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AnalyzeSkeleton specifications

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Unique identifier OMICS_19399
Name AnalyzeSkeleton
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A binary image.
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 3.1.3
Stability Stable
Source code URL https://codeload.github.com/fiji/AnalyzeSkeleton/tar.gz/AnalyzeSkeleton_-3.1.3
Maintained Yes

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Maintainer


  • person_outline Ignacio Arganda-Carreras

Publication for AnalyzeSkeleton

AnalyzeSkeleton citations

 (33)
library_books

A screen for deeply conserved non coding GWAS SNPs uncovers a MIR 9 2 functional mutation associated to retinal vasculature defects in human

2018
Nucleic Acids Res
PMCID: 5909433
PMID: 29518216
DOI: 10.1093/nar/gky166

[…] images were prepared using photoshop software (adobe). for quantification of blood vessels number and branching in the retina, images were analyzed using imagej software with skeletonize and analyzeskeleton plugins. statistical analyses associated with each figure are reported in the figure legends., we began by extracting nearly 40 000 references snp cluster id (rsid) entries […]

library_books

Quantitative microglia analyses reveal diverse morphologic responses in the rat cortex after diffuse brain injury

2017
Sci Rep
PMCID: 5643511
PMID: 29038483
DOI: 10.1038/s41598-017-13581-z

[…] images. in addition to creating skeletonized images, cell somas were manually counted for each photomicrograph. the analyze skeleton plugin (developed by and maintained here: http://imagej.net/analyzeskeleton31) was then applied to the skeleton image which tags skeletal features relevant to microglia ramification: slab voxels (orange, process length) and endpoints (blue). figure  […]

library_books

TREM2 deficiency exacerbates tau pathology through dysregulated kinase signaling in a mouse model of tauopathy

2017
Mol Neurodegener
PMCID: 5644120
PMID: 29037207
DOI: 10.1186/s13024-017-0216-6

[…] ca3 region of the hippocampus from each genotype. individual cells were thresholded and analyzed for soma area and total cell area. thresholded cells were then skeletonized and analyzed using imagej analyzeskeleton plugin which outputs total number of branches along with branch junctions. 2-way anova with sidek multiple comparison correction was utilized to compare differences between genotypes, […]

library_books

FiloQuant reveals increased filopodia density during breast cancer progression

2017
PMCID: 5626550
PMID: 28765364
DOI: 10.1083/jcb.201704045

[…] cell-edge image to specifically isolate filopodia at the cell boundary (). the number and length of these cell-edge filopodia are then automatically analyzed by filoquant using the skeletonize and analyzeskeleton algorithms (). filopodia density can also be determined by calculating the ratio of filopodia number to edge length (extracted by filoquant from the edge detection image; )., to make […]

library_books

Cortical and trabecular morphology is altered in the limb bones of mice artificially selected for faster skeletal growth

2017
Sci Rep
PMCID: 5585176
PMID: 28874773
DOI: 10.1038/s41598-017-10317-x

[…] as 3d objects, and running the “thickness” function in the bonej plugin. to obtain canal orientation, the 3d canal stack was processed using the “skeletonize (2d/3d)” function, followed by the “analyzeskeleton” plugin in fiji. the output of these functions comprises canal branch information with lengths and 3d coordinates of the ends of the branch. these data were exported to matlab 2016 […]

library_books

Myosin activity drives actomyosin bundle formation and organization in contractile cells of the Caenorhabditis elegans spermatheca

2017
Mol Biol Cell
PMCID: 5541844
PMID: 28331075
DOI: 10.1091/mbc.E17-01-0029

[…] was used for computer-guided tracing of individual bundles to allow for tortuosity measurements and to generate a skeletonized image. network connectivity of skeletonized images was measured using analyzeskeleton () to determine the number of junction (more than two neighbors), endpoint (less than two neighbors), and slab (exactly two neighbors) pixels per image. connectivity was calculated […]


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AnalyzeSkeleton institution(s)
Biocomputing Unit, National Centre for Biotechnology (CNB-CSIC), Universidad Autonoma de Madrid, Madrid, Spain; Developmental Biology Program, Sloan-Kettering Institute, New York, NY, USA; Cancer Imaging Laboratory, Centre for Applied Medical Research (CIMA), Pamplona, Spain
AnalyzeSkeleton funding source(s)
Supported by Spanish Ministry of Education (MCYT Program); TEC2005-04732; Spanish Science and Innovation Ministry; MCIIN PSS-010000- 2008-2; Marie Curie International Reintegration Grant; MIRG-CT-2005-028342; Department of Defense and University of California Breast Cancer Research Programs; DAMD17-00-1-0227, DAMD17-00-1-0306, 8WB-0150; UTE project CIMA, Spanish Ministry of Education (Ramon y Cajal fellowship).

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