
- Anatomy and Physiology of Macaque Visual Cortical Areas V1, V2, and V5/MT: Bases for Biologically Realistic Models.Cerebral cortex (New York, N.Y. : 1991) · 2020Review
- Laminar Differences in Responses to Naturalistic Texture in Macaque V1 and V2.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2019Article
- Densities and Laminar Distributions of Kv3.1b-, PV-, GABA-, and SMI-32-Immunoreactive Neurons in Macaque Area V1.Cerebral cortex (New York, N.Y. : 1991) · 2019Article
- Major Feedforward Thalamic Input Into Layer 4C of Primary Visual Cortex in Primate.Cerebral cortex (New York, N.Y. : 1991) · 2019Article
- Neural crest stem cells protect spinal cord neurons from excitotoxic damage and inhibit glial activation by secretion of brain-derived neurotrophic factor.Cell and tissue research · 2018Article
- Total Number Is Important: Using the Disector Method in Design-Based Stereology to Understand the Structure of the Rodent Brain.Frontiers in neuroanatomy · 2018Review
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2 authors.
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Abstract
A new framework for measuring densities of immunolabeled neurons across cortical layers was implemented that combines a confocal microscopy sampling strategy with automated analysis of 3D image stacks. Its utility was demonstrated by quantifying neuronal density in macaque cortical areas V1 and V2. A series of overlapping confocal image stacks were acquired, each spanning from the pial surface to the white matter. DAPI channel images were automatically thresholded, and contiguous regions that included multiple clumped nuclear profiles were split using k-means clustering of image pixels for a set of candidate k values determined based on the clump's area; the most likely candidate segmentation was selected based on criteria that capture expected nuclear profile shape and size. The centroids of putative nuclear profiles estimated from 2D images were then grouped across z planes in an image stack to identify the positions of nuclei in x-y-z. 3D centroids falling outside user-specified exclusion boundaries were deleted, nuclei were classified by the presence or absence of signal in a channel corresponding to an immunolabeled antigen (e.g., the pan-neuronal marker NeuN) at the nuclear centroid location, and the set of classified cells was combined across image stacks to estimate density across cortical depth. The method was validated by comparison with conventional stereological methods. The average neuronal density across cortical layers was 230 × 10
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