Literature DB >> 25653123

The importance of metadata to assess information content in digital reconstructions of neuronal morphology.

Ruchi Parekh1, Rubén Armañanzas, Giorgio A Ascoli.   

Abstract

Digital reconstructions of axonal and dendritic arbors provide a powerful representation of neuronal morphology in formats amenable to quantitative analysis, computational modeling, and data mining. Reconstructed files, however, require adequate metadata to identify the appropriate animal species, developmental stage, brain region, and neuron type. Moreover, experimental details about tissue processing, neurite visualization and microscopic imaging are essential to assess the information content of digital morphologies. Typical morphological reconstructions only partially capture the underlying biological reality. Tracings are often limited to certain domains (e.g., dendrites and not axons), may be incomplete due to tissue sectioning, imperfect staining, and limited imaging resolution, or can disregard aspects irrelevant to their specific scientific focus (such as branch thickness or depth). Gauging these factors is critical in subsequent data reuse and comparison. NeuroMorpho.Org is a central repository of reconstructions from many laboratories and experimental conditions. Here, we introduce substantial additions to the existing metadata annotation aimed to describe the completeness of the reconstructed neurons in NeuroMorpho.Org. These expanded metadata form a suitable basis for effective description of neuromorphological data.

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Year:  2015        PMID: 25653123      PMCID: PMC4722868          DOI: 10.1007/s00441-014-2103-6

Source DB:  PubMed          Journal:  Cell Tissue Res        ISSN: 0302-766X            Impact factor:   5.249


  32 in total

1.  Regional dendritic and spine variation in human cerebral cortex: a quantitative golgi study.

Authors:  B Jacobs; M Schall; M Prather; E Kapler; L Driscoll; S Baca; J Jacobs; K Ford; M Wainwright; M Treml
Journal:  Cereb Cortex       Date:  2001-06       Impact factor: 5.357

2.  Neuronal morphology data bases: morphological noise and assesment of data quality.

Authors:  Anton V Kaspirzhny; Paul Gogan; Ginette Horcholle-Bossavit; Suzanne Tyc-Dumont
Journal:  Network       Date:  2002-08       Impact factor: 1.273

3.  Developmental changes in spinal motoneuron dendrites in neonatal mice.

Authors:  Yan Li; Diana Brewer; Robert E Burke; Giorgio A Ascoli
Journal:  J Comp Neurol       Date:  2005-03-14       Impact factor: 3.215

4.  Three-dimensional reconstruction of the axon arbor of a CA3 pyramidal cell recorded and filled in vivo.

Authors:  Lucia Wittner; Darrell A Henze; László Záborszky; György Buzsáki
Journal:  Brain Struct Funct       Date:  2007-06-12       Impact factor: 3.270

5.  Anatomical, physiological, molecular and circuit properties of nest basket cells in the developing somatosensory cortex.

Authors:  Yun Wang; Anirudh Gupta; Maria Toledo-Rodriguez; Cai Zhi Wu; Henry Markram
Journal:  Cereb Cortex       Date:  2002-04       Impact factor: 5.357

6.  Status epilepticus enhances tonic GABA currents and depolarizes GABA reversal potential in dentate fast-spiking basket cells.

Authors:  Jiandong Yu; Archana Proddutur; Fatima S Elgammal; Takahiro Ito; Vijayalakshmi Santhakumar
Journal:  J Neurophysiol       Date:  2013-01-16       Impact factor: 2.714

Review 7.  Neuronal morphology goes digital: a research hub for cellular and system neuroscience.

Authors:  Ruchi Parekh; Giorgio A Ascoli
Journal:  Neuron       Date:  2013-03-20       Impact factor: 17.173

8.  Digital morphometry of rat cerebellar climbing fibers reveals distinct branch and bouton types.

Authors:  Kerry M Brown; Izumi Sugihara; Yoshikazu Shinoda; Giorgio A Ascoli
Journal:  J Neurosci       Date:  2012-10-17       Impact factor: 6.167

9.  Quantitative morphometry of electrophysiologically identified CA3b interneurons reveals robust local geometry and distinct cell classes.

Authors:  Giorgio A Ascoli; Kerry M Brown; Eduardo Calixto; J Patrick Card; E J Galván; T Perez-Rosello; Germán Barrionuevo
Journal:  J Comp Neurol       Date:  2009-08-20       Impact factor: 3.215

10.  Morphology and physiology of excitatory neurons in layer 6b of the somatosensory rat barrel cortex.

Authors:  Manuel Marx; Dirk Feldmeyer
Journal:  Cereb Cortex       Date:  2012-09-03       Impact factor: 5.357

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  15 in total

1.  From DIADEM to BigNeuron.

Authors:  Hanchuan Peng; Erik Meijering; Giorgio A Ascoli
Journal:  Neuroinformatics       Date:  2015-07

2.  Highlights from the Era of Open Source Web-Based Tools.

Authors:  Kristin R Anderson; Julie A Harris; Lydia Ng; Pjotr Prins; Sara Memar; Bengt Ljungquist; Daniel Fürth; Robert W Williams; Giorgio A Ascoli; Dani Dumitriu
Journal:  J Neurosci       Date:  2021-01-20       Impact factor: 6.167

3.  Comprehensive Estimates of Potential Synaptic Connections in Local Circuits of the Rodent Hippocampal Formation by Axonal-Dendritic Overlap.

Authors:  Carolina Tecuatl; Diek W Wheeler; Nate Sutton; Giorgio A Ascoli
Journal:  J Neurosci       Date:  2020-12-23       Impact factor: 6.167

4.  Win-win data sharing in neuroscience.

Authors:  Giorgio A Ascoli; Patricia Maraver; Sumit Nanda; Sridevi Polavaram; Rubén Armañanzas
Journal:  Nat Methods       Date:  2017-01-31       Impact factor: 28.547

5.  Quantitative techniques for imaging cells and tissues.

Authors:  Christopher S von Bartheld; Fred S Wouters
Journal:  Cell Tissue Res       Date:  2015-04       Impact factor: 5.249

6.  Efficient metadata mining of web-accessible neural morphologies.

Authors:  Masood A Akram; Bengt Ljungquist; Giorgio A Ascoli
Journal:  Prog Biophys Mol Biol       Date:  2021-05-19       Impact factor: 3.667

7.  Topological characterization of neuronal arbor morphology via sequence representation: I--motif analysis.

Authors:  Todd A Gillette; Giorgio A Ascoli
Journal:  BMC Bioinformatics       Date:  2015-07-10       Impact factor: 3.169

8.  An ontology-based search engine for digital reconstructions of neuronal morphology.

Authors:  Sridevi Polavaram; Giorgio A Ascoli
Journal:  Brain Inform       Date:  2017-03-23

9.  Sharing Neuron Data: Carrots, Sticks, and Digital Records.

Authors:  Giorgio A Ascoli
Journal:  PLoS Biol       Date:  2015-10-08       Impact factor: 8.029

10.  An open repository for single-cell reconstructions of the brain forest.

Authors:  Masood A Akram; Sumit Nanda; Patricia Maraver; Rubén Armañanzas; Giorgio A Ascoli
Journal:  Sci Data       Date:  2018-02-27       Impact factor: 6.444

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