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

Akram, Masood A.; Nanda, Sumit; Maraver, Patricia; Armañanzas, Rubén; Ascoli, Giorgio A.

doi:10.1038/sdata.2018.6

Cited by 77 publications

(68 citation statements)

References 59 publications

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“…The digital neuronal reconstructions of all neurons together with the associated brain contours are freely available at the CERN database Zenodo ( https://zenodo.org/communities/petersen-lab-data ) with direct link http://doi.org/10.5281/zenodo.1220711 . The data have also been submitted to NeuroMorpho.Org (Akram et al, 2018 ).…”

Section: Methodsmentioning

confidence: 99%

Diverse Long-Range Axonal Projections of Excitatory Layer 2/3 Neurons in Mouse Barrel Cortex

et al. 2018

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Excitatory projection neurons of the neocortex are thought to play important roles in perceptual and cognitive functions of the brain by directly connecting diverse cortical and subcortical areas. However, many aspects of the anatomical organization of these inter-areal connections are unknown. Here, we studied long-range axonal projections of excitatory layer 2/3 neurons with cell bodies located in mouse primary somatosensory barrel cortex (wS1). As a population, these neurons densely projected to secondary whisker somatosensory cortex (wS2) and primary/secondary whisker motor cortex (wM1/2), with additional axon in the dysgranular zone surrounding the barrel field, perirhinal temporal association cortex and striatum. In three-dimensional reconstructions of 6 individual wS2-projecting neurons and 9 individual wM1/2-projecting neurons, we found that both classes of neurons had extensive local axon in layers 2/3 and 5 of wS1. Neurons projecting to wS2 did not send axon to wM1/2, whereas a small subset of wM1/2-projecting neurons had relatively weak projections to wS2. A small fraction of projection neurons solely targeted wS2 or wM1/2. However, axon collaterals from wS2-projecting and wM1/2-projecting neurons were typically also found in subsets of various additional areas, including the dysgranular zone, perirhinal temporal association cortex and striatum. Our data suggest extensive diversity in the axonal targets selected by individual nearby cortical long-range projection neurons with somata located in layer 2/3 of wS1.

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Section: Methodsmentioning

confidence: 99%

Diverse Long-Range Axonal Projections of Excitatory Layer 2/3 Neurons in Mouse Barrel Cortex

et al. 2018

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“…Computational models are being optimized to aid with the biological interpretation but also to benchmark new image analysis algorithms, and this in turn is supported by improved simulations of cellular models and networks ( Loew and Schaff, 2001 ; Lenk et al, 2016 ). Finally, the models, images and morphofunctional data should be bundled and centralized to make them openly available to the neuroscience community, as was recently done for neuronal morphology ( Parekh and Ascoli, 2013 ; Akram et al, 2018 ).…”

Section: Future Perspectivementioning

confidence: 99%

Image-Based Profiling of Synaptic Connectivity in Primary Neuronal Cell Culture

et al. 2018

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Neurological disorders display a broad spectrum of clinical manifestations. Yet, at the cellular level, virtually all these diseases converge into a common phenotype of dysregulated synaptic connectivity. In dementia, synapse dysfunction precedes neurodegeneration and cognitive impairment by several years, making the synapse a crucial entry point for the development of diagnostic and therapeutic strategies. Whereas high-resolution imaging and biochemical fractionations yield detailed insight into the molecular composition of the synapse, standardized assays are required to quickly gauge synaptic connectivity across large populations of cells under a variety of experimental conditions. Such screening capabilities have now become widely accessible with the advent of high-throughput, high-content microscopy. In this review, we discuss how microscopy-based approaches can be used to extract quantitative information about synaptic connectivity in primary neurons with deep coverage. We elaborate on microscopic readouts that may serve as a proxy for morphofunctional connectivity and we critically analyze their merits and limitations. Finally, we allude to the potential of alternative culture paradigms and integrative approaches to enable comprehensive profiling of synaptic connectivity.

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“…Here, we introduce a resource developed to promote and facilitate data sharing and metadata annotation for NeuroMorpho.Org, a repository providing unrestricted access to digital reconstructions of neuronal and glial morphology [2,3]. The acquisition and release of morphological tracings begin with the continuous identification of newly published scientific reports describing data of interest [19,26].…”

Section: Introductionmentioning

confidence: 99%

An open-source framework for neuroscience metadata management applied to digital reconstructions of neuronal morphology

2020

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Research advancements in neuroscience entail the production of a substantial amount of data requiring interpretation, analysis, and integration. The complexity and diversity of neuroscience data necessitate the development of specialized databases and associated standards and protocols. NeuroMorpho.Org is an online repository of over one hundred thousand digitally reconstructed neurons and glia shared by hundreds of laboratories worldwide. Every entry of this public resource is associated with essential metadata describing animal species, anatomical region, cell type, experimental condition, and additional information relevant to contextualize the morphological content. Until recently, the lack of a user-friendly, structured metadata annotation system relying on standardized terminologies constituted a major hindrance in this effort, limiting the data release pace. Over the past 2 years, we have transitioned the original spreadsheet-based metadata annotation system of NeuroMorpho.Org to a custom-developed, robust, web-based framework for extracting, structuring, and managing neuroscience information. Here we release the metadata portal publicly and explain its functionality to enable usage by data contributors. This framework facilitates metadata annotation, improves terminology management, and accelerates data sharing. Moreover, its open-source development provides the opportunity of adapting and extending the code base to other related research projects with similar requirements. This metadata portal is a beneficial web companion to NeuroMorpho.Org which saves time, reduces errors, and aims to minimize the barrier for direct knowledge sharing by domain experts. The underlying framework can be progressively augmented with the integration of increasingly autonomous machine intelligence components.

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

Cited by 77 publications

References 59 publications

Diverse Long-Range Axonal Projections of Excitatory Layer 2/3 Neurons in Mouse Barrel Cortex

Diverse Long-Range Axonal Projections of Excitatory Layer 2/3 Neurons in Mouse Barrel Cortex

Image-Based Profiling of Synaptic Connectivity in Primary Neuronal Cell Culture

An open-source framework for neuroscience metadata management applied to digital reconstructions of neuronal morphology

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