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neuTube specifications

Information


Unique identifier OMICS_10498
Name neuTube
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 1.0
Stability Stable
Maintained Yes

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  • person_outline Ting Zhao <>

Publication for neuTube

neuTube in publications

 (4)
PMCID: 5827689
PMID: 29485626
DOI: 10.1038/sdata.2018.6

[…] complete standardization process is also posted on neuromorpho.org along with the open-source checking software. inconsistencies are edited using a variety of programs, including cvapp, neuromantic, neutube, vaa3d, trees toolbox, and several more as needed. importantly, all edits are tracked in accompanying log reports., after completing morphological editing, data processing is finalized […]

PMCID: 5779069
PMID: 29360104
DOI: 10.1038/sdata.2017.207

[…] eswc reconstructions were generated starting from the multi-channel image data and the standard swc reconstructions. first the basic swc file was created by tracing the overall neuronal structure in neutube. this file was then used as input in the multichannel_compute plugin of vaa3d along with the image stacks for each channel. the plugin interface asks for a primary channel, a secondary […]

PMCID: 5384829
PMID: 28244870
DOI: 10.7554/eLife.21012.021

[…] fluoview laser scanning confocal microscope (0.5 um optical thickness). vias software was used to align confocal images taken at 40x and 60x in the same plane (x,y,z). neurons were then traced using neutube software, which uses fixed radii small tubes to estimate the dendritic branches length and thickness ()., dbx1cre+/-;rosa26yfp+/+ male and female mice 3–7 months old were used […]

PMCID: 4599031
PMID: 26344548
DOI: 10.7554/eLife.08758.036

[…] only brightness and contrast adjusted. confocal stacks of brains imaged with a 63× objective were used to reconstruct each neuronal class shown in . we traced each neuron from different brains with neutube software () and assembled the neuronal circuit manually., male flies were dissected in saline containing 103 mm nacl, 3 mm kcl, 5 mm tes, 8 mm trehalose dihydrate, 10 mm glucose, 26 mm […]


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neuTube institution(s)
Center for Functional Connectomics, Korea Institute of Science and Technology (KIST), Seoul, Korea; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; Neuroscience Program, University of Science and Technology, Daejeon, Korea

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