NeuroMorpho.Org: A Central Resource for Neuronal Morphologies

Ascoli, Giorgio A.; Donohue, Duncan; Halavi, Maryam

doi:10.1523/jneurosci.2055-07.2007

Cited by 659 publications

(647 citation statements)

References 11 publications

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“…In the case of digital reconstructions of neuronal morphology, the most comprehensive database is NeuroMorpho.org (13,130), an online (its name derives straight from its URL) and centrally curated inventory containing contributions from dozens of labs. The database can be browsed by animal species, brain region, cell type (see Fig.…”

Section: Morphology Databasesmentioning

confidence: 99%

Neuron tracing in perspective

2010

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The study of the structure and function of neuronal cells and networks is of crucial importance in the endeavor to understand how the brain works. A key component in this process is the extraction of neuronal morphology from microscopic imaging data. In the past four decades, many computational methods and tools have been developed for digital reconstruction of neurons from images, with limited success. As witnessed by the growing body of literature on the subject, as well as the organization of challenging competitions in the field, the quest for a robust and fully automated system of more general applicability still continues. The aim of this work, is to contribute by surveying recent developments in the field for anyone interested in taking up the challenge. Relevant aspects discussed in the article include proposed image segmentation methods, quantitative measures of neuronal morphology, currently available software tools for various related purposes, and morphology databases. ' 2010 International Society for Advancement of Cytometry

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Section: Morphology Databasesmentioning

confidence: 99%

Neuron tracing in perspective

2010

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“…or the response to new experimental protocols. The experimental data used as the basis of a model and for validation may come directly from a research group, from the literature, or from a database such as NeuronDB, NeuroElectro (Tripathy et al 2014), or NeuroMorpho.Org (Ascoli et al 2007). ModelDB provides the infrastructure to allow researchers to build on prior published models instead of having to create a new virtual model system de novo.…”

Section: Figurementioning

confidence: 99%

Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience

et al. 2016

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Neuron modeling may be said to have originated with the Hodgkin and Huxley action potential model in 1952 and Rall's models of integrative activity of dendrites in 1964. Over the ensuing decades, these approaches have led to a massive development of increasingly accurate and complex data-based models of neurons and neuronal circuits. ModelDB was founded in 1996 to support this new field and enhance the scientific credibility and utility of computational neuroscience models by providing a convenient venue for sharing them. It has grown to include over 1100 published models covering more than 130 research topics. It is actively curated and developed to help researchers discover and understand models of interest. ModelDB also provides mechanisms to assist running models both locally and remotely, and has a graphical tool that enables users to explore the anatomical and biophysical properties that are represented in a model. Each of its capabilities is undergoing continued refinement and improvement in response to user experience. Large research groups (Allen Brain Institute, EU Human Brain Project, etc.) are emerging that collect data across multiple scales and integrate that data into many complex models, presenting new challenges of scale. We end by predicting a future for neuroscience increasingly fueled by new technology and high performance computation, and increasingly in need of comprehensive user-friendly databases such as ModelDB to provide the means to integrate the data for deeper insights into brain function in health and disease.

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“…Similarly, the German Neuroinformatics Node (G-Node) is a web portal for data access, data storage and data annotation focusing on cellular and systems neurophysiology data (Herz, et al, 2008). NeuroMorpho.Org (Ascoli, Donohue & Halavi, 2007) is a large repository of digital neuromorphological reconstructions. The reconstructed neurons can be hyperlinked to the publications describing them and are available for use in different research projects.…”

Section: Background and Overviewmentioning

confidence: 99%

“…The NIF (Marenco et al, 2008) and the Neuromorpho.org (Ascoli, Donohue & Halavi, 2007) portals both allow users to link publications with data described in those publications. More multifaceted publication repositories are under development that allow data and software to not only be stored, shared and associated with academic publications, but the software can also executed in situ.…”

Section: Background and Overviewmentioning

confidence: 99%

A Digital Repository and Execution Platform for Interactive Scholarly Publications in Neuroscience

et al. 2015

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Abstract:The CARMEN Virtual Laboratory (VL) is a cloud-based platform which allows neuroscientists to store, share, develop, execute, reproduce and publicise their work. This paper describes new functionality in the CARMEN VL: an interactive publications repository. This new facility allows users to link data and software to publications. This enables other users to examine data and software associated with the publication and execute the associated software within the VL using the same data as the authors used in the publication. The cloud-based architecture and SaaS (Software as a Service) framework allows vast data sets to be uploaded and analysed using software services. Thus, this new interactive publications facility allows others to build on research results through reuse. This aligns with recent developments by funding agencies, institutions, and publishers with a move to open access research. Open access provides reproducibility and verification of research resources and results. Publications and their associated data and software will be assured of long-term preservation and curation in the repository. Further, analysing research data and the evaluations described in publications frequently requires a number of execution stages many of which are iterative. The VL provides a scientific workflow environment to combine software services into a processing tree. These workflows can also be associated with publications and executed by users. The VL also provides a secure environment where users can decide the access rights for each resource to ensure copyright and privacy restrictions are met.

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NeuroMorpho.Org: A Central Resource for Neuronal Morphologies

Cited by 659 publications

References 11 publications

Neuron tracing in perspective

Neuron tracing in perspective

Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience

A Digital Repository and Execution Platform for Interactive Scholarly Publications in Neuroscience

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