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chevron_left Biological network reconstruction 3D image analysis 3D image analysis 2D image visualization Biological network reconstruction chevron_right

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SOAX specifications


Unique identifier OMICS_18873
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Mac OS, Windows
Programming languages Perl, Python
Computer skills Advanced
Version 3.6.1
Stability Stable
Maintained Yes




No version available



  • person_outline Dimitrios Vavylonis
  • person_outline Xiaolei Huang

Additional information

Publication for SOAX

SOAX citations


Stromule extension along microtubules coordinated with actin mediated anchoring guides perinuclear chloroplast movement during innate immunity

PMCID: 5815851
PMID: 29338837
DOI: 10.7554/eLife.23625.055

[…] mt organization was significantly altered in the leaves of nbgcp4-silenced plants compared to the control () in a similar way to amir-atgcp4 in arabidopsis (). to quantify these changes, we used soax software that uses stretching open active contours (soacs) to quantify filamentous networks (). soax analysis showed that mts were more parallel or aligned in nbgcp4-silenced plants compared […]


Resliced image space construction for coronary artery collagen fibers

PLoS One
PMCID: 5617181
PMID: 28953913
DOI: 10.1371/journal.pone.0184972

[…] the negative value around 0° was regarded as belonging to the distribution where the second peak was 18.4°., finally, typical fiber structure was processed by open source software vaa3d, neutu and soax as illustrated in . the tortuosity was not recognized correctly in some locations while the fuzzy regions were ignored. the high curvature regions were overlooked by neutu and vaa3d in , […]

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SOAX institution(s)
Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA, USA; Department of Physics, Lehigh University, Bethlehem, PA, USA; FOM Institute AMOLF, Systems Biophysics department, Amsterdam, Netherlands; Surya College of Education, SURE Center, Tangerang, Indonesia; IPH Schools, Surabaya, Indonesia; Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
SOAX funding source(s)
Supported by NIH grants R01GM098430 and R01GM086546; a VIDI grant from the Netherlands Organization for Scientific Research (NWO) and by the Foundation for Fundamental Research on Matter (FOM), which is part of NOW; the Fulbright Visiting Scholar Program and TheWorld Academy of Sciences (TWAS).

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