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Automated quantification of morphodynamics for high-throughput live cell time-lapse datasets

German Gonzalez, Ludovico Fusco, Fethallah Benmansour, Pascal Fua, Olivier Pertz, Kevin Smith
2013 2013 IEEE 10th International Symposium on Biomedical Imaging  
We present a fully automatic method to track and quantify the morphodynamics of differentiating neurons in fluorescence time-lapse datasets.  ...  Our approach opens the door to rich dynamic analysis of complex cellular behavior in high-throughput time-lapse data.  ...  initiative for Systems Biology, through the SyBIT project.  ... 
doi:10.1109/isbi.2013.6556562 dblp:conf/isbi/GonzalezFBFPS13 fatcat:cz73dusmznhnhnnuties2nncwi

Automated quantification of morphodynamics for high-throughput live cell time-lapse dataset

German Gonzalez, Ludovico Fusco, Fethallah Benmansour, Pascal Fua, Olivier Pertz, Kevin Smith
2011
Our approach opens the door to rich dynamic analysis of complex cellular behavior in high-throughput time-lapse data.  ...  We present a fully automatic method to track and quantify the morphodynamics of differentiating neurons in uorescence time-lapse microscopy datasets.  ...  initiative for Systems Biology, through the SyBIT project.  ... 
doi:10.5167/uzh-76548 fatcat:ftpr2e3bfjeifoc6qyp4ksbyne

Filopodyan: An open-source pipeline for the analysis of filopodia

Vasja Urbančič, Richard Butler, Benjamin Richier, Manuel Peter, Julia Mason, Frederick J. Livesey, Christine E. Holt, Jennifer L. Gallop
2017 Journal of Cell Biology  
Filopodyan supports high-throughput phenotype characterization as well as detailed interactive editing of filopodia reconstructions through an intuitive graphical user interface.  ...  different responses to changes in the accumulation of ENA and VASP fluorescence in their tips over time.  ...  and Edouard Hanezzo and Ulrich Dobramysl for critical reading of the manuscript.  ... 
doi:10.1083/jcb.201705113 pmid:28760769 pmcid:PMC5626553 fatcat:vpnyi6g6nbevnmsn3ockiojpt4

Quantification of Local Morphodynamics and Local GTPase Activity by Edge Evolution Tracking

Yuki Tsukada, Kazuhiro Aoki, Takeshi Nakamura, Yuichi Sakumura, Michiyuki Matsuda, Shin Ishii, Kozo Kaibuchi
2008 PLoS Computational Biology  
A problem underlying the analysis of time-lapse cell images is the lack of rigorous methods to extract morphodynamic properties.  ...  Although the techniques themselves have promoted the understanding of dynamic cellular functions, the vast number of images acquired has generated a need for automated processing tools to extract statistical  ...  Acknowledgments We thank Naoki Honda, Shigeyuki Oba, and Justin Dauwels for helpful discussions and Yuko Fujisawa and Ian Smith for reviewing the manuscript. Author Contributions  ... 
doi:10.1371/journal.pcbi.1000223 pmid:19008941 pmcid:PMC2573959 fatcat:bz3co5bc5ffnpakrqtumfqem7i

Computer vision profiling of neurite outgrowth dynamics reveals spatiotemporal modularity of Rho GTPase signaling

Ludovico Fusco, Riwal Lefort, Kevin Smith, Fethallah Benmansour, German Gonzalez, Caterina Barillari, Bernd Rinn, Francois Fleuret, Pascal Fua, Olivier Pertz
2016 Journal of Experimental Medicine  
Abbreviations used in this paper: CV, computer vision; FRET, Förster resonance energy transfer; GAP, GTPase-activating protein; GEF, guanine nucleotide-exchange factor; HDS, hierarchical data structure; HS, high  ...  stringency; KD, knockdown; LS, low stringency; MDS, morphodynamic signature; MLCK, myosin light chain kinase; MP, morphogenetic process; MRCK, myotonin-related dystrophyn kinase myosin light chain kinase  ...  Acknowledgments We are grateful to Chris Bakal for constructive comments on the manuscript.  ... 
doi:10.1084/jem.2131oia128 fatcat:4dy6s6mt7be3zmuuhkkfxj2afi

Computer vision profiling of neurite outgrowth dynamics reveals spatiotemporal modularity of Rho GTPase signaling

Ludovico Fusco, Riwal Lefort, Kevin Smith, Fethallah Benmansour, German Gonzalez, Caterina Barillari, Bernd Rinn, Francois Fleuret, Pascal Fua, Olivier Pertz
2016 Journal of Cell Biology  
Abbreviations used in this paper: CV, computer vision; FRET, Förster resonance energy transfer; GAP, GTPase-activating protein; GEF, guanine nucleotide-exchange factor; HDS, hierarchical data structure; HS, high  ...  stringency; KD, knockdown; LS, low stringency; MDS, morphodynamic signature; MLCK, myosin light chain kinase; MP, morphogenetic process; MRCK, myotonin-related dystrophyn kinase myosin light chain kinase  ...  Acknowledgments We are grateful to Chris Bakal for constructive comments on the manuscript.  ... 
doi:10.1083/jcb.201506018 pmid:26728857 pmcid:PMC4700477 fatcat:2toviieybbhyzejzjqxwhm6obm

Deciphering tissue morphodynamics using bioimage informatics

Alexandre C. Dufour, Anneliene H. Jonker, Jean-Christophe Olivo-Marin
2017 Philosophical Transactions of the Royal Society of London. Biological Sciences  
One contribution of 13 to a theme issue 'Systems morphodynamics: understanding the development of tissue hardware'.  ...  -MorphoGraphX [41] is a platform developed for the quantification of four-dimensional (three-dimensional time-lapse) analysis of growth dynamics in plant morphogenesis, focused on computational efficiency  ...  -Real-time accurate cell shape extractor (RACE) [28] is a highperformance image analysis framework for automated three-dimensional cell segmentation, with a particular focus on massive SPIM datasets.  ... 
doi:10.1098/rstb.2015.0512 pmid:28348249 pmcid:PMC5379021 fatcat:cuy735thevfchbqbvttl3pzyjy

DynaMorph: learning morphodynamic states of human cells with live imaging and sc-RNAseq [article]

Zhenqin Wu, Bryant B. Chhun, Galina Schmunk, Chang Kim, Li-Hao Yeh, Tomasz J. Nowakowski, James Zou, Shalin B. Mehta
2020 bioRxiv   pre-print
We propose a computational framework, DynaMorph, that combines quantitative label-free imaging and deep learning for automated discovery of morphodynamic states.  ...  As a case study, we apply DynaMorph to study the morphodynamic states of live primary human microglia, which are mobile immune cells of the brain that exhibit complex functional states.  ...  Acknowledgements We thank Syuan-Ming Guo for discussions around machine learning and dimensionality reduction. We thank Greg Huber for discussions around the physical models of cell states.  ... 
doi:10.1101/2020.07.20.213074 fatcat:yw3fdjiwdrhhpca6b6i63btshe

Open source software for quantification of cell migration, protrusions, and fluorescence intensities

David J. Barry, Charlotte H. Durkin, Jasmine V. Abella, Michael Way
2015 Journal of Cell Biology  
The authors would like to thank Paul Bates and Erik Sahai for their comments on the manuscript.  ...  This work has been supported by postdoctoral fellowship awards from Cancer Research UK and the Canadian Institutes of Health Research (number 234201).  ...  We now describe software designed for the automated quantification of cell migration and morphodynamics.  ... 
doi:10.1083/jcb.201501081 pmid:25847537 pmcid:PMC4395480 fatcat:l3ohgwpdbvcznp3jmrnabpzaxy

Distinct predictive performance of Rac1 and Cdc42 in cell migration

Masataka Yamao, Honda Naoki, Katsuyuki Kunida, Kazuhiro Aoki, Michiyuki Matsuda, Shin Ishii
2015 Scientific Reports  
In this approach, we performed FRET time-lapse imaging of Rac1 and Cdc42, members of Rho GTPases which are responsible for cell motility, and quantitatively identified the response functions that describe  ...  Over the past decade, live-cell imaging techniques have been developed to visualize the dynamics of molecular activity in situ by means of biosensors, for example, based on the principle of Förster (or  ...  Acknowledgements This study was supported by the Platform for Dynamic Approaches to Living System (H.N., K.A., M.M., and S.I.) and the Strategic Research Program for Brain Sciences (M.Y., H.N., and S.I  ... 
doi:10.1038/srep17527 pmid:26634649 pmcid:PMC4669460 fatcat:poosatasmnb2to4iuq6vdgxuue

Quantitative Multiscale Cell Imaging in Controlled 3D Microenvironments

Erik S. Welf, Meghan K. Driscoll, Kevin M. Dean, Claudia Schäfer, Jun Chu, Michael W. Davidson, Michael Z. Lin, Gaudenz Danuser, Reto Fiolka
2016 Developmental Cell  
and high speed enable the quantification of 3D cell signaling and morphodynamics d Multiscale quantification of microenvironmental reorganization by cells SUMMARY The microenvironment determines cell  ...  Here we introduce microenvironmental selective plane illumination microscopy (meSPIM) for imaging and quantification of intracellular signaling and submicrometer cellular structures as well as large-scale  ...  ACKNOWLEDGMENTS We would like to thank John Hammer for the GFP-tractin construct, Magnus Hö ö k for the CNA35 peptide, John Minna for the Kras V12 construct, Bob Fischer for the td-Tomato membrane marker  ... 
doi:10.1016/j.devcel.2016.01.022 pmid:26906741 pmcid:PMC4784259 fatcat:vanrgow56vfhbhpe6pv4hsctj4

Reconstructing embryonic development

Khaled Khairy, Philipp J. Keller
2011 Genesis  
We review state-of-the-art technology for live imaging, focusing on fluorescence light microscopy techniques for system-level investigations of animal development, and discuss computational approaches  ...  to image segmentation, cell tracking, automated data annotation, and biophysical modeling.  ...  ACKNOWLEDGMENTS The authors thank the authors of McMahon et al. 2008 , Fowlkes et al. 2008 , Fernandez et al. 2010 for kindly sharing their figure materials and permitting us to reprint their figures  ... 
doi:10.1002/dvg.20698 pmid:21140407 fatcat:g6aznif7ivec5nwgakw5zflnha

A Fyn biosensor reveals pulsatile, spatially localized kinase activity and signaling crosstalk in live mammalian cells

Ananya Mukherjee, Randhir Singh, Sreeram Udayan, Sayan Biswas, Pothula Purushotham Reddy, Saumya Manmadhan, Geen George, Shilpa Kumar, Ranabir Das, Balaji M Rao, Akash Gulyani
2020 eLife  
Here, we report a biosensor for specifically visualizing active conformation of SFK-Fyn in live cells.  ...  Nuclear-magnetic-resonance (NMR) analysis provides the structural basis of F29 specificity for Fyn over homologous SFKs.  ...  We thank Professor Jyotsna Dhawan (inStem,CCMB), Professor Satyajit Mayor (NCBS) and Professor Apurva Sarin (inStem) for sharing cell lines and reagents.  ... 
doi:10.7554/elife.50571 pmid:32017701 pmcid:PMC7000222 fatcat:5g3lfvegnzdbveslxspf5vwz3e

Light-Regulated allosteric switch enables temporal and subcellular control of enzyme activity

Mark Shaaya, Jordan Fauser, Anastasia Zhurikhina, Jason E Conage-Pough, Vincent Huyot, Martin Brennan, Cameron T Flower, Jacob Matsche, Shazeb Khan, Viswanathan Natarajan, Jalees Rehman, Pradeep Kota (+3 others)
2020 eLife  
A fast cycling variant enables the stimulation of transient pulses and local regulation of activity in a selected region of a cell.  ...  Engineered allosteric regulation of protein activity provides significant advantages for the development of robust and broadly applicable tools.  ...  ., A biosensor generated via high-throughput screening quantifies cell 1360 edge Src dynamics. Nat Chem Biol, 2011. 7(7): p. 437-44. 1361 64.  ... 
doi:10.7554/elife.60647 pmid:32965214 pmcid:PMC7577742 fatcat:apwk4t3kdng3ropg3zjdwfbnoy

An integrated enhancement and reconstruction strategy for the quantitative extraction of actin stress fibers from fluorescence micrographs

Zhen Zhang, Shumin Xia, Pakorn Kanchanawong
2017 BMC Bioinformatics  
Conclusion: We present an open-source graphically-interfaced computational tool for the extraction and quantification of stress fibers in adherent cells with minimal user input.  ...  This poses a challenge for the automation of their detection, segmentation, and quantitative analysis.  ...  Acknowledgements We thank the staffs of the microscopy, computing, and open lab core facilities in Mechanobiology Institute.  ... 
doi:10.1186/s12859-017-1684-y pmid:28532442 pmcid:PMC5440974 fatcat:ak3dowtvibbxpetho5yfx5565i
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