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AnalyzeSkeleton specifications


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
Maintained Yes




No version available


  • person_outline Ignacio Arganda-Carreras

Publication for AnalyzeSkeleton

AnalyzeSkeleton citations


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

Nucleic Acids Res
PMCID: 5909433
PMID: 29518216
DOI: 10.1093/nar/gky166
call_split See protocol

[…] cility). 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. […]


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

Sci Rep
PMCID: 5643511
PMID: 29038483
DOI: 10.1038/s41598-017-13581-z
call_split See protocol

[…] onized images. In addition to creating skeletonized images, cell somas were manually counted for each photomicrograph. The Analyze Skeleton Plugin (developed by and maintained here: was then applied to the skeleton image which tags skeletal features relevant to microglia ramification: slab voxels (orange, process length) and endpoints (blue). Figure  illustrate […]


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

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, […]


FiloQuant reveals increased filopodia density during breast cancer progression

PMCID: 5626550
PMID: 28765364
DOI: 10.1083/jcb.201704045
call_split See protocol

[…] ImageJ, users need to install the following dependencies: Enhanced Local Contrast (CLAHE.class;, Skeletonize3D.jar (, AnalyzeSkeleton.jar (; ), and Temporal-Color Code ( […]


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

Sci Rep
PMCID: 5585176
PMID: 28874773
DOI: 10.1038/s41598-017-10317-x
call_split See protocol

[…] anals 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 (Ma […]


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

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

[…] () 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 by […]


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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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