ArticleOpen biology2021
An open-source pipeline for analysing changes in microglial morphology.
Article in Open biology, 2021. 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.
- Subplate neuron dendritic morphology during development in gyrencephalic and lissencephalic brains.Scientific reports · 2026Article
- Comparison of automated and manual approaches for microglial quantification and classification: A focus on the HALO digital pathology platform.Brain pathology (Zurich, Switzerland) · 2026Article
- Inflammatory mechanisms contribute to long-term cognitive deficits induced by perinatal asphyxia via interleukin-1.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2026Article
- Characterizing Microglial Morphology: Methodological Advances in Confocal Imaging and Analysis.Cells · 2025Article
- Chronic Stress Modulates Microglial Activation Dynamics, Shaping Priming Responses to Subsequent Stress.Brain sciences · 2025Article
- Article
- The Complementary Role of Morphology in Understanding Microglial Functional Heterogeneity.International journal of molecular sciences · 2025Review
- Streamlined Quantification of Microglial Morphology in Mouse Brains Using 3D Immunofluorescence Analysis.Bio-protocol · 2025Article
- Development of a High-Throughput Pipeline to Characterize Microglia Morphological States at a Single-Cell Resolution.eNeuro · 2024Article
- Microglial reactivity in brainstem chemosensory nuclei in response to hypercapnia.Frontiers in physiology · 2024Article
- Monoclonal Antibody Therapy in Alzheimer's Disease.Pharmaceutics · 2023Review
- A deep convolutional neural network for efficient microglia detection.Scientific reports · 2023Article
- Forty-hertz light stimulation does not entrain native gamma oscillations in Alzheimer's disease model mice.Nature neuroscience · 2023Article
- Article
- Microglial morphometric analysis: so many options, so little consistency.Frontiers in neuroinformatics · 2023Review
- Characterization of microglia behaviour in healthy and pathological conditions with image analysis tools.Open biology · 2023Article
- A novel automated morphological analysis of Iba1+ microglia using a deep learning assisted model.Frontiers in cellular neuroscience · 2022Article
- The Shape of μ-How Morphological Analyses Shape the Study of Microglia.Frontiers in cellular neuroscience · 2022Review
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3 authors.
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Abstract
Changes in microglial morphology are powerful indicators of the inflammatory state of the brain. Here, we provide an open-source microglia morphology analysis pipeline that first cleans and registers images of microglia, before extracting 62 parameters describing microglial morphology. It then compares control and 'inflammation' training data and uses dimensionality reduction to generate a single metric of morphological change (an 'inflammation index'). This index can then be calculated for test data to assess inflammation, as we demonstrate by investigating the effect of short-term high-fat diet consumption in heterozygous Cx3CR1-GFP mice, finding no significant effects of diet. Our pipeline represents the first open-source microglia morphology pipeline combining semi-automated image processing and dimensionality reduction. It uses free software (ImageJ and R) and can be applied to a wide variety of experimental paradigms. We anticipate it will enable others to more easily take advantage of the powerful insights microglial morphology analysis provides.
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