SOAX: a software for quantification of 3D biopolymer networks

Scientific Reports
Ting XuXiaolei Huang

Abstract

Filamentous biopolymer networks in cells and tissues are routinely imaged by confocal microscopy. Image analysis methods enable quantitative study of the properties of these curvilinear networks. However, software tools to quantify the geometry and topology of these often dense 3D networks and to localize network junctions are scarce. To fill this gap, we developed a new software tool called "SOAX", which can accurately extract the centerlines of 3D biopolymer networks and identify network junctions using Stretching Open Active Contours (SOACs). It provides an open-source, user-friendly platform for network centerline extraction, 2D/3D visualization, manual editing and quantitative analysis. We propose a method to quantify the performance of SOAX, which helps determine the optimal extraction parameter values. We quantify several different types of biopolymer networks to demonstrate SOAX's potential to help answer key questions in cell biology and biophysics from a quantitative viewpoint.

References

Apr 2, 2004·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·E MeijeringM Unser
Feb 3, 2005·Journal of the American Medical Informatics Association : JAMIA·George Hripcsak, Adam S Rothschild
Jun 20, 2006·Current Biology : CB·Sophie G Martin, Fred Chang
Oct 10, 2006·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Laure Ménétrier-Deremble, Patrick Tabeling
Apr 14, 2007·IEEE Transactions on Pattern Analysis and Machine Intelligence·Ranjith UnnikrishnanMartial Hebert
Jul 7, 2007·Methods in Cell Biology·Andrew D BicekDavid J Odde
Oct 4, 2007·Proceedings of the National Academy of Sciences of the United States of America·Clifford P BrangwynneDavid A Weitz
Oct 16, 2007·Journal of Neuroscience Methods·Madeline PoolAlyson E Fournier
Jun 4, 2008·Physical Review Letters·Clifford P BrangwynneDavid A Weitz
Dec 20, 2008·Journal of Microscopy·Andrew M SteinLeonard M Sander
May 21, 2010·Biophysical Journal·Izabela K PiechockaGijsje H Koenderink
Sep 4, 2010·Cytoskeleton·Matthew B SmithDimitrios Vavylonis
Sep 28, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Katja OstermeirErwin Frey
Mar 15, 2011·Neuroinformatics·Yu WangBadrinath Roysam
Mar 23, 2011·The Journal of Cell Biology·Damien LaporteJian-Qiu Wu
Apr 26, 2011·Nature Materials·Simone KöhlerAndreas R Bausch
Sep 13, 2011·Journal of Structural Biology·Alexander RigortHans-Christian Hege
Oct 13, 2011·BMC Neuroscience·Leif DehmeltShelley Halpain
Dec 14, 2011·Advances in Experimental Medicine and Biology·Tyler DrakeDimitrios Vavylonis
Mar 6, 2012·Journal of Structural Biology·Christoph WinklerChristian Schmeiser
Mar 27, 2012·Journal of Colloid and Interface Science·Kazuya NishimuraTetsuya Yomo
Apr 14, 2012·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Julian WeichselUlrich S Schwarz
May 25, 2012·BMC Bioinformatics·David MayerichBadrinath Roysam
Jun 9, 2012·Science·Anne-Cécile ReymannLaurent Blanchoin
Jun 30, 2012·Nature Methods·Albert Cardona, Pavel Tomancak
Oct 9, 2012·Current Biology : CB·Dan ZhangSnezhana Oliferenko
Nov 9, 2012·Nature·Tim SanchezZvonimir Dogic
Mar 6, 2013·Journal of Microscopy·S BasuG K Rohde
Sep 26, 2013·Integrative Biology : Quantitative Biosciences From Nano to Macro·Megan BaileyJennifer L Ross
Dec 10, 2013·Medical Image Analysis·Ting XuXiaolei Huang
Mar 14, 2014·Soft Matter·José AlvaradoGijsje H Koenderink

❮ Previous
Next ❯

Citations

Nov 26, 2015·Trends in Cell Biology·Meghan K Driscoll, Gaudenz Danuser
Aug 24, 2016·PLoS Computational Biology·Mitchel Alioscha-PerezHichem Sahli
Sep 7, 2016·Journal of Microscopy·T LuoG S Kassab
Oct 27, 2016·Cytoskeleton·Philip R NicovichTill Böcking
Nov 18, 2016·Molecular Biology of the Cell·Zhen ZhangPakorn Kanchanawong
Dec 17, 2015·Scientific Reports·David Breuer, Zoran Nikoloski
Sep 1, 2018·Wiley Interdisciplinary Reviews. Developmental Biology·Hannah G Yevick, Adam C Martin
Sep 28, 2017·PloS One·Tong LuoGhassan S Kassab
Aug 5, 2018·The Journal of Cell Biology·Mikael V GarabedianBruce L Goode
Jun 29, 2017·Proceedings of the National Academy of Sciences of the United States of America·David BreuerZoran Nikoloski
Nov 15, 2016·Physical Review. E·A SharmaF C MacKintosh
Feb 10, 2019·Scientific Reports·Ting XuDimitrios Vavylonis
Jun 25, 2020·Molecular Biology of the Cell·Mikael V GarabedianBruce L Goode
Apr 30, 2017·Nature Plants·Tian ZhangDaniel J Cosgrove
Feb 27, 2021·Frontiers in Cell and Developmental Biology·Thomas J Rands, Bruce L Goode
Jun 7, 2018·Biophysical Journal·Karin A JansenGijsje H Koenderink
Apr 10, 2021·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Daniel A D FlormannFranziska Lautenschläger
Apr 17, 2021·Nature Communications·Thomas LitschelPetra Schwille
Jul 9, 2021·Scientific Reports·Yen-Chen ChenKun-Ta Wu
Aug 12, 2021·Scientific Reports·Hannah T PerkinsThomas A Waigh
Oct 9, 2018·Nano Letters·Haiyang JiaPetra Schwille
Aug 20, 2021·Biophysical Journal·Ninna Struck RossenLene Broeng Oddershede

❮ Previous
Next ❯

Methods Mentioned

BETA
fluorescence microscopy
confocal microscopy

Software Mentioned

Neuron
SOAX
Vaa3D
Farsight Toolkit
Network Extractor

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Gerlind HerberichTil Aach
Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Alexandre L CunhaElliot M Meyerowitz
© 2021 Meta ULC. All rights reserved