ArticleFrontiers in neuroanatomy2018
NeuroMorph: A Software Toolset for 3D Analysis of Neurite Morphology and Connectivity.
Article in Frontiers in neuroanatomy, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 42 citations in OpenAlex.
- Article
- Astrocyte glypican 5 regulates synapse maturation and stabilization.Cell reports · 2025Article
- The endoplasmic reticulum connects to the nucleus by constricted junctions that mature after mitosis.EMBO reports · 2024Article
- Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets.Nature protocols · 2024Review
- SV2B defines a subpopulation of synaptic vesicles.Journal of molecular cell biology · 2024Article
- Oligodendrocyte calcium signaling promotes actin-dependent myelin sheath extension.Nature communications · 2024Article
- CellWalker: a user-friendly and modular computational pipeline for morphological analysis of microscopy images.Bioinformatics (Oxford, England) · 2023Article
- Article
- Dense 4D nanoscale reconstruction of living brain tissue.Nature methods · 2023Article
- CellRemorph: A Toolkit for Transforming, Selecting, and Slicing 3D Cell Structures on the Road to Morphologically Detailed Astrocyte Simulations.Neuroinformatics · 2023Article
- A subpopulation of cortical VIP-expressing interneurons with highly dynamic spines.Communications biology · 2022Article
- Ultrastructural analysis of dendritic spine necks reveals a continuum of spine morphologies.Developmental neurobiology · 2021Article
- Maturation of Complex Synaptic Connections of Layer 5 Cortical Axons in the Posterior Thalamic Nucleus Requires SNAP25.Cerebral cortex (New York, N.Y. : 1991) · 2021Article
- 3D Ultrastructure of Synaptic Inputs to Distinct GABAergic Neurons in the Mouse Primary Visual Cortex.Cerebral cortex (New York, N.Y. : 1991) · 2021Article
- Ultrastructural comparison of dendritic spine morphology preserved with cryo and chemical fixation.eLife · 2020Article
- Microglial physiological properties and interactions with synapses are altered at presymptomatic stages in a mouse model of Huntington's disease pathology.Journal of neuroinflammation · 2020Article
- Somatostatin enhances visual processing and perception by suppressing excitatory inputs to parvalbumin-positive interneurons in V1.Science advances · 2020Article
- ilastik: interactive machine learning for (bio)image analysis.Nature methods · 2019Review
- Three-Dimensional Nanostructure of an Intact Microglia Cell.Frontiers in neuroanatomy · 2018Article
- Block Face Scanning Electron Microscopy of Fluorescently Labeled Axons Without Using Near Infra-Red Branding.Frontiers in neuroanatomy · 2018Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The geometries of axons, dendrites and their synaptic connections provide important information about their functional properties. These can be collected directly from measurements made on serial electron microscopy images. However, manual and automated segmentation methods can also yield large and accurate models of neuronal architecture from which morphometric data can be gathered in 3D space. This technical paper presents a series of software tools, operating in the Blender open source software, for the quantitative analysis of axons and their synaptic connections. These allow the user to annotate serial EM images to generate models of different cellular structures, or to make measurements of models generated in other software. The paper explains how the tools can measure the cross-sectional surface area at regular intervals along the length of an axon, and the amount of contact with other cellular elements in the surrounding neuropil, as well as the density of organelles, such as vesicles and mitochondria, that it contains. Nearest distance measurements, in 3D space, can also be made between any features. This provides many capabilities such as the detection of boutons and the evaluation of different vesicle pool sizes, allowing users to comprehensively describe many aspects of axonal morphology and connectivity.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.