neuTube 1.0: A New Design for Efficient Neuron Reconstruction Software Based on the SWC Format

Feng, Linqing; Zhao, Ting; Kim, J.

doi:10.1523/eneuro.0049-14.2015

Cited by 61 publications

(58 citation statements)

References 3 publications

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“…HICAP axons and Granule dendrites are colocated, as are the Basket axons and the granule perisomatic region; therefore, these neurons give rise to two distinct inhibitory potential connections. Morphologies rendered with neuTube (Feng, Zhao, & Kim, ) using data from the Bausch (Granule) and Lien (Basket and HICAP) archives (Bausch, He, Petrova, Wang, & McNamara, ; Liu, Cheng, & Lien, ) of NeuroMorpho.Org (Ascoli, Donohue, & Halavi, ). (b) The presynaptic spikes (upper traces) generate postsynaptic signals (lower traces) digitized and plotted from pair recording (Liu et al, ), from which we identified “fast‐spiking” as DG Basket and “non‐fast‐spiking” as DG HICAP (IN: interneuron and GC: Granule cell).…”

Section: Resultsmentioning

confidence: 99%

A comprehensive knowledge base of synaptic electrophysiology in the rodent hippocampal formation

Moradi

Ascoli

2019

Hippocampus

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The cellular and synaptic architecture of the rodent hippocampus has been described in thousands of peer‐reviewed publications. However, no human‐ or machine‐readable public catalog of synaptic electrophysiology data exists for this or any other neural system. Harnessing state‐of‐the‐art information technology, we have developed a cloud‐based toolset for identifying empirical evidence from the scientific literature pertaining to synaptic electrophysiology, for extracting the experimental data of interest, and for linking each entry to relevant text or figure excerpts. Mining more than 1,200 published journal articles, we have identified eight different signal modalities quantified by 90 different methods to measure synaptic amplitude, kinetics, and plasticity in hippocampal neurons. We have designed a data structure that both reflects the differences and maintains the existing relations among experimental modalities. Moreover, we mapped every annotated experiment to identified potential connections, that is, specific pairs of presynaptic and postsynaptic neuron types. To this aim, we leveraged http://hippocampome.org, an open‐access knowledge base of morphologically, electrophysiologically, and molecularly characterized neuron types in the rodent hippocampal formation. Specifically, we have implemented a computational pipeline to systematically translate neuron type properties into formal queries in order to find all compatible potential connections. With this system, we have collected nearly 40,000 synaptic data entities covering 88% of the 3,120 potential connections in http://hippocampome.org. Correcting membrane potentials with respect to liquid junction potentials significantly reduced the difference between theoretical and experimental reversal potentials, thereby enabling the accurate conversion of all synaptic amplitudes to conductance. This data set allows for large‐scale hypothesis testing of the general rules governing synaptic signals. To illustrate these applications, we confirmed several expected correlations between synaptic measurements and their covariates while suggesting previously unreported ones. We release all data open‐source at http://hippocampome.org in order to further research across disciplines.

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Section: Resultsmentioning

confidence: 99%

A comprehensive knowledge base of synaptic electrophysiology in the rodent hippocampal formation

Moradi

Ascoli

2019

Hippocampus

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“…Neurons were traced using Simple Neurite Tracer plugin of ImageJ (NIH). Reconstructions were represented using NeuTube (Feng, Zhao, & Kim, ) software.…”

Section: Methodsmentioning

confidence: 99%

Characterization of perinatally born glutamatergic neurons of the mouse olfactory bulb based on NeuroD6 expression reveals their resistance to sensory deprivation

Angelova

Platel

Béclin

et al. 2019

J of Comparative Neurology

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During postnatal olfactory bulb (OB) neurogenesis, predetermined stem cells residing in the ventricular–subventricular zone continuously generate progenitors that migrate in the rostral migratory stream and integrate into the OB. Although the vast majority of these postnatally generated interneurons are inhibitory, a sub‐fraction represents glutamatergic neurons that integrate into the superficial glomerular layer. In the present work, we demonstrate that the bHLH transcription factor NeuroD6 is specifically and transitorily expressed in the dorsal neurogenic lineage that generates glutamatergic juxtaglomerular cells (JGCs) for the OB. Using lineage tracing combined with whole brain clearing, we provide new insight into timing of generation, morphology, and connectivity of glutamatergic JGCs. Specifically, we show that all glutamatergic JGCs send complex axons with varying projection patterns into different layers of the OB. Moreover, we find that, contrary to GABAergic OB interneurons, glutamatergic JGCs survive under sensory deprivation, indicating that inhibitory and excitatory populations are differentially susceptible to environmental stimulation.

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“…For general image analysis, we recommend Fiji 60 (a distribution of ImageJ 61 ) and Vaa3D 62,63 , which are open-source, extensible platforms for image analysis and visualization that have a rich collection of plug-ins for carrying out specific tasks including stitching and fiber tracing 64–66 . We recommend neuTube 67 for semiautomated tracing of neurites (Fig. 10a and Supplementary Fig.…”

Section: Introductionmentioning

confidence: 99%

“…Alternatively, one can use special-purpose software such as Neurolucida 68 , neuTube 67 , Neural Circuit Tracer 82 , flNeuronTool 83 , Farsight trace editor 84 , Neuron Studio 84 and Neuromantic 85 . Several of these tools provide automated or semiautomated workflows that allow a user to trace neurites by clicking on a few points along a given neurite, which can greatly accelerate initial tracing of long-range projections.…”

Section: Introductionmentioning

confidence: 99%

Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping

et al. 2015

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To facilitate fine-scale phenotyping of whole specimens, we describe here a set of tissue fixation-embedding, detergent-clearing and staining protocols that can be used to transform excised organs and whole organisms into optically transparent samples within 1–2 weeks without compromising their cellular architecture or endogenous fluorescence. PACT (passive CLARITY technique) and PARS (perfusion-assisted agent release in situ) use tissue-hydrogel hybrids to stabilize tissue biomolecules during selective lipid extraction, resulting in enhanced clearing efficiency and sample integrity. Furthermore, the macromolecule permeability of PACT- and PARS-processed tissue hybrids supports the diffusion of immunolabels throughout intact tissue, whereas RIMS (refractive index matching solution) grants high-resolution imaging at depth by further reducing light scattering in cleared and uncleared samples alike. These methods are adaptable to difficult-to-image tissues, such as bone (PACT-deCAL), and to magnified single-cell visualization (ePACT). Together, these protocols and solutions enable phenotyping of subcellular components and tracing cellular connectivity in intact biological networks.

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neuTube 1.0: A New Design for Efficient Neuron Reconstruction Software Based on the SWC Format

Cited by 61 publications

References 3 publications

A comprehensive knowledge base of synaptic electrophysiology in the rodent hippocampal formation

A comprehensive knowledge base of synaptic electrophysiology in the rodent hippocampal formation

Characterization of perinatally born glutamatergic neurons of the mouse olfactory bulb based on NeuroD6 expression reveals their resistance to sensory deprivation

Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping

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