Soma-Segmentation specifications


Unique identifier OMICS_21856
Name Soma-Segmentation
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Qian Liu <>

Publication for Soma-Segmentation

Soma-Segmentation in publications

PMCID: 5915526
PMID: 29691458
DOI: 10.1038/s41598-018-24753-w

[…] computing time for the shearlet-based denoising was approximately 7 seconds; the average computing time for the 2d segmentation routine was approximately 8 seconds; the average computing time of the soma segmentation routine was approximately 5 seconds; the average computing time of the tracing routine for a cell containing 3 branches was approximately 130 seconds. note that our soma […]

PMCID: 5662727
PMID: 29085023
DOI: 10.1038/s41598-017-14699-w

[…] within the som population in different regions might be functionally significant. these results provide a distribution reference for the functional study of som-expressing neurons.figure 4 , soma segmentation not only provides the central location of the cell body but also morphological characteristics of neuronal somas. we observed that som-expressing neurons in the same nuclei […]

PMCID: 5024436
PMID: 27628179
DOI: 10.1186/s12859-016-1252-x

[…] [–]. to achieve this goal, many computational techniques are required such as the localization and segmentation of neuronal somas, which is the first step in digital neuronal circuit reconstruction. soma segmentation can provide the spatial distribution and morphometrics of somas, which are quantitative aspects of some brain disease diagnosis [, ]. for example, in alzheimer's disease […]

PMCID: 4700477
PMID: 26728857
DOI: 10.1083/jcb.201506018

[…] segmentation areas in each frame are divided into regions and assigned a label from the following list: (a) ok: the nucleus/soma is correctly segmented; (b) fp (false positive): area of nucleus/soma segmentation that does not exist in the annotation; (c) fn (false negative): area of the nucleus/soma annotation that is not recovered by the segmentation., the results of the validation […]

PMCID: 4670727
PMID: 26613961
DOI: 10.15252/msb.20156458

[…] different pulse regimes for 13 h followed by additional 24 h in gf‐free medium, and quantified steady‐state neurite outgrowth as a measure of differentiation (fig a and b) using an automated neurite/soma segmentation algorithm (). statistical analysis of this dataset is also shown (). as expected, sustained egf and ngf stimulation, respectively, led to undifferentiated and differentiated states. […]

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Soma-Segmentation institution(s)
Britton Chance Center for Biomedical Photonics, School of Engineering Sciences, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, China; MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
Soma-Segmentation funding source(s)
Supported by the National Natural Science Foundation of China (Grant No.91432116).

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