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An imaging system for standardized quantitative analysis of C. elegans behavior

Zhaoyang Feng, Christopher J Cronin, John H Wittig, Paul W Sternberg, William R Schafer
2004 BMC Bioinformatics  
Here we describe a tracking and imaging system for the automated analysis of C. elegans morphology and behavior.  ...  Because traditional methods for evaluating behavioral phenotypes are qualitative and imprecise, there is a need for tools that allow quantitation and standardization of C. elegans behavioral assays.  ...  ZF and CJC jointly wrote the software and developed the system described here. JHW developed an early version of the system and designed the hardware configuration.  ... 
doi:10.1186/1471-2105-5-115 pmid:15331023 pmcid:PMC517925 fatcat:6lqwcpamuzb55g42apgkonm5gy

WormScan: A Technique for High-Throughput Phenotypic Analysis of Caenorhabditis elegans

Mark D. Mathew, Neal D. Mathew, Paul R. Ebert, Ben Lehner
2012 PLoS ONE  
We have developed WormScan, an automated image acquisition system that allows quantitative analysis of each of these four phenotypes on standard NGM plates seeded with E. coli.  ...  Conclusions/Significance: There are existing systems for the automated phenotypic data collection of C. elegans.  ...  Acknowledgments We appreciate the assistance and advice of Andrew Tuck and David Schlipalius in the development of this method. Author Contributions  ... 
doi:10.1371/journal.pone.0033483 pmid:22457766 pmcid:PMC3311640 fatcat:nixkc7tjqfdsbodiargqll2q6a

Addiction research in a simple animal model: the nematode Caenorhabditis elegans

William R. Schafer
2004 Neuropharmacology  
Genetic analysis in the nematode C. elegans has provided important insights into many aspects of neuronal cell biology, including functions related to addiction.  ...  This review presents a personal view of addiction-related research in C. elegans, and includes a discussion of technical innovations that have facilitated neurobiological analyses in C. elegans and a look  ...  The development of behavioral imaging tools addresses an increasing need within the C. elegans research community for rigorous and quantitative assays for behavioral phenotypes, especially those that are  ... 
doi:10.1016/j.neuropharm.2004.06.026 pmid:15464131 fatcat:mxmzbkdt4zhotpgjsga45m4ez4

Nemo: a computational tool for analyzing nematode locomotion

George D Tsibidis, Nektarios Tavernarakis
2007 BMC Neuroscience  
It can be downloaded, printed and distributed freely for any purposes (see copyright notice below). Articles in BMC journals are listed in PubMed and archived at PubMed Central.  ...  Acknowledgements We thank Giannis Voglis and Nikos Kourtis for help with data acquisition.  ...  The nematode strain used in this work was provided by the Caenorhabditis Genetics Center, which is funded by the NIH National Center for Research Resources (NCRR).  ... 
doi:10.1186/1471-2202-8-86 pmid:17941975 pmcid:PMC2148042 fatcat:vefdgm73vbd25kzh4bp4ec4x6e

3-D Worm Tracker for Freely Moving C. elegans

Namseop Kwon, Jaeyeon Pyo, Seung-Jae Lee, Jung Ho Je, Michael Hendricks
2013 PLoS ONE  
To address this question, C. elegans has been widely used as a model animal for the analysis of various animal behaviors.  ...  Here, we develop a 3-D worm tracker (3DWT) for freely moving C. elegans in 3-D environments, based on a stereoscopic configuration.  ...  Hwang for her help in understanding worm movement. The N2 strain used for this research was provided by the Caenorhabditis Genetics Center (CGC).  ... 
doi:10.1371/journal.pone.0057484 pmid:23437394 pmcid:PMC3578814 fatcat:x3nn4hr22jgt3lleybhqkboexa

Quantitative classification and natural clustering of Caenorhabditis elegans behavioral phenotypes

Wei Geng, Pamela Cosman, Joong-Hwan Baek, Charles C Berry, William R Schafer
2003 Genetics  
Here we describe the application of machine learning to quantitatively define and classify the behavioral patterns of C. elegans nervous system mutants.  ...  However, standard methods for classifying the behavioral patterns of mutant Caenorhabditis elegans rely on human observation and are therefore subjective and imprecise.  ...  clustering of C. elegans behavioral phenotypes.  ... 
pmid:14668369 pmcid:PMC1462821 fatcat:7j25dybq5fdc3hafyvkjhtg6r4

Light-microscopy methods in C. elegans research

Laura Breimann, Friedrich Preusser, Stephan Preibisch
2019 Current Opinion in Systems Biology  
This review will discuss state-of-the-art developments in quantitative light microscopy in the context of C. elegans research as well as the impact these technologies have on the field.  ...  Ever since Caenorhabditis elegans was introduced as a model system it has been tightly linked to microscopy, which has led to significant advances in understanding biology over the last decades.  ...  mintbody line, and the Caenorhabditis Genetics Center at the University of Minnesota for providing C. elegans strains.  ... 
doi:10.1016/j.coisb.2018.11.004 fatcat:q2bwk3zdlzcazhex3utqk6mxru

Ratiometric Calcium Imaging of Individual Neurons in Behaving Caenorhabditis Elegans

Bhavya Ravi, Layla M. Nassar, Richard J. Kopchock, Pravat Dhakal, Michael Scheetz, Kevin M. Collins
2018 Journal of Visualized Experiments  
Here we describe methods for ratiometric Ca 2+ imaging of single neurons in freely behaving Caenorhabditis elegans worms.  ...  By integrating these microscopic techniques and data streams, we can record Ca 2+ activity in the C. elegans egg-laying circuit as it progresses between inactive and active behavior states over tens of  ...  Strains used in this study C. elegans Genetics Center, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). We thank James Baker and Mason Klein for helpful discussions.  ... 
doi:10.3791/56911 pmid:29443112 pmcid:PMC5912386 fatcat:34droxb7qbhp3pxkcnmfzxrhxm

NemaFlex: a microfluidics-based technology for standardized measurement of muscular strength of C. elegans

Mizanur Rahman, Jennifer E. Hewitt, Frank Van-Bussel, Hunter Edwards, Jerzy Blawzdziewicz, Nathaniel J. Szewczyk, Monica Driscoll, Siva A. Vanapalli
2018 Lab on a Chip  
NemaFlex measures a behavior- and gait-independent measure of C. elegans strength analogous to maximum voluntary force in humans.  ...  Laranjeiro for useful discussions on exercise training of C. elegans and critical reading of the manuscript, and Alex Trindade for help with data analysis and statistics.  ...  We also thank members of the Driscoll and Blawzdziewicz lab for useful discussions.  ... 
doi:10.1039/c8lc00103k pmid:29892747 fatcat:twredtskpffilnb7jsy6ukm6ou

Automated Analysis of C. elegans Swim Behavior Using CeleST Software

Carolina Ibáñez-Ventoso, Christopher Herrera, Esteban Chen, Douglas Motto, Monica Driscoll
2016 Journal of Visualized Experiments  
The steps of a simple procedure, and use of a software that enables high-resolution analysis of C. elegans swim behavior, are presented here.  ...  new challenges for quantitation.  ...  Software like CeleST is intended to fill the gap for detailed analysis of C. elegans behavior in liquid, permitting quantitation of motion-associated parameters that are not readily measured by the un-aided  ... 
doi:10.3791/54359 pmid:28060275 pmcid:PMC5226367 fatcat:shqc7wmgifhxvialv2snp63e7q

A Deep Learning Analysis Reveals Nitrogen-Doped Graphene Quantum Dots Damage Neurons of Nematode Caenorhabditis elegans

Hongsheng Xu, Xinyu Wang, Xiaomeng Zhang, Jin Cheng, Jixiang Zhang, Min Chen, Tianshu Wu
2021 Nanomaterials  
When assessing the morphological changes of neurons caused by N-GQDs, a quantitative image-based analysis based on a deep neural network algorithm (YOLACT) was used because traditional image-based analysis  ...  track subtle morphological changes of neurons at an unbiased level in a nanotoxicological study using C. elegans.  ...  The quantitative analysis of morphological changes in dopaminergic neurons in transgenic strain of BZ555 C. elegans by using YOLACT algorithm.  ... 
doi:10.3390/nano11123314 pmid:34947663 pmcid:PMC8703693 fatcat:ndvvkp3usbcbxfhadlspds7yam

Gravity Studies of C. elegans

Jenny Magnes, Kathleen M. Raley-Susman, Alicia Jago, Karl Spuhler, Dylan Wine, Tewa Kpulun
2013 Biophysical Journal  
Single particle tracking (SPT) is an important tool for investigating the mobility of proteins on cell surfaces.  ...  Typically, the analysis of such trajectories involves the calculation of the Mean Squared Displacement (MSD) versus time interval and the resulting curve is fit to extract the diffusion constant.  ...  Despite the simplicity of its nervous system, C. elegans exhibits many sensory modalities and behaviors, allowing researchers to perform relatively simple yet highly insightful experiments that probe both  ... 
doi:10.1016/j.bpj.2012.11.3694 fatcat:jrsyi6buyncdzisohfnxzyotke

Automated imaging of neuronal activity in freely behaving Caenorhabditis elegans

Juliette Ben Arous, Yoshinori Tanizawa, Ithai Rabinowitch, Didier Chatenay, William R. Schafer
2010 Journal of Neuroscience Methods  
Here, using a new automated system for simultaneous recording of behavior and neuronal activity in freely moving Caenorhabditis elegans on standard agar plates, we show that spontaneous reversals from  ...  We also witness spontaneous activity transients in the PLM sensory neurons during free behavior of the worm in standard conditions.  ...  I.R. is funded by an Israel Science Foundation Bikura postdoctoral fellowship.  ... 
doi:10.1016/j.jneumeth.2010.01.011 pmid:20096306 fatcat:n5knan6isfaljmg2fv5oznhm6u

Optimization of FRET Microscopy for Live-Cell Imaging of Multiple Protein-Protein Interactions

Brandon L. Scott, Adam D. Hoppe
2013 Biophysical Journal  
Single particle tracking (SPT) is an important tool for investigating the mobility of proteins on cell surfaces.  ...  Typically, the analysis of such trajectories involves the calculation of the Mean Squared Displacement (MSD) versus time interval and the resulting curve is fit to extract the diffusion constant.  ...  Despite the simplicity of its nervous system, C. elegans exhibits many sensory modalities and behaviors, allowing researchers to perform relatively simple yet highly insightful experiments that probe both  ... 
doi:10.1016/j.bpj.2012.11.3696 fatcat:xit4cu3wi5gdzcbyd6z5gw7yn4

Three-Dimensional Thermal Noise Imaging of Collagen Networks

Tobias F. Bartsch, Martin D. Kochanczyk, Janina Lange, Ernst-Ludwig Florin
2013 Biophysical Journal  
Single particle tracking (SPT) is an important tool for investigating the mobility of proteins on cell surfaces.  ...  Typically, the analysis of such trajectories involves the calculation of the Mean Squared Displacement (MSD) versus time interval and the resulting curve is fit to extract the diffusion constant.  ...  Despite the simplicity of its nervous system, C. elegans exhibits many sensory modalities and behaviors, allowing researchers to perform relatively simple yet highly insightful experiments that probe both  ... 
doi:10.1016/j.bpj.2012.11.3692 fatcat:gvyuhhlpjff5xlcr4wpejbyvki
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