Mobilizing the base of neuroscience data: the case of neuronal morphologies

Despite the explosive growth of bioinformatics, data sharing has not yet become routine in neuroscience, possibly because of several broad-spanning issues, from data heterogeneity to privacy regulations. We present the case of neuronal morphology as an ideal example of shareable data. Drawing from recent experience, we argue that the tremendous research potential of existing (and largely unused) digital reconstructions should diffuse any reticence to sharing this type of data.

[1]  Joseph J. Capowski,et al.  Computer Techniques in Neuroanatomy , 1989, Springer US.

[2]  E M Glaser,et al.  Neuron imaging with Neurolucida--a PC-based system for image combining microscopy. , 1990, Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society.

[3]  M. Nelen,et al.  Abnormal behavior associated with a point mutation in the structural gene for monoamine oxidase A. , 1993, Science.

[4]  S. Snyder,et al.  Behavioural abnormalities in male mice lacking neuronal nitric oxide synthase , 1995, Nature.

[5]  T. Sejnowski,et al.  [Letters to nature] , 1996, Nature.

[6]  Nicholas T. Carnevale,et al.  The NEURON Simulation Environment , 1997, Neural Computation.

[7]  Perry L. Miller,et al.  Database tools for integrating and searching membrane property data correlated with neuronal morphology , 1998, Journal of Neuroscience Methods.

[8]  D A Turner,et al.  Dendrites of classes of hippocampal neurons differ in structural complexity and branching patterns , 1999, The Journal of comparative neurology.

[9]  Stephen H. Koslow,et al.  Should the neuroscience community make a paradigm shift to sharing primary data? , 2000, Nature Neuroscience.

[10]  Jeffrey L. Krichmar,et al.  L-neuron: A modeling tool for the efficient generation and parsimonious description of dendritic morphology , 2000, Neurocomputing.

[11]  Giorgio A. Ascoli,et al.  Algorithmic Extraction of Morphological Statistics from Electronic Archives of Neuroanatomy , 2001, IWANN.

[12]  Daniel H. Geschwind,et al.  Sharing gene expression data: an array of options , 2001, Nature Reviews Neuroscience.

[13]  R. Nelson,et al.  Molecular basis of aggression , 2001, Trends in Neurosciences.

[14]  Michael F. Miles,et al.  Microarrays: lost in a storm of data? , 2001, Nature Reviews Neuroscience.

[15]  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.

[16]  R. Nelson,et al.  Brain serotonin dysfunction accounts for aggression in male mice lacking neuronal nitric oxide synthase. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Kevin G. Becker,et al.  The sharing of cDNA microarray data , 2001, Nature Reviews Neuroscience.

[18]  Nigel H. Goddard,et al.  Non-curated distributed databases for experimental data and models in neuroscience , 2002, Network.

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

[20]  A. Caspi,et al.  Role of Genotype in the Cycle of Violence in Maltreated Children , 2002, Science.

[21]  Stuart D. Washington,et al.  Effects of dendritic morphology on CA3 pyramidal cell electrophysiology: a simulation study , 2002, Brain Research.

[22]  Irwin D Waldman,et al.  Genetic and environmental influences on antisocial behavior: a meta-analysis of twin and adoption studies. , 2002, Psychological bulletin.

[23]  Stephen H Koslow,et al.  Sharing primary data: a threat or asset to discovery? , 2002, Nature Reviews Neuroscience.

[24]  T. Moffitt,et al.  Toward an Animal Model for Antisocial Behavior: Parallels Between Mice and Humans , 2003, Behavior genetics.

[25]  Badrinath Roysam,et al.  Automated Three-Dimensional Tracing of Neurons in Confocal and Brightfield Images , 2003, Microscopy and Microanalysis.

[26]  Nora D Volkow,et al.  Neuroscience Networks , 2003, PLoS biology.

[27]  Ulla Ruotsalainen,et al.  Neuroscience data and tool sharing , 2003, Neuroinformatics.

[28]  Rolf Kötter,et al.  Neuroscience databases : a practical guide , 2003 .

[29]  David N. Kennedy,et al.  An information science infrastructure for neuroscience , 2003, Neuroinformatics.

[30]  Douglas B. Ehlenberger,et al.  Automated reconstruction of three-dimensional neuronal morphology from laser scanning microscopy images. , 2003, Methods.

[31]  G. Ascoli,et al.  Quantitative morphometry of hippocampal pyramidal cells: Differences between anatomical classes and reconstructing laboratories , 2004, The Journal of comparative neurology.

[32]  Scott T. Grafton,et al.  Sharing neuroimaging studies of human cognition , 2004, Nature Neuroscience.

[33]  L. Eaves,et al.  Childhood adversity, monoamine oxidase a genotype, and risk for conduct disorder. , 2004, Archives of general psychiatry.

[34]  Nicholas T. Carnevale,et al.  ModelDB: A Database to Support Computational Neuroscience , 2004, Journal of Computational Neuroscience.

[35]  Michael Scholz,et al.  New methods for the computer-assisted 3-D reconstruction of neurons from confocal image stacks , 2004, NeuroImage.

[36]  Explore Configuring,et al.  A Simulation Study to , 2004 .

[37]  D. Chklovskii,et al.  Neurogeometry and potential synaptic connectivity , 2005, Trends in Neurosciences.

[38]  Giorgio A Ascoli,et al.  Developmental changes in spinal motoneuron dendrites in neonatal mice , 2005, The Journal of comparative neurology.

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

[40]  Giorgio A Ascoli,et al.  Signal propagation in oblique dendrites of CA1 pyramidal cells. , 2005, Journal of neurophysiology.

[41]  G. Ascoli,et al.  Morphological homeostasis in cortical dendrites , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[42]  H. Markram.  The Blue Brain Project , 2006, Nature Reviews Neuroscience.

[43]  Giorgio A. Ascoli,et al.  A cross-platform freeware tool for digital reconstruction of neuronal arborizations from image stacks , 2007, Neuroinformatics.

[44]  Stephen H. Koslow,et al.  Celebrating a decade of neuroscience databases , 2007, Neuroinformatics.

[45]  Simone Santini,et al.  The cell-centered database , 2007, Neuroinformatics.

[46]  Larry W. Swanson,et al.  Brain architecture management system , 2007, Neuroinformatics.

[47]  David N. Kennedy,et al.  The impact of Neuroinformatics , 2007, Neuroinformatics.

[48]  Anders M. Dale,et al.  Towards effective and rewarding data sharing , 2003, Neuroinformatics.

[49]  Rolf Kötter,et al.  Online retrieval, processing, and visualization of primate connectivity data from the CoCoMac Database , 2007, Neuroinformatics.

[50]  Daniel Gardner,et al.  A gateway to the future of neuroinformatics , 2007, Neuroinformatics.