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Wolcott NS, Redman WT, Karpinska M, Jacobs EG, Goard MJ. The estrous cycle modulates hippocampal spine dynamics, dendritic processing, and spatial coding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606418. [PMID: 39131375 PMCID: PMC11312567 DOI: 10.1101/2024.08.02.606418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Histological evidence suggests that the estrous cycle exerts a powerful effect on CA1 neurons in mammalian hippocampus. Decades have passed since this landmark observation, yet how the estrous cycle shapes dendritic spine dynamics and hippocampal spatial coding in vivo remains a mystery. Here, we used a custom hippocampal microperiscope and two-photon calcium imaging to track CA1 pyramidal neurons in female mice over multiple cycles. Estrous cycle stage had a potent effect on spine dynamics, with heightened density during periods of greater estradiol (proestrus). These morphological changes were accompanied by greater somatodendritic coupling and increased infiltration of back-propagating action potentials into the apical dendrite. Finally, tracking CA1 response properties during navigation revealed enhanced place field stability during proestrus, evident at the single-cell and population level. These results establish the estrous cycle as a driver of large-scale structural and functional plasticity in hippocampal circuits essential for learning and memory.
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Abdellah M, Foni A, Cantero JJG, Guerrero NR, Boci E, Fleury A, Coggan JS, Keller D, Planas J, Courcol JD, Khazen G. Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for in silico modeling. Brief Bioinform 2024; 25:bbae393. [PMID: 39129363 PMCID: PMC11317524 DOI: 10.1093/bib/bbae393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/06/2024] [Accepted: 07/29/2024] [Indexed: 08/13/2024] Open
Abstract
Understanding the intracellular dynamics of brain cells entails performing three-dimensional molecular simulations incorporating ultrastructural models that can capture cellular membrane geometries at nanometer scales. While there is an abundance of neuronal morphologies available online, e.g. from NeuroMorpho.Org, converting those fairly abstract point-and-diameter representations into geometrically realistic and simulation-ready, i.e. watertight, manifolds is challenging. Many neuronal mesh reconstruction methods have been proposed; however, their resulting meshes are either biologically unplausible or non-watertight. We present an effective and unconditionally robust method capable of generating geometrically realistic and watertight surface manifolds of spiny cortical neurons from their morphological descriptions. The robustness of our method is assessed based on a mixed dataset of cortical neurons with a wide variety of morphological classes. The implementation is seamlessly extended and applied to synthetic astrocytic morphologies that are also plausibly biological in detail. Resulting meshes are ultimately used to create volumetric meshes with tetrahedral domains to perform scalable in silico reaction-diffusion simulations for revealing cellular structure-function relationships. Availability and implementation: Our method is implemented in NeuroMorphoVis, a neuroscience-specific open source Blender add-on, making it freely accessible for neuroscience researchers.
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Affiliation(s)
- Marwan Abdellah
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Alessandro Foni
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Juan José García Cantero
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Nadir Román Guerrero
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Elvis Boci
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Adrien Fleury
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Jay S Coggan
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Daniel Keller
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Judit Planas
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Jean-Denis Courcol
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
| | - Georges Khazen
- Blue Brain Project, École Polytecnique Fédérale de Lausanne (EPFL), Campus Biotech, Chemin des Mines 9, Genève 1202, Switzerland
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3
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Zhu F, Shi Q, Jiang YH, Zhang YQ, Zhao H. Impaired synaptic function and hyperexcitability of the pyramidal neurons in the prefrontal cortex of autism-associated Shank3 mutant dogs. Mol Autism 2024; 15:9. [PMID: 38297387 PMCID: PMC10829216 DOI: 10.1186/s13229-024-00587-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/22/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND SHANK3 gene is a highly replicated causative gene for autism spectrum disorder and has been well characterized in multiple Shank3 mutant rodent models. When compared to rodents, domestic dogs are excellent animal models in which to study social cognition as they closely interact with humans and exhibit similar social behaviors. Using CRISPR/Cas9 editing, we recently generated a dog model carrying Shank3 mutations, which displayed a spectrum of autism-like behaviors, such as social impairment and heightened anxiety. However, the neural mechanism underlying these abnormal behaviors remains to be identified. METHODS We used Shank3 mutant dog models to examine possible relationships between Shank3 mutations and neuronal dysfunction. We studied electrophysiological properties and the synaptic transmission of pyramidal neurons from acute brain slices of the prefrontal cortex (PFC). We also examined dendrite elaboration and dendritic spine morphology in the PFC using biocytin staining and Golgi staining. We analyzed the postsynaptic density using electron microscopy. RESULTS We established a protocol for the electrophysiological recording of canine brain slices and revealed that excitatory synaptic transmission onto PFC layer 2/3 pyramidal neurons in Shank3 heterozygote dogs was impaired, and this was accompanied by reduced dendrite complexity and spine density when compared to wild-type dogs. Postsynaptic density structures were also impaired in Shank3 mutants; however, pyramidal neurons exhibited hyperexcitability. LIMITATIONS Causal links between impaired PFC pyramidal neuron function and behavioral alterations remain unclear. Further experiments such as manipulating PFC neuronal activity or restoring synaptic transmission in Shank3 mutant dogs are required to assess PFC roles in altered social behaviors. CONCLUSIONS Our study demonstrated the feasibility of using canine brain slices as a model system to study neuronal circuitry and disease. Shank3 haploinsufficiency causes morphological and functional abnormalities in PFC pyramidal neurons, supporting the notion that Shank3 mutant dogs are new and valid animal models for autism research.
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Affiliation(s)
- Feipeng Zhu
- State Key Laboratory for Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Shi
- State Key Laboratory for Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong-Hui Jiang
- Department of Genetics and Neuroscience, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Yong Q Zhang
- State Key Laboratory for Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Life Sciences, Hubei University, Wuhan, 430415, China.
| | - Hui Zhao
- State Key Laboratory for Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Department of Neurobiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
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4
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Choi J, Lee SE, Lee Y, Cho E, Chang S, Jeong WK. DXplorer: A Unified Visualization Framework for Interactive Dendritic Spine Analysis Using 3D Morphological Features. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2023; 29:1424-1437. [PMID: 34591770 DOI: 10.1109/tvcg.2021.3116656] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Dendritic spines are dynamic, submicron-scale protrusions on neuronal dendrites that receive neuronal inputs. Morphological changes in the dendritic spine often reflect alterations in physiological conditions and are indicators of various neuropsychiatric conditions. However, owing to the highly dynamic and heterogeneous nature of spines, accurate measurement and objective analysis of spine morphology are major challenges in neuroscience research. Most conventional approaches for analyzing dendritic spines are based on two-dimensional (2D) images, which barely reflect the actual three-dimensional (3D) shapes. Although some recent studies have attempted to analyze spines with various 3D-based features, it is still difficult to objectively categorize and analyze spines based on 3D morphology. Here, we propose a unified visualization framework for an interactive 3D dendritic spine analysis system, DXplorer, that displays 3D rendering of spines and plots the high-dimensional features extracted from the 3D mesh of spines. With this system, users can perform the clustering of spines interactively and explore and analyze dendritic spines based on high-dimensional features. We propose a series of high-dimensional morphological features extracted from a 3D mesh of dendritic spines. In addition, an interactive machine learning classifier with visual exploration and user feedback using an interactive 3D mesh grid view ensures a more precise classification based on the spine phenotype. A user study and two case studies were conducted to quantitatively verify the performance and usability of the DXplorer. We demonstrate that the system performs the entire analytic process effectively and provides high-quality, accurate, and objective analysis.
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5
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Redman WT, Wolcott NS, Montelisciani L, Luna G, Marks TD, Sit KK, Yu CH, Smith S, Goard MJ. Long-term transverse imaging of the hippocampus with glass microperiscopes. eLife 2022; 11:75391. [PMID: 35775393 PMCID: PMC9249394 DOI: 10.7554/elife.75391] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 06/12/2022] [Indexed: 11/19/2022] Open
Abstract
The hippocampus consists of a stereotyped neuronal circuit repeated along the septal-temporal axis. This transverse circuit contains distinct subfields with stereotyped connectivity that support crucial cognitive processes, including episodic and spatial memory. However, comprehensive measurements across the transverse hippocampal circuit in vivo are intractable with existing techniques. Here, we developed an approach for two-photon imaging of the transverse hippocampal plane in awake mice via implanted glass microperiscopes, allowing optical access to the major hippocampal subfields and to the dendritic arbor of pyramidal neurons. Using this approach, we tracked dendritic morphological dynamics on CA1 apical dendrites and characterized spine turnover. We then used calcium imaging to quantify the prevalence of place and speed cells across subfields. Finally, we measured the anatomical distribution of spatial information, finding a non-uniform distribution of spatial selectivity along the DG-to-CA1 axis. This approach extends the existing toolbox for structural and functional measurements of hippocampal circuitry.
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Affiliation(s)
- William T Redman
- Interdepartmental Graduate Program in Dynamical Neuroscience, University of California, Santa Barbara, United States
| | - Nora S Wolcott
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, United States
| | - Luca Montelisciani
- Cognitive and Systems Neuroscience Group, University of Amsterdam, Amsterdam, Netherlands
| | - Gabriel Luna
- Neuroscience Research Institute, University of California, Santa Barbara, United States
| | - Tyler D Marks
- Neuroscience Research Institute, University of California, Santa Barbara, United States
| | - Kevin K Sit
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, United States
| | - Che-Hang Yu
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, Santa Barbara, United States
| | - Spencer Smith
- Neuroscience Research Institute, University of California, Santa Barbara, United States.,Department of Electrical and Computer Engineering, University of California, Santa Barbara, Santa Barbara, United States
| | - Michael J Goard
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, United States.,Department of Psychological and Brain Sciences, University of California, Santa Barbara, United States
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Vidaurre-Gallart I, Fernaud-Espinosa I, Cosmin-Toader N, Talavera-Martínez L, Martin-Abadal M, Benavides-Piccione R, Gonzalez-Cid Y, Pastor L, DeFelipe J, García-Lorenzo M. A Deep Learning-Based Workflow for Dendritic Spine Segmentation. Front Neuroanat 2022; 16:817903. [PMID: 35370569 PMCID: PMC8967951 DOI: 10.3389/fnana.2022.817903] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/11/2022] [Indexed: 11/13/2022] Open
Abstract
The morphological analysis of dendritic spines is an important challenge for the neuroscientific community. Most state-of-the-art techniques rely on user-supervised algorithms to segment the spine surface, especially those designed for light microscopy images. Therefore, processing large dendritic branches is costly and time-consuming. Although deep learning (DL) models have become one of the most commonly used tools in image segmentation, they have not yet been successfully applied to this problem. In this article, we study the feasibility of using DL models to automatize spine segmentation from confocal microscopy images. Supervised learning is the most frequently used method for training DL models. This approach requires large data sets of high-quality segmented images (ground truth). As mentioned above, the segmentation of microscopy images is time-consuming and, therefore, in most cases, neuroanatomists only reconstruct relevant branches of the stack. Additionally, some parts of the dendritic shaft and spines are not segmented due to dyeing problems. In the context of this research, we tested the most successful architectures in the DL biomedical segmentation field. To build the ground truth, we used a large and high-quality data set, according to standards in the field. Nevertheless, this data set is not sufficient to train convolutional neural networks for accurate reconstructions. Therefore, we implemented an automatic preprocessing step and several training strategies to deal with the problems mentioned above. As shown by our results, our system produces a high-quality segmentation in most cases. Finally, we integrated several postprocessing user-supervised algorithms in a graphical user interface application to correct any possible artifacts.
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Affiliation(s)
| | - Isabel Fernaud-Espinosa
- Instituto Cajal, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Madrid, Spain
| | | | | | - Miguel Martin-Abadal
- Departament de Matemàtiques i Informàtica, Universitat de les Illes Balears, Palma, Spain
| | - Ruth Benavides-Piccione
- Instituto Cajal, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Madrid, Spain
- *Correspondence: Ruth Benavides-Piccione
| | - Yolanda Gonzalez-Cid
- Departament de Matemàtiques i Informàtica, Universitat de les Illes Balears, Palma, Spain
- E-Health and Multidisciplinary Telemedicine Through Cyber-Physical Intelligent Systems, IdISBa, Palma, Spain
| | - Luis Pastor
- VG-LAB, Universidad Rey Juan Carlos, Móstoles, Spain
- Research Center for Computational Simulation (CCS), Madrid, Spain
| | - Javier DeFelipe
- Instituto Cajal, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Madrid, Spain
| | - Marcos García-Lorenzo
- VG-LAB, Universidad Rey Juan Carlos, Móstoles, Spain
- Research Center for Computational Simulation (CCS), Madrid, Spain
- Marcos García-Lorenzo
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Okabe S. Recent advances in computational methods for measurement of dendritic spines imaged by light microscopy. Microscopy (Oxf) 2021; 69:196-213. [PMID: 32244257 DOI: 10.1093/jmicro/dfaa016] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 02/04/2020] [Accepted: 03/23/2020] [Indexed: 12/13/2022] Open
Abstract
Dendritic spines are small protrusions that receive most of the excitatory inputs to the pyramidal neurons in the neocortex and the hippocampus. Excitatory neural circuits in the neocortex and hippocampus are important for experience-dependent changes in brain functions, including postnatal sensory refinement and memory formation. Several lines of evidence indicate that synaptic efficacy is correlated with spine size and structure. Hence, precise and accurate measurement of spine morphology is important for evaluation of neural circuit function and plasticity. Recent advances in light microscopy and image analysis techniques have opened the way toward a full description of spine nanostructure. In addition, large datasets of spine nanostructure can be effectively analyzed using machine learning techniques and other mathematical approaches, and recent advances in super-resolution imaging allow researchers to analyze spine structure at an unprecedented level of precision. This review summarizes computational methods that can effectively identify, segment and quantitate dendritic spines in either 2D or 3D imaging. Nanoscale analysis of spine structure and dynamics, combined with new mathematical approaches, will facilitate our understanding of spine functions in physiological and pathological conditions.
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Affiliation(s)
- Shigeo Okabe
- Department of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
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8
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Pchitskaya E, Bezprozvanny I. Dendritic Spines Shape Analysis-Classification or Clusterization? Perspective. Front Synaptic Neurosci 2020; 12:31. [PMID: 33117142 PMCID: PMC7561369 DOI: 10.3389/fnsyn.2020.00031] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/02/2020] [Indexed: 12/11/2022] Open
Abstract
Dendritic spines are small protrusions from the dendrite membrane, where contact with neighboring axons is formed in order to receive synaptic input. Changes in size, shape, and density of synaptic spines are associated with learning and memory, and observed after drug abuse in a variety of neurodegenerative, neurodevelopmental, and psychiatric disorders. Due to the preeminent importance of synaptic spines, there have been major efforts into developing techniques that enable visualization and analysis of dendritic spines in cultured neurons, in fixed slices and in intact brain tissue. The classification of synaptic spines into predefined morphological groups is a standard approach in neuroscience research, where spines are divided into fixed categories such as thin, mushroom, and stubby subclasses. This study examines accumulated evidence that supports the existence of dendritic spine shapes as a continuum rather than separated classes. Using new approaches and software tools we reflect on complex dendritic spine shapes, positing that understanding of their highly dynamic nature is required to perform analysis of their morphology. The study discusses and compares recently developed algorithms that rely on clusterization rather than classification, therefore enabling new levels of spine shape analysis. We reason that improved methods of analysis may help to investigate a link between dendritic spine shape and its function, facilitating future studies of learning and memory as well as studies of brain disorders.
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Affiliation(s)
- Ekaterina Pchitskaya
- Laboratory of Molecular Neurodegeneration, Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Ilya Bezprozvanny
- Laboratory of Molecular Neurodegeneration, Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.,Department of Physiology, UT Southwestern Medical Center at Dallas, Dallas, TX, United States
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A rapid and accurate method to quantify neurite outgrowth from cell and tissue cultures: Two image analytic approaches using adaptive thresholds or machine learning. J Neurosci Methods 2019; 331:108522. [PMID: 31734324 DOI: 10.1016/j.jneumeth.2019.108522] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/23/2019] [Accepted: 11/13/2019] [Indexed: 11/23/2022]
Abstract
BACKGROUND Assessments of axonal outgrowth and dendritic development are essential readouts in many in vitro models in the field of neuroscience. Available analysis software is based on the assessment of fixed immunolabelled tissue samples, making it impossible to follow the dynamic development of neurite outgrowth. Thus, automated algorithms that efficiently analyse brightfield images, such as those obtained during time-lapse microscopy, are needed. NEW METHOD We developed and validated algorithms to quantitatively assess neurite outgrowth from living and unstained spinal cord slice cultures (SCSCs) and dorsal root ganglion cultures (DRGCs) based on an adaptive thresholding approach called NeuriteSegmantation. We used a machine learning approach to evaluate dendritic development from dissociate neuron cultures. RESULTS NeuriteSegmentation successfully recognized axons in brightfield images of SCSCs and DRGCs. The temporal pattern of axonal growth was successfully assessed. In dissociate neuron cultures the total number of cells and their outgrowth of dendrites were successfully assessed using machine learning. COMPARISON WITH EXISTING METHODS The methods were positively correlated and were more time-saving than manual counts, having performing times varying from 0.5-2 min. In addition, NeuriteSegmentation was compared to NeuriteJ®, that uses global thresholding, being more reliable in recognizing axons in areas of intense background. CONCLUSION The developed image analysis methods were more time-saving and user-independent than established approaches. Moreover, by using adaptive thresholding, we could assess images with large variations in background intensity. These tools may prove valuable in the quantitative analysis of axonal and dendritic outgrowth from numerous in vitro models used in neuroscience.
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10
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Quantitative 3-D morphometric analysis of individual dendritic spines. Sci Rep 2018; 8:3545. [PMID: 29476060 PMCID: PMC5825014 DOI: 10.1038/s41598-018-21753-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 02/05/2018] [Indexed: 01/09/2023] Open
Abstract
The observation and analysis of dendritic spines morphological changes poses a major challenge in neuroscience studies. The alterations of their density and/or morphology are indicators of the cellular processes involved in neural plasticity underlying learning and memory, and are symptomatic in neuropsychiatric disorders. Despite ongoing intense investigations in imaging approaches, the relationship between changes in spine morphology and synaptic function is still unknown. The existing quantitative analyses are difficult to perform and require extensive user intervention. Here, we propose a new method for (1) the three-dimensional (3-D) segmentation of dendritic spines using a multi-scale opening approach and (2) define 3-D morphological attributes of individual spines for the effective assessment of their structural plasticity. The method was validated using confocal light microscopy images of dendritic spines from dissociated hippocampal cultures and brain slices (1) to evaluate accuracy relative to manually labeled ground-truth annotations and relative to the state-of-the-art Imaris tool, (2) to analyze reproducibility of user-independence of the segmentation method, and (3) to quantitatively analyze morphological changes in individual spines before and after chemically induced long-term potentiation. The method was monitored and used to precisely describe the morphology of individual spines in real-time using consecutive images of the same dendritic fragment.
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Ghani MU, Mesadi F, Kanık SD, Argunşah AÖ, Hobbiss AF, Israely I, Ünay D, Taşdizen T, Çetin M. Dendritic spine classification using shape and appearance features based on two-photon microscopy. J Neurosci Methods 2016; 279:13-21. [PMID: 27998713 DOI: 10.1016/j.jneumeth.2016.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 11/30/2022]
Abstract
BACKGROUND Neuronal morphology and function are highly coupled. In particular, dendritic spine morphology is strongly governed by the incoming neuronal activity. The first step towards understanding the structure-function relationships is to classify spine shapes into the main spine types suggested in the literature. Due to the lack of reliable automated analysis tools, classification is mostly performed manually, which is a time-intensive task and prone to subjectivity. NEW METHOD We propose an automated method to classify dendritic spines using shape and appearance features based on challenging two-photon laser scanning microscopy (2PLSM) data. Disjunctive Normal Shape Models (DNSM) is a recently proposed parametric shape representation. We perform segmentation of spine images by applying DNSM and use the resulting representation as shape features. Furthermore, we use Histogram of oriented gradients (HOG) to extract appearance features. In this context, we propose a kernel density estimation (KDE) based framework for dendritic spine classification, which uses these shape and appearance features. RESULTS Our shape and appearance features based approach combined with Neural Network (NN) correctly classifies 87.06% of spines on a dataset of 456 spines. COMPARISON WITH EXISTING METHODS Our proposed method outperforms standard morphological feature based approaches. Our KDE based framework also enables neuroscientists to analyze the separability of spine shape classes in the likelihood ratio space, which leads to further insights about nature of the spine shape analysis problem. CONCLUSIONS Results validate that performance of our proposed approach is comparable to a human expert. It also enable neuroscientists to study shape statistics in the likelihood ratio space.
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Affiliation(s)
- Muhammad Usman Ghani
- Signal Processing and Information Systems Lab., Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.
| | - Fitsum Mesadi
- Electrical and Computer Engineering Department, University of Utah, Salt Lake City, UT, USA
| | - Sümeyra Demir Kanık
- Signal Processing and Information Systems Lab., Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Ali Özgür Argunşah
- Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Lisbon, Portugal.
| | - Anna Felicity Hobbiss
- Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Inbal Israely
- Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Lisbon, Portugal.
| | - Devrim Ünay
- Biomedical Engineering Department, Faculty of Engineering, Izmir University of Economics, Izmir, Turkey
| | - Tolga Taşdizen
- Electrical and Computer Engineering Department, University of Utah, Salt Lake City, UT, USA
| | - Müjdat Çetin
- Signal Processing and Information Systems Lab., Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
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12
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Basu S, Plewczynski D, Saha S, Roszkowska M, Magnowska M, Baczynska E, Wlodarczyk J. 2dSpAn: semiautomated 2-d segmentation, classification and analysis of hippocampal dendritic spine plasticity. ACTA ACUST UNITED AC 2016; 32:2490-8. [PMID: 27153678 DOI: 10.1093/bioinformatics/btw172] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 03/26/2016] [Indexed: 12/18/2022]
Abstract
MOTIVATION Accurate and effective dendritic spine segmentation from the dendrites remains as a challenge for current neuroimaging research community. In this article, we present a new method (2dSpAn) for 2-d segmentation, classification and analysis of structural/plastic changes of hippocampal dendritic spines. A user interactive segmentation method with convolution kernels is designed to segment the spines from the dendrites. Formal morphological definitions are presented to describe key attributes related to the shape of segmented spines. Spines are automatically classified into one of four classes: Stubby, Filopodia, Mushroom and Spine-head Protrusions. RESULTS The developed method is validated using confocal light microscopy images of dendritic spines from dissociated hippocampal cultures for: (i) quantitative analysis of spine morphological changes, (ii) reproducibility analysis for assessment of user-independence of the developed software and (iii) accuracy analysis with respect to the manually labeled ground truth images, and also with respect to the available state of the art. The developed method is monitored and used to precisely describe the morphology of individual spines in real-time experiments, i.e. consequent images of the same dendritic fragment. AVAILABILITY AND IMPLEMENTATION The software and the source code are available at https://sites.google.com/site/2dspan/ under open-source license for non-commercial use. CONTACT subhadip@cse.jdvu.ac.in or j.wlodarczyk@nencki.gov.pl SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Subhadip Basu
- Department of Computer Science and Engineering, Jadavpur University, Kolkata 700032, India
| | | | - Satadal Saha
- Department of Electronics and Communication Engineering, MCKV Institute of Engineering, Howrah 711204, India
| | - Matylda Roszkowska
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Marta Magnowska
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Ewa Baczynska
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Jakub Wlodarczyk
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
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Dendritic Spine Shape Analysis: A Clustering Perspective. LECTURE NOTES IN COMPUTER SCIENCE 2016. [DOI: 10.1007/978-3-319-46604-0_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Maiti P, Manna J, McDonald MP. Merging advanced technologies with classical methods to uncover dendritic spine dynamics: A hot spot of synaptic plasticity. Neurosci Res 2015; 96:1-13. [DOI: 10.1016/j.neures.2015.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 01/08/2023]
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Workman JL, Brummelte S, Galea LAM. Postpartum corticosterone administration reduces dendritic complexity and increases the density of mushroom spines of hippocampal CA3 arbours in dams. J Neuroendocrinol 2013; 25:119-30. [PMID: 22935038 DOI: 10.1111/j.1365-2826.2012.02380.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 08/15/2012] [Accepted: 08/24/2012] [Indexed: 12/01/2022]
Abstract
Postpartum depression (PPD) affects approximately 15% of mothers after giving birth. A complete understanding of depression during the postpartum period has yet to be established, although disruptions in the hypothalamic-pituitary-adrenal axis and stress during the postpartum may be involved. To model these components in rats, we administered high corticosterone (CORT) postpartum, which increases immobility in the forced swim test (FST), and reduces maternal care, body weight and hippocampal cell proliferation in dams. The hippocampus is altered in response to chronic stress, exposure to high glucocorticoids and in major depression in humans. In the present study, we examined whether high CORT reduced dendritic complexity and spines in the CA3 region of the hippocampus. Additionally, housing complexity was manipulated so that dams and litters were housed either with tubes (complex) or without tubes (impoverished) to investigate the consequences of new animal care regulations. Dams received 40 mg/kg/day of CORT or oil starting on day 2 postpartum for 23 days. Maternal behaviours were assessed on postpartum days 2-8 and dams were tested using the FST on days 21 and 22. Dams were killed on day 24 and brains were processed for Golgi impregnation. Pyramidal cells in the CA3 subfield were traced using a camera lucida and analysed for branch points and dendritic complexity, as well as spine density and type on both basal and apical arbours. As previously established, high CORT postpartum reduced maternal care and increased immobility in the FST, which is a measure of depressive-like behaviour. High CORT postpartum reduced the complexity of basal arbours and increased mushroom spines on both apical and basal dendrites. Housing complexity had no effect on spines of CA3 pyramidal cells but modest effects on cell morphology. These data show that chronic high CORT in postpartum females alters hippocampal morphology and may provide insight regarding the neurobiological consequences of high stress or CORT during the postpartum period, as well as be relevant for postpartum stress or depression.
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Affiliation(s)
- J L Workman
- Department of Psychology, University of British Columbia, Vancouver, BC, Canada
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Bibliography Current World Literature. CURRENT ORTHOPAEDIC PRACTICE 2012. [DOI: 10.1097/bco.0b013e318256e7f2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Mancuso JJ, Chen Y, Li X, Xue Z, Wong STC. Methods of dendritic spine detection: from Golgi to high-resolution optical imaging. Neuroscience 2012; 251:129-40. [PMID: 22522468 DOI: 10.1016/j.neuroscience.2012.04.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 03/30/2012] [Accepted: 04/05/2012] [Indexed: 12/18/2022]
Abstract
Dendritic spines, the bulbous protrusions that form the postsynaptic half of excitatory synapses, are one of the most prominent features of neurons and have been imaged and studied for over a century. In that time, changes in the number and morphology of dendritic spines have been correlated to the developmental process as well as the pathophysiology of a number of neurodegenerative diseases. Due to the sheer scale of synaptic connectivity in the brain, work to date has merely scratched the surface in the study of normal spine function and pathology. This review will highlight traditional approaches to the imaging of dendritic spines and newer approaches made possible by advances in microscopy, protein engineering, and image analysis. The review will also describe recent work that is leading researchers toward the possibility of a systematic and comprehensive study of spine anatomy throughout the brain.
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Affiliation(s)
- J J Mancuso
- Department of Systems Medicine and Bioengineering, The Methodist Hospital Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA; Ting Tsung and Wei Fong Chao Center for Bioinformatics Research and Imaging in Neurosciences, USA
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