Automated Sholl analysis of digitized neuronal morphology at multiple scales: Whole cell Sholl analysis versus Sholl analysis of arbor subregions

The morphology of dendrites and the axon determines how a neuron processes and transmits information. Neurite morphology is frequently analyzed by Sholl analysis or by counting the total number of neurites and branch tips. However, the time and resources required to perform such analysis by hand is prohibitive for the processing of large data sets and introduces problems with data auditing and reproducibility. Furthermore, analyses performed by hand or using course‐grained morphometric data extraction tools can obscure subtle differences in data sets because they do not store the data in a form that facilitates the application of multiple analytical tools. To address these shortcomings, we have developed a program (titled “Bonfire”) to facilitate digitization of neurite morphology and subsequent Sholl analysis. Our program builds upon other available open‐source morphological analysis tools by performing Sholl analysis on subregions of the neuritic arbor, enabling the detection of local level changes in dendrite and axon branching behavior. To validate this new tool, we applied Bonfire analysis to images of hippocampal neurons treated with 25 ng/ml brain‐derived neurotrophic factor (BDNF) and untreated control neurons. Consistent with prior findings, conventional Sholl analysis revealed that global exposure to BDNF increases the number of neuritic intersections proximal to the soma. Bonfire analysis additionally uncovers that BDNF treatment affects both root processes and terminal processes with no effect on intermediate neurites. Taken together, our data suggest that global exposure of hippocampal neurons to BDNF results in a reorganization of neuritic segments within their arbors, but not necessarily a change in their number or length. These findings were only made possible by the neurite‐specific Sholl data returned by Bonfire analysis. © 2010 International Society for Advancement of Cytometry

[1]  J. van Pelt,et al.  Growth of pyramidal, but not non‐pyramidal, dendrites in long‐term organotypic explants of neonatal rat neocortex chronically exposed to neurotrophin‐3 , 1998, The European journal of neuroscience.

[2]  B. Firestein,et al.  NOS1AP Regulates Dendrite Patterning of Hippocampal Neurons through a Carboxypeptidase E-Mediated Pathway , 2009, The Journal of Neuroscience.

[3]  Douglas B. Ehlenberger,et al.  Rayburst sampling, an algorithm for automated three-dimensional shape analysis from laser scanning microscopy images , 2006, Nature Protocols.

[4]  J. McNamara,et al.  Increased Expression of Brain-Derived Neurotrophic Factor Induces Formation of Basal Dendrites and Axonal Branching in Dentate Granule Cells in Hippocampal Explant Cultures , 2002, The Journal of Neuroscience.

[5]  Paul J. Harrison.  The neuropathology of schizophrenia , 2008 .

[6]  Giorgio A. Ascoli,et al.  Algorithmic reconstruction of complete axonal arborizations in rat hippocampal neurons , 2005, Neurocomputing.

[7]  B. Lom,et al.  Local and Target-Derived Brain-Derived Neurotrophic Factor Exert Opposing Effects on the Dendritic Arborization of Retinal Ganglion Cells In Vivo , 2002, The Journal of Neuroscience.

[8]  Sten Grillner,et al.  Global Neuroinformatics: The International Neuroinformatics Coordinating Facility , 2007, The Journal of Neuroscience.

[9]  Alexander E. Dityatev,et al.  Natural variability in the number of dendritic segments: Model‐based inferences about branching during neurite outgrowth , 1997, The Journal of comparative neurology.

[10]  G. Ascoli,et al.  NeuroMorpho.Org: A Central Resource for Neuronal Morphologies , 2007, The Journal of Neuroscience.

[11]  J. McNamara,et al.  Selective enhancement of axonal branching of cultured dentate gyrus neurons by neurotrophic factors , 1995, Neuroscience.

[12]  M. Pool,et al.  NeuriteTracer: A novel ImageJ plugin for automated quantification of neurite outgrowth , 2008, Journal of Neuroscience Methods.

[13]  Giorgio A. Ascoli,et al.  A Comparative Computer Simulation of Dendritic Morphology , 2008, PLoS Comput. Biol..

[14]  Christof Koch,et al.  The role of single neurons in information processing , 2000, Nature Neuroscience.

[15]  J. van Pelt,et al.  Analysis of binary trees when occasional multifurcations can be considered as aggregates of bifurcations. , 1990, Bulletin of mathematical biology.

[16]  Bartlett W. Mel,et al.  Impact of Active Dendrites and Structural Plasticity on the Memory Capacity of Neural Tissue , 2001, Neuron.

[17]  R. C Cannon,et al.  An on-line archive of reconstructed hippocampal neurons , 1998, Journal of Neuroscience Methods.

[18]  L. C. Katz,et al.  Destabilization of Cortical Dendrites and Spines by BDNF , 1999, Neuron.

[19]  W. Welsh,et al.  Structural characterization of the zinc binding domain in cytosolic PSD‐95 interactor (cypin): Role of zinc binding in guanine deamination and dendrite branching , 2008, Proteins.

[20]  B. Firestein,et al.  The Yin–Yang of Dendrite Morphology: Unity of Actin and Microtubules , 2008, Molecular Neurobiology.

[21]  J. van Pelt,et al.  Growth models (including terminal and segmental branching) for topological binary trees. , 1985, Bulletin of mathematical biology.

[22]  Nelson Spruston,et al.  Dendritic Signal Integration , 2009 .

[23]  Kaoru Sugimura,et al.  Self-organizing Mechanism for Development of Space-filling Neuronal Dendrites , 2007, PLoS Comput. Biol..

[24]  Y. Barde,et al.  Binding of brain-derived neurotrophic factor to the nerve growth factor receptor , 1990, Neuron.

[25]  Changming Sun,et al.  Automated analysis of neurite branching in cultured cortical neurons using HCA‐Vision , 2007, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[26]  Douglas B. Ehlenberger,et al.  New techniques for imaging, digitization and analysis of three-dimensional neural morphology on multiple scales , 2005, Neuroscience.

[27]  Anirvan Ghosh,et al.  Molecular control of cortical dendrite development. , 2002, Annual review of neuroscience.

[28]  A. McAllister.  Neurotrophins and neuronal differentiation in the central nervous system , 2001, Cellular and Molecular Life Sciences CMLS.

[29]  M. Dragunow.  High-content analysis in neuroscience , 2008, Nature Reviews Neuroscience.

[30]  N. Spruston,et al.  Diversity and dynamics of dendritic signaling. , 2000, Science.

[31]  T. Arendt,et al.  Dendritic changes in the basal nucleus of meynert and in the diagonal band nucleus in Alzheimer's disease—A quantitative Golgi investigation , 1986, Neuroscience.

[32]  H. Moser,et al.  Dendritic anomalies in disorders associated with mental retardation. , 1999, Cerebral cortex.

[33]  Barbara F. Akum,et al.  Activity-Independent Regulation of Dendrite Patterning by Postsynaptic Density Protein PSD-95 , 2006, The Journal of Neuroscience.

[34]  Slawomir Nasuto.  Three-Dimensional Reconstruction of Neurons with Neuromantic , 2007 .

[35]  D. Ristanovic,et al.  The Sholl analysis of neuronal cell images: semi-log or log-log method? , 2007, Journal of theoretical biology.

[36]  M. Lykissas,et al.  The role of neurotrophins in axonal growth, guidance, and regeneration. , 2007, Current neurovascular research.

[37]  Jaap van Pelt,et al.  Topological analysis of binary tree structures when occasional multifurcations occur , 1985 .

[38]  E. Shooter,et al.  BDNF overexpression increases dendrite complexity in hippocampal dentate gyrus , 2002, Neuroscience.

[39]  J. Pierri,et al.  Altered Cortical Glutamate Neurotransmission in Schizophrenia , 2003 .

[40]  Gang-yi Wu,et al.  Regulation of Dendritic Morphogenesis by Ras–PI3K–Akt–mTOR and Ras–MAPK Signaling Pathways , 2005, The Journal of Neuroscience.

[41]  H. Lee,et al.  Quantitative neurite outgrowth measurement based on image segmentation with topological dependence , 2009, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[42]  D. Bredt,et al.  Cypin A Cytosolic Regulator of PSD-95 Postsynaptic Targeting , 1999, Neuron.

[43]  Sholl Da.  Dendritic organization in the neurons of the visual and motor cortices of the cat. , 1953 .

[44]  Andreas Schierwagen,et al.  Morphological analysis and modeling of neuronal dendrites. , 2004, Mathematical biosciences.

[45]  Jaap van Pelt,et al.  Measures for quantifying dendritic arborizations , 2002, Network.

[46]  Nicholas T. Carnevale,et al.  Simulation of networks of spiking neurons: A review of tools and strategies , 2006, Journal of Computational Neuroscience.

[47]  Giorgio A Ascoli,et al.  Neuroanatomical algorithms for dendritic modelling , 2002, Network.

[48]  M. Häusser,et al.  Propagation of action potentials in dendrites depends on dendritic morphology. , 2001, Journal of neurophysiology.

[49]  E Meijering,et al.  Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images , 2004, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[50]  J. Pierri,et al.  Altered cortical glutamate neurotransmission in schizophrenia: evidence from morphological studies of pyramidal neurons. , 2003, Annals of the New York Academy of Sciences.

[51]  Jonathan Popko,et al.  Automated analysis of NeuronJ tracing data , 2009, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[52]  The Newsletter of the Society for the Study of Artificial Intelligence and Simulation of Behaviour Quarterly Three-Dimensional Reconstruction of Neurons with Neuromantic , 2007 .

[53]  Barbara F. Akum,et al.  Cypin regulates dendrite patterning in hippocampal neurons by promoting microtubule assembly , 2004, Nature Neuroscience.

[54]  Andreas T. Schaefer,et al.  Coincidence detection in pyramidal neurons is tuned by their dendritic branching pattern. , 2003, Journal of neurophysiology.

[55]  G. Ascoli,et al.  L-Measure: a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies , 2008, Nature Protocols.

[56]  G A Ascoli,et al.  Generation, description and storage of dendritic morphology data. , 2001, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[57]  Humberto Gutierrez,et al.  A fast and accurate procedure for deriving the Sholl profile in quantitative studies of neuronal morphology , 2007, Journal of Neuroscience Methods.

[58]  S. Zeiler,et al.  Development/Plasticity/Repair Brain-Derived Neurotrophic Factor Is Required for the Maintenance of Cortical Dendrites , 2022 .

[59]  B. Firestein,et al.  RhoA Regulates Dendrite Branching in Hippocampal Neurons by Decreasing Cypin Protein Levels , 2007, The Journal of Neuroscience.

[60]  Anirvan Ghosh,et al.  BDNF regulates primary dendrite formation in cortical neurons via the PI3-kinase and MAP kinase signaling pathways. , 2005, Journal of neurobiology.

[61]  Lawrence C. Katz,et al.  Neurotrophins regulate dendritic growth in developing visual cortex , 1995, Neuron.

[62]  J. Pelt,et al.  Growth models (including terminal and segmental branching) for topological binary trees , 1985 .

[63]  C. Hoogenraad,et al.  Control of Dendritic Arborization by the Phosphoinositide-3′-Kinase–Akt–Mammalian Target of Rapamycin Pathway , 2005, The Journal of Neuroscience.

[64]  Katherine C. Chen,et al.  Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. , 2003, Current opinion in cell biology.

[65]  Giorgio A Ascoli,et al.  Statistical determinants of dendritic morphology in hippocampal pyramidal neurons: A hidden Markov model , 2005, Hippocampus.

[66]  Idan Segev,et al.  Optimization principles of dendritic structure , 2007, Theoretical Biology and Medical Modelling.

[67]  G. Elston.  Pyramidal Cells of the Frontal Lobe: All the More Spinous to Think With , 2000, The Journal of Neuroscience.

[68]  Wen G. Chen,et al.  BDNF Regulates the Translation of a Select Group of mRNAs by a Mammalian Target of Rapamycin-Phosphatidylinositol 3-Kinase-Dependent Pathway during Neuronal Development , 2004, The Journal of Neuroscience.