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Zhang H, Chen W. Automated recognition and analysis of body bending behavior in C. elegans. BMC Bioinformatics 2023; 24:175. [PMID: 37118676 PMCID: PMC10148436 DOI: 10.1186/s12859-023-05307-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/26/2023] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND Locomotion behaviors of Caenorhabditis elegans play an important role in drug activity screening, anti-aging research, and toxicological assessment. Previous studies have provided important insights into drug activity screening, anti-aging, and toxicological research by manually counting the number of body bends. However, manual counting is often low-throughput and takes a lot of time and manpower. And it is easy to cause artificial bias and error in counting results. RESULTS In this paper, an algorithm is proposed for automatic counting and analysis of the body bending behavior of nematodes. First of all, the numerical coordinate regression method with convolutional neural network is used to obtain the head and tail coordinates. Next, curvature-based feature point extraction algorithm is used to calculate the feature points of the nematode centerline. Then the maximum distance between the peak point and the straight line between the pharynx and the tail is calculated. The number of body bends is counted according to the change in the maximum distance per frame. CONCLUSION Experiments are performed to prove the effectiveness of the proposed algorithm. The accuracy of head coordinate prediction is 0.993, and the accuracy of tail coordinate prediction is 0.990. The Pearson correlation coefficient between the results of the automatic count and manual count of the number of body bends is 0.998 and the mean absolute error is 1.931. Different strains of nematodes are selected to analyze differences in body bending behavior, demonstrating a relationship between nematode vitality and lifespan. The code is freely available at https://github.com/hthana/Body-Bend-Count .
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Affiliation(s)
- Hui Zhang
- School of Cyber Science and Engineering, Qufu Normal University, Qufu, China
- School of Computer Science and Technology, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Weiyang Chen
- School of Cyber Science and Engineering, Qufu Normal University, Qufu, China.
- School of Computer Science and Technology, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China.
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Sohrabi S, Mor DE, Kaletsky R, Keyes W, Murphy CT. High-throughput behavioral screen in C. elegans reveals Parkinson's disease drug candidates. Commun Biol 2021; 4:203. [PMID: 33589689 PMCID: PMC7884385 DOI: 10.1038/s42003-021-01731-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 12/18/2020] [Indexed: 12/17/2022] Open
Abstract
We recently linked branched-chain amino acid transferase 1 (BCAT1) dysfunction with the movement disorder Parkinson's disease (PD), and found that RNAi-mediated knockdown of neuronal bcat-1 in C. elegans causes abnormal spasm-like 'curling' behavior with age. Here we report the development of a machine learning-based workflow and its application to the discovery of potentially new therapeutics for PD. In addition to simplifying quantification and maintaining a low data overhead, our simple segment-train-quantify platform enables fully automated scoring of image stills upon training of a convolutional neural network. We have trained a highly reliable neural network for the detection and classification of worm postures in order to carry out high-throughput curling analysis without the need for user intervention or post-inspection. In a proof-of-concept screen of 50 FDA-approved drugs, enasidenib, ethosuximide, metformin, and nitisinone were identified as candidates for potential late-in-life intervention in PD. These findings point to the utility of our high-throughput platform for automated scoring of worm postures and in particular, the discovery of potential candidate treatments for PD.
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Affiliation(s)
- Salman Sohrabi
- Department of Molecular Biology & Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Danielle E Mor
- Department of Molecular Biology & Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Rachel Kaletsky
- Department of Molecular Biology & Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - William Keyes
- Department of Molecular Biology & Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Coleen T Murphy
- Department of Molecular Biology & Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
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4
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A survey for the applications of content-based microscopic image analysis in microorganism classification domains. Artif Intell Rev 2017. [DOI: 10.1007/s10462-017-9572-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Guo B, Zhu Y, Luo G, Zuo X. A Dynamic Survival Detection and Analysis System for Mosquito Larvae Viability in Drug Assays. SLAS Technol 2017; 22:557-564. [PMID: 28314109 DOI: 10.1177/2472630317698633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bioinformatics studies have emerged in the domain of larval behavior analysis in recent years. A dynamic survival detection and analysis system for automatically monitoring a large amount of mosquito larvae in bioassays with multiwell plates by acquiring and processing videos is proposed in this article. In our system, equipment is designed for acquiring the video of the mosquito larvae in several multiwell plates simultaneously by a camera, and a video analysis module is developed for detecting the survival states of larvae in each well in real time. Also, a novel model and a new image registration algorithm are proposed to accurately obtain the survival state by analyzing the larval motion activities and the weights of larvae in each well. In our experiments, several spinosad bioassays against 2-instar Aedes aegypti with 96-well plates are used to evaluate the proposed system, and the accuracy of the larval survival state in our system is more than 85%. Moreover, this investigation has indicated that the developed system not only can be used in the mosquito larval bioassays but also can be suitable to detect and analyze the behaviors of large amount of other larvae.
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Affiliation(s)
- Biao Guo
- 1 Communication and Information Security Laboratory, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, China
| | - Yuesheng Zhu
- 1 Communication and Information Security Laboratory, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, China
| | - Guibo Luo
- 1 Communication and Information Security Laboratory, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, China
| | - Xiaorong Zuo
- 2 Academy of State Administration of Grain, Beijing, China
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Wakabayashi T, Sakata K, Togashi T, Itoi H, Shinohe S, Watanabe M, Shingai R. Navigational choice between reversal and curve during acidic pH avoidance behavior in Caenorhabditis elegans. BMC Neurosci 2015; 16:79. [PMID: 26584677 PMCID: PMC4653917 DOI: 10.1186/s12868-015-0220-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/05/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Under experimental conditions, virtually all behaviors of Caenorhabditis elegans are achieved by combinations of simple locomotion, including forward, reversal movement, turning by deep body bending, and gradual shallow turning. To study how worms regulate these locomotion in response to sensory information, acidic pH avoidance behavior was analyzed by using worm tracking system. RESULTS In the acidic pH avoidance, we characterized two types of behavioral maneuvers that have similar behavioral sequences in chemotaxis and thermotaxis. A stereotypic reversal-turn-forward sequence of reversal avoidance caused an abrupt random reorientation, and a shallow gradual turn in curve avoidance caused non-random reorientation in a less acidic direction to avoid the acidic pH. Our results suggest that these two maneuvers were each triggered by a distinct threshold pH. A simulation study using the two-distinct-threshold model reproduced the avoidance behavior of the real worm, supporting the presence of the threshold. Threshold pH for both reversal and curve avoidance was altered in mutants with reduced or enhanced glutamatergic signaling from acid-sensing neurons. CONCLUSIONS C. elegans employ two behavioral maneuvers, reversal (klinokinesis) and curve (klinotaxis) to avoid acidic pH. Unlike the chemotaxis in C. elegans, reversal and curve avoidances were triggered by absolute pH rather than temporal derivative of stimulus concentration in this behavior. The pH threshold is different between reversal and curve avoidance. Mutant studies suggested that the difference results from a differential amount of glutamate released from ASH and ASK chemosensory neurons.
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Affiliation(s)
- Tokumitsu Wakabayashi
- Department of Chemistry and Biological Sciences, Faculty of Engineering, Iwate University, Iwate, 020-8551, Japan.
| | - Kazumi Sakata
- Department of Chemistry and Biological Sciences, Faculty of Engineering, Iwate University, Iwate, 020-8551, Japan.
| | - Takuya Togashi
- Department of Chemistry and Biological Sciences, Faculty of Engineering, Iwate University, Iwate, 020-8551, Japan.
| | - Hiroaki Itoi
- Department of Chemistry and Biological Sciences, Faculty of Engineering, Iwate University, Iwate, 020-8551, Japan.
| | - Sayaka Shinohe
- Department of Chemistry and Biological Sciences, Faculty of Engineering, Iwate University, Iwate, 020-8551, Japan.
| | - Miwa Watanabe
- Department of Chemistry and Biological Sciences, Faculty of Engineering, Iwate University, Iwate, 020-8551, Japan.
| | - Ryuzo Shingai
- Department of Chemistry and Biological Sciences, Faculty of Engineering, Iwate University, Iwate, 020-8551, Japan.
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Roussel N, Sprenger J, Tappan SJ, Glaser JR. Robust tracking and quantification of C. elegans body shape and locomotion through coiling, entanglement, and omega bends. WORM 2015; 3:e982437. [PMID: 26435884 DOI: 10.4161/21624054.2014.982437] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/17/2014] [Accepted: 10/27/2014] [Indexed: 01/27/2023]
Abstract
The behavior of the well-characterized nematode, Caenorhabditis elegans (C. elegans), is often used to study the neurologic control of sensory and motor systems in models of health and neurodegenerative disease. To advance the quantification of behaviors to match the progress made in the breakthroughs of genetics, RNA, proteins, and neuronal circuitry, analysis must be able to extract subtle changes in worm locomotion across a population. The analysis of worm crawling motion is complex due to self-overlap, coiling, and entanglement. Using current techniques, the scope of the analysis is typically restricted to worms to their non-occluded, uncoiled state which is incomplete and fundamentally biased. Using a model describing the worm shape and crawling motion, we designed a deformable shape estimation algorithm that is robust to coiling and entanglement. This model-based shape estimation algorithm has been incorporated into a framework where multiple worms can be automatically detected and tracked simultaneously throughout the entire video sequence, thereby increasing throughput as well as data validity. The newly developed algorithms were validated against 10 manually labeled datasets obtained from video sequences comprised of various image resolutions and video frame rates. The data presented demonstrate that tracking methods incorporated in WormLab enable stable and accurate detection of these worms through coiling and entanglement. Such challenging tracking scenarios are common occurrences during normal worm locomotion. The ability for the described approach to provide stable and accurate detection of C. elegans is critical to achieve unbiased locomotory analysis of worm motion.
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Greenblum A, Sznitman R, Fua P, Arratia PE, Sznitman J. Caenorhabditis elegans segmentation using texture-based models for motility phenotyping. IEEE Trans Biomed Eng 2014; 61:2278-89. [PMID: 25051545 DOI: 10.1109/tbme.2014.2298612] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With widening interests in using model organisms for reverse genetic approaches and biomimmetic microrobotics, motility phenotyping of the nematode Caenorhabditis elegans is expanding across a growing array of locomotive environments. One ongoing bottleneck lies in providing users with automatic nematode segmentations of C. elegans in image sequences featuring complex and dynamic visual cues, a first and necessary step prior to extracting motility phenotypes. Here, we propose to tackle such automatic segmentation challenges by introducing a novel texture factor model (TFM). Our approach revolves around the use of combined intensity- and texture-based features integrated within a probabilistic framework. This strategy first provides a coarse nematode segmentation from which a Markov random field model is used to refine the segmentation by inferring pixels belonging to the nematode using an approximate inference technique. Finally, informative priors can then be estimated and integrated in our framework to provide coherent segmentations across image sequences. We validate our TFM method across a wide range of motility environments. Not only does TFM assure comparative performances to existing segmentation methods on traditional environments featuring static backgrounds, it importantly provides state-of-the-art C. elegans segmentations for dynamic environments such as the recently introduced wet granular media. We show how such segmentations may be used to compute nematode "skeletons" from which motility phenotypes can then be extracted. Overall, our TFM method provides users with a tangible solution to tackle the growing needs of C. elegans segmentation in challenging motility environments.
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Buckingham SD, Partridge FA, Sattelle DB. Automated, high-throughput, motility analysis in Caenorhabditis elegans and parasitic nematodes: Applications in the search for new anthelmintics. Int J Parasitol Drugs Drug Resist 2014; 4:226-32. [PMID: 25516833 PMCID: PMC4266775 DOI: 10.1016/j.ijpddr.2014.10.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The scale of the damage worldwide to human health, animal health and agricultural crops resulting from parasitic nematodes, together with the paucity of treatments and the threat of developing resistance to the limited set of widely-deployed chemical tools, underlines the urgent need to develop novel drugs and chemicals to control nematode parasites. Robust chemical screens which can be automated are a key part of that discovery process. Hitherto, the successful automation of nematode behaviours has been a bottleneck in the chemical discovery process. As the measurement of nematode motility can provide a direct scalar readout of the activity of the neuromuscular system and an indirect measure of the health of the animal, this omission is acute. Motility offers a useful assay for high-throughput, phenotypic drug/chemical screening and several recent developments have helped realise, at least in part, the potential of nematode-based drug screening. Here we review the challenges encountered in automating nematode motility and some important developments in the application of machine vision, statistical imaging and tracking approaches which enable the automated characterisation of nematode movement. Such developments facilitate automated screening for new drugs and chemicals aimed at controlling human and animal nematode parasites (anthelmintics) and plant nematode parasites (nematicides).
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Affiliation(s)
| | | | - David B. Sattelle
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
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Salvador LCM, Bartumeus F, Levin SA, Ryu WS. Mechanistic analysis of the search behaviour of Caenorhabditis elegans. J R Soc Interface 2014; 11:20131092. [PMID: 24430127 PMCID: PMC3899880 DOI: 10.1098/rsif.2013.1092] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Accepted: 12/16/2013] [Indexed: 11/12/2022] Open
Abstract
A central question in movement research is how animals use information and movement to promote encounter success. Current random search theory identifies reorientation patterns as key to the compromise between optimizing encounters for both nearby and faraway targets, but how the balance between intrinsic motor programmes and previous environmental experience determines the occurrence of these reorientation behaviours remains unknown. We used high-resolution tracking and imaging data to describe the complete motor behaviour of Caenorhabditis elegans when placed in a novel environment (one in which food is absent). Movement in C. elegans is structured around different reorientation behaviours, and we measured how these contributed to changing search strategies as worms became familiar with their new environment. This behavioural transition shows that different reorientation behaviours are governed by two processes: (i) an environmentally informed 'extrinsic' strategy that is influenced by recent experience and that controls for area-restricted search behaviour, and (ii) a time-independent, 'intrinsic' strategy that reduces spatial oversampling and improves random encounter success. Our results show how movement strategies arise from a balance between intrinsic and extrinsic mechanisms, that search behaviour in C. elegans is initially determined by expectations developed from previous environmental experiences, and which reorientation behaviours are modified as information is acquired from new environments.
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Affiliation(s)
- Liliana C. M. Salvador
- Department of Ecology and Evolutionary Biology, Princeton University, Guyot Hall, Princeton, NJ 08542, USA
- ICREA-Movement Ecology Laboratory, Centre for Advanced Studies of Blanes (CEAB-CSIC), Cala St Francesc 14, Blanes 17300, Spain
- Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Frederic Bartumeus
- ICREA-Movement Ecology Laboratory, Centre for Advanced Studies of Blanes (CEAB-CSIC), Cala St Francesc 14, Blanes 17300, Spain
- CREAF, Cerdanyola del Vallès, Barcelona 08193, Spain
| | - Simon A. Levin
- Department of Ecology and Evolutionary Biology, Princeton University, Guyot Hall, Princeton, NJ 08542, USA
| | - William S. Ryu
- Department of Physics and the Donnelly Centre, University of Toronto, 60 St George St., Toronto, CanadaM5S1A7
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Sasakura H, Tsukada Y, Takagi S, Mori I. Japanese studies on neural circuits and behavior of Caenorhabditis elegans. Front Neural Circuits 2013; 7:187. [PMID: 24348340 PMCID: PMC3842693 DOI: 10.3389/fncir.2013.00187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 11/03/2013] [Indexed: 01/25/2023] Open
Abstract
The nematode Caenorhabditis elegans is an ideal organism for studying neural plasticity and animal behaviors. A total of 302 neurons of a C. elegans hermaphrodite have been classified into 118 neuronal groups. This simple neural circuit provides a solid basis for understanding the mechanisms of the brains of higher animals, including humans. Recent studies that employ modern imaging and manipulation techniques enable researchers to study the dynamic properties of nervous systems with great precision. Behavioral and molecular genetic analyses of this tiny animal have contributed greatly to the advancement of neural circuit research. Here, we will review the recent studies on the neural circuits of C. elegans that have been conducted in Japan. Several laboratories have established unique and clever methods to study the underlying neuronal substrates of behavioral regulation in C. elegans. The technological advances applied to studies of C. elegans have allowed new approaches for the studies of complex neural systems. Through reviewing the studies on the neuronal circuits of C. elegans in Japan, we will analyze and discuss the directions of neural circuit studies.
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Affiliation(s)
- Hiroyuki Sasakura
- Laboratory of Molecular Neurobiology, Division of Biological Science, Nagoya University Nagoya, Japan
| | - Yuki Tsukada
- Laboratory of Molecular Neurobiology, Division of Biological Science, Nagoya University Nagoya, Japan
| | - Shin Takagi
- Laboratory of Brain Function and Structure, Division of Biological Science, Nagoya University Nagoya, Japan
| | - Ikue Mori
- Laboratory of Molecular Neurobiology, Division of Biological Science, Nagoya University Nagoya, Japan
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A method for selective ablation of neurons in C. elegans using the phototoxic fluorescent protein, KillerRed. Neurosci Lett 2013; 548:261-4. [DOI: 10.1016/j.neulet.2013.05.053] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 05/16/2013] [Accepted: 05/20/2013] [Indexed: 11/15/2022]
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Antony PMA, Trefois C, Stojanovic A, Baumuratov AS, Kozak K. Light microscopy applications in systems biology: opportunities and challenges. Cell Commun Signal 2013; 11:24. [PMID: 23578051 PMCID: PMC3627909 DOI: 10.1186/1478-811x-11-24] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 03/28/2013] [Indexed: 01/05/2023] Open
Abstract
Biological systems present multiple scales of complexity, ranging from molecules to entire populations. Light microscopy is one of the least invasive techniques used to access information from various biological scales in living cells. The combination of molecular biology and imaging provides a bottom-up tool for direct insight into how molecular processes work on a cellular scale. However, imaging can also be used as a top-down approach to study the behavior of a system without detailed prior knowledge about its underlying molecular mechanisms. In this review, we highlight the recent developments on microscopy-based systems analyses and discuss the complementary opportunities and different challenges with high-content screening and high-throughput imaging. Furthermore, we provide a comprehensive overview of the available platforms that can be used for image analysis, which enable community-driven efforts in the development of image-based systems biology.
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Affiliation(s)
- Paul Michel Aloyse Antony
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Christophe Trefois
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Aleksandar Stojanovic
- Interdisciplinary Centre for Security, Reliability and Trust (SnT), University of Luxembourg, Luxembourg City, Luxembourg
| | | | - Karol Kozak
- Light Microscopy Centre (LMSC), Institute for Biochemistry, ETH Zurich, Zurich, Switzerland
- Medical Faculty, Technical University Dresden, Dresden, Germany
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Shingai R, Furudate M, Hoshi K, Iwasaki Y. Evaluation of Head Movement Periodicity and Irregularity during Locomotion of Caenorhabditis elegans. Front Behav Neurosci 2013; 7:20. [PMID: 23518645 PMCID: PMC3604732 DOI: 10.3389/fnbeh.2013.00020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Accepted: 02/28/2013] [Indexed: 11/24/2022] Open
Abstract
Caenorhabditis elegans is suitable for studying the nervous system, which controls behavior. C. elegans shows sinusoidal locomotion on an agar plate. The head moves not only sinusoidally but also more complexly, which reflects regulation of the head muscles by the nervous system. The head movement becomes more irregular with senescence. To date, the head movement complexity has not been quantitatively analyzed. We propose two simple methods for evaluation of the head movement regularity on an agar plate using image analysis. The methods calculate metrics that are a measure of how the head end movement is correlated with body movement. In the first method, the length along the trace of the head end on the agar plate between adjacent intersecting points of the head trace and the quasi-midline of the head trace, which was made by sliding an averaging window of 1/2 the body wavelength, was obtained. Histograms of the lengths showed periodic movement of the head and deviation from it. In the second method, the intersections between the trace of the head end and the trace of the 5 (near the pharynx) or 50% (the mid-body) point from the head end in the centerline length of the worm image were marked. The length of the head trace between adjacent intersections was measured, and a histogram of the lengths was produced. The histogram for the 5% point showed deviation of the head end movement from the movement near the pharynx. The histogram for the 50% point showed deviation of the head movement from the sinusoidal movement of the body center. Application of these methods to wild type and several mutant strains enabled evaluation of their head movement periodicity and irregularity, and revealed a difference in the age-dependence of head movement irregularity between the strains. A set of five parameters obtained from the histograms reliably identifies differences in head movement between strains.
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Affiliation(s)
- Ryuzo Shingai
- Laboratory of Bioscience, Faculty of Engineering, Iwate University Morioka, Iwate, Japan
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15
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Izquierdo EJ, Beer RD. Connecting a connectome to behavior: an ensemble of neuroanatomical models of C. elegans klinotaxis. PLoS Comput Biol 2013; 9:e1002890. [PMID: 23408877 PMCID: PMC3567170 DOI: 10.1371/journal.pcbi.1002890] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 12/03/2012] [Indexed: 11/23/2022] Open
Abstract
Increased efforts in the assembly and analysis of connectome data are providing new insights into the principles underlying the connectivity of neural circuits. However, despite these considerable advances in connectomics, neuroanatomical data must be integrated with neurophysiological and behavioral data in order to obtain a complete picture of neural function. Due to its nearly complete wiring diagram and large behavioral repertoire, the nematode worm Caenorhaditis elegans is an ideal organism in which to explore in detail this link between neural connectivity and behavior. In this paper, we develop a neuroanatomically-grounded model of salt klinotaxis, a form of chemotaxis in which changes in orientation are directed towards the source through gradual continual adjustments. We identify a minimal klinotaxis circuit by systematically searching the C. elegans connectome for pathways linking chemosensory neurons to neck motor neurons, and prune the resulting network based on both experimental considerations and several simplifying assumptions. We then use an evolutionary algorithm to find possible values for the unknown electrophsyiological parameters in the network such that the behavioral performance of the entire model is optimized to match that of the animal. Multiple runs of the evolutionary algorithm produce an ensemble of such models. We analyze in some detail the mechanisms by which one of the best evolved circuits operates and characterize the similarities and differences between this mechanism and other solutions in the ensemble. Finally, we propose a series of experiments to determine which of these alternatives the worm may be using.
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Cohen E, Yemini E, Schafer W, Feitelson DG, Treinin M. Locomotion analysis identifies roles of mechanosensory neurons in governing locomotion dynamics of C. elegans. J Exp Biol 2012; 215:3639-48. [DOI: 10.1242/jeb.075416] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Summary
The simple and well-characterized nervous system of C. elegans facilitates analysis of mechanisms controlling behavior. Locomotion is a major behavioral output governed by multiple external and internal signals. Here we examine the roles of low- and high-threshold mechanosensors in locomotion, using high-resolution and detailed analysis of locomotion and its dynamics. This analysis reveals a new role for touch receptor neurons in suppressing an intrinsic direction bias of locomotion. We also examine the response to noxious mechanical stimuli, showing a response entailing several locomotion properties and lasting several minutes. Effects on different locomotion properties have different half-lives and depend on different partly overlapping sets of sensory neurons. PVD and FLP, high-threshold mechanosensors, play a major role in some of these responses. Overall, our results demonstrate the power of detailed, prolonged, and high-resolution analysis of locomotion and locomotion dynamics in enabling better understanding of gene and neuron function.
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Chung K, Zhan M, Srinivasan J, Sternberg PW, Gong E, Schroeder FC, Lu H. Microfluidic chamber arrays for whole-organism behavior-based chemical screening. LAB ON A CHIP 2011; 11:3689-3697. [PMID: 21935539 PMCID: PMC3924777 DOI: 10.1039/c1lc20400a] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The nematode Caenorhabditis elegans is an important model organism in genetic research and drug screening because of its relative simplicity, ease of maintenance, amenability to simple genetic manipulation, and relevance to human biology. However, their small size and mobility make nematodes difficult to physically manipulate, particularly with spatial and temporal precision. We have developed a microfluidic device to overcome these challenges and enable fast behavior-based chemical screening in C. elegans. The key components of this easy-to-use device allow rapid loading and housing of C. elegans in a chamber array for chemical screening. A simple two-step loading process enables simultaneous loading of a large number of animals within a few minutes without using any expensive/active off-chip components. In addition, chemicals can be precisely delivered to the worms and exchanged with high temporal precision. To demonstrate this feature and the ability to measure time dependent responses to chemicals, we characterize the transient response of worms exposed to different concentrations of anesthetics. We then use the device to study the effect of chemical signals from hermaphrodite worms on male behavior. The ability of the device to maintain a large number of free moving animals in one field of view over a long period of time permits us to demonstrate an increase in the incidence of a specific behavior in males subjected to worm-conditioned medium. Because our device allows monitoring of a large number of worms with single-animal resolution, we envision that this platform will greatly expedite chemical screening in C. elegans.
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Affiliation(s)
- Kwanghun Chung
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Dr, NW, Atlanta, GA, 30332-0100, USA
| | - Mei Zhan
- Interdisciplinary Program of Bioengineering, Georgia Institute of Technology, 311 Ferst Dr, NW, Atlanta, GA, 30332-0100, USA
| | - Jagan Srinivasan
- MC156-29, Biology Division, California Institute of Technology, 1200 East California Blvd, Pasadena, CA, 91125, USA
| | - Paul W. Sternberg
- MC156-29, Biology Division, California Institute of Technology, 1200 East California Blvd, Pasadena, CA, 91125, USA
| | - Emily Gong
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Dr, NW, Atlanta, GA, 30332-0100, USA
| | - Frank C. Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Dr, NW, Atlanta, GA, 30332-0100, USA
- Interdisciplinary Program of Bioengineering, Georgia Institute of Technology, 311 Ferst Dr, NW, Atlanta, GA, 30332-0100, USA
- ; Fax: +1-404-894-8473; Tel: +1-404-894-8473
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Sznitman R, Gupta M, Hager GD, Arratia PE, Sznitman J. Multi-environment model estimation for motility analysis of Caenorhabditis elegans. PLoS One 2010; 5:e11631. [PMID: 20661478 PMCID: PMC2908547 DOI: 10.1371/journal.pone.0011631] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 06/23/2010] [Indexed: 11/30/2022] Open
Abstract
The nematode Caenorhabditis elegans is a well-known model organism used to investigate fundamental questions in biology. Motility assays of this small roundworm are designed to study the relationships between genes and behavior. Commonly, motility analysis is used to classify nematode movements and characterize them quantitatively. Over the past years, C. elegans' motility has been studied across a wide range of environments, including crawling on substrates, swimming in fluids, and locomoting through microfluidic substrates. However, each environment often requires customized image processing tools relying on heuristic parameter tuning. In the present study, we propose a novel Multi-Environment Model Estimation (MEME) framework for automated image segmentation that is versatile across various environments. The MEME platform is constructed around the concept of Mixture of Gaussian (MOG) models, where statistical models for both the background environment and the nematode appearance are explicitly learned and used to accurately segment a target nematode. Our method is designed to simplify the burden often imposed on users; here, only a single image which includes a nematode in its environment must be provided for model learning. In addition, our platform enables the extraction of nematode ‘skeletons’ for straightforward motility quantification. We test our algorithm on various locomotive environments and compare performances with an intensity-based thresholding method. Overall, MEME outperforms the threshold-based approach for the overwhelming majority of cases examined. Ultimately, MEME provides researchers with an attractive platform for C. elegans' segmentation and ‘skeletonizing’ across a wide range of motility assays.
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Affiliation(s)
- Raphael Sznitman
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Manaswi Gupta
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Gregory D. Hager
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Paulo E. Arratia
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Josué Sznitman
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
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19
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OCHOA D, GAUTAMA S, PHILIPS W. Automatic identification ofCaenorhabditis elegansin population images by shape energy features. J Microsc 2010; 238:173-84. [DOI: 10.1111/j.1365-2818.2009.03339.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Identifying prototypical components in behaviour using clustering algorithms. PLoS One 2010; 5:e9361. [PMID: 20179763 PMCID: PMC2825265 DOI: 10.1371/journal.pone.0009361] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 02/02/2010] [Indexed: 02/08/2023] Open
Abstract
Quantitative analysis of animal behaviour is a requirement to understand the task solving strategies of animals and the underlying control mechanisms. The identification of repeatedly occurring behavioural components is thereby a key element of a structured quantitative description. However, the complexity of most behaviours makes the identification of such behavioural components a challenging problem. We propose an automatic and objective approach for determining and evaluating prototypical behavioural components. Behavioural prototypes are identified using clustering algorithms and finally evaluated with respect to their ability to represent the whole behavioural data set. The prototypes allow for a meaningful segmentation of behavioural sequences. We applied our clustering approach to identify prototypical movements of the head of blowflies during cruising flight. The results confirm the previously established saccadic gaze strategy by the set of prototypes being divided into either predominantly translational or rotational movements, respectively. The prototypes reveal additional details about the saccadic and intersaccadic flight sections that could not be unravelled so far. Successful application of the proposed approach to behavioural data shows its ability to automatically identify prototypical behavioural components within a large and noisy database and to evaluate these with respect to their quality and stability. Hence, this approach might be applied to a broad range of behavioural and neural data obtained from different animals and in different contexts.
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21
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Meijering E, Dzyubachyk O, Smal I, van Cappellen WA. Tracking in cell and developmental biology. Semin Cell Dev Biol 2009; 20:894-902. [PMID: 19660567 DOI: 10.1016/j.semcdb.2009.07.004] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Revised: 07/10/2009] [Accepted: 07/28/2009] [Indexed: 11/30/2022]
Abstract
The past decade has seen an unprecedented data explosion in biology. It has become evident that in order to take full advantage of the potential wealth of information hidden in the data produced by even a single experiment, visual inspection and manual analysis are no longer adequate. To ensure efficiency, consistency, and completeness in data processing and analysis, computational tools are essential. Of particular importance to many modern live-cell imaging experiments is the ability to automatically track and analyze the motion of objects in time-lapse microscopy images. This article surveys the recent literature in this area. Covering all scales of microscopic observation, from cells, down to molecules, and up to entire organisms, it discusses the latest trends and successes in the development and application of computerized tracking methods in cell and developmental biology.
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Affiliation(s)
- Erik Meijering
- Biomedical Imaging Group Rotterdam, Erasmus MC - University Medical Center Rotterdam, Department of Medical Informatics, P. O. Box 2040, 3000 CA Rotterdam, The Netherlands.
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22
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Boyd WA, Smith MV, Kissling GE, Freedman JH. Medium- and high-throughput screening of neurotoxicants using C. elegans. Neurotoxicol Teratol 2009; 32:68-73. [PMID: 19166924 DOI: 10.1016/j.ntt.2008.12.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 11/17/2008] [Accepted: 12/06/2008] [Indexed: 11/25/2022]
Abstract
The U.S. National Toxicology Program, the U.S. Environmental Protection Agency, and other national and international agencies are committing significant resources towards the development of alternative species to be used as replacements for mammalian models in toxicological studies. Caenorhabditis elegans is a well-characterized soil nematode that is becoming a useful model in the assessment of neurotoxicants. To determine the effects of potential neurotoxicants on C. elegans, four medium-throughput (feeding, growth, reproduction and locomotion) and two high-throughput (growth and reproduction) assays have been developed. Three of these assays use the COPAS Biosort, a flow cytometer capable of rapidly measuring thousands of nematodes in minutes. Medium-throughput feeding, growth, and reproduction assays were used to assess the toxicity of eight suspected neurotoxicants. For several of the neurotoxicants examined, significant effects were observed at similar concentrations between assays. High-throughput reproduction and growth assays were used to estimate the toxicity of thousands of chemicals in two libraries. These assays will prove useful in evaluating the role of alternative toxicological models in tiered toxicity testing of thousands of chemicals.
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Affiliation(s)
- Windy A Boyd
- National Toxicology Program, Research Triangle Park, NC 27709, USA
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Leung MCK, Williams PL, Benedetto A, Au C, Helmcke KJ, Aschner M, Meyer JN. Caenorhabditis elegans: an emerging model in biomedical and environmental toxicology. Toxicol Sci 2008; 106:5-28. [PMID: 18566021 PMCID: PMC2563142 DOI: 10.1093/toxsci/kfn121] [Citation(s) in RCA: 662] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 06/10/2008] [Indexed: 12/21/2022] Open
Abstract
The nematode Caenorhabditis elegans has emerged as an important animal model in various fields including neurobiology, developmental biology, and genetics. Characteristics of this animal model that have contributed to its success include its genetic manipulability, invariant and fully described developmental program, well-characterized genome, ease of maintenance, short and prolific life cycle, and small body size. These same features have led to an increasing use of C. elegans in toxicology, both for mechanistic studies and high-throughput screening approaches. We describe some of the research that has been carried out in the areas of neurotoxicology, genetic toxicology, and environmental toxicology, as well as high-throughput experiments with C. elegans including genome-wide screening for molecular targets of toxicity and rapid toxicity assessment for new chemicals. We argue for an increased role for C. elegans in complementing other model systems in toxicological research.
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Affiliation(s)
- Maxwell C. K. Leung
- Nicholas School of the Environment, Duke University, Durham, North Carolina 27750
| | - Phillip L. Williams
- Department of Environmental Health Science, College of Public University of Georgia, Athens, Georgia 30602
| | - Alexandre Benedetto
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37240
| | - Catherine Au
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37240
| | - Kirsten J. Helmcke
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37240
| | - Michael Aschner
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37240
| | - Joel N. Meyer
- Nicholas School of the Environment, Duke University, Durham, North Carolina 27750
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24
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Adachi R, Osada H, Shingai R. Phase-dependent preference of thermosensation and chemosensation during simultaneous presentation assay in Caenorhabditis elegans. BMC Neurosci 2008; 9:106. [PMID: 18976490 PMCID: PMC2614431 DOI: 10.1186/1471-2202-9-106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Accepted: 11/01/2008] [Indexed: 11/19/2022] Open
Abstract
Background Multi-sensory integration is necessary for organisms to discriminate different environmental stimuli and thus determine behavior. Caenorhabditis elegans has 12 pairs of amphid sensory neurons, which are involved in generating behaviors such as thermotaxis toward cultivation temperature, and chemotaxis toward chemical stimuli. This arrangement of known sensory neurons and measurable behavioral output makes C. elegans suitable for addressing questions of multi-sensory integration in the nervous system. Previous studies have suggested that C. elegans can process different chemoattractants simultaneously. However, little is known about how these organisms can integrate information from stimuli of different modality, such as thermal and chemical stimuli. Results We studied the behavior of a population of C. elegans during simultaneous presentation of thermal and chemical stimuli. First, we examined thermotaxis within the radial temperature gradient produced by a feedback-controlled thermoregulator. Separately, we examined chemotaxis toward sodium chloride or isoamyl alcohol. Then, assays for simultaneous presentations of 15°C (colder temperature than 20°C room temperature) and chemoattractant were performed with 15°C-cultivated wild-type worms. Unlike the sum of behavioral indices for each separate behavior, simultaneous presentation resulted in a biased migration to cold regions in the first 10 min of the assay, and sodium chloride-regions in the last 40 min. However, when sodium chloride was replaced with isoamyl alcohol in the simultaneous presentation, the behavioral index was very similar to the sum of separate single presentation indices. We then recorded tracks of single worms and analyzed their behavior. For behavior toward sodium chloride, frequencies of forward and backward movements in simultaneous presentation were significantly different from those in single presentation. Also, migration toward 15°C in simultaneous presentation was faster than that in 15°C-single presentation. Conclusion We conclude that worms preferred temperature to chemoattractant at first, but preferred the chemoattractant sodium chloride thereafter. This preference was not seen for isoamyl alcohol presentation. We attribute this phase-dependent preference to the result of integration of thermosensory and chemosensory signals received by distinct sensory neurons.
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Affiliation(s)
- Ryota Adachi
- Laboratory of Bioscience, Faculty of Engineering, Iwate University, 4-3-5 Ueda, Morioka 020-8551, Japan.
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Buckingham SD, Sattelle DB. Strategies for automated analysis of C. elegans locomotion. INVERTEBRATE NEUROSCIENCE 2008; 8:121-31. [PMID: 18688666 DOI: 10.1007/s10158-008-0077-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Accepted: 07/24/2008] [Indexed: 12/29/2022]
Abstract
Automated analysis of C. elegans behaviour is a rapidly developing field, offering the possibility of behaviour-based, high-throughput drug screens and systematic phenotyping. Standard methods for parameterizing worm shapes and movements are emerging, and progress has been made towards overcoming the difficulties introduced by interactions between worms, as well as worm coiling and omega turning. Current methods have facilitated the identification of subtle phenotypes and the characterisation of roles of neurones in forward locomotion and chemotaxis, as well as the quantitative characterisation of behaviour choice and circadian patterns of activity. Given the speed with which C. elegans has been deployed in genetic screens and chemical screens, it is to be hoped that wormtrackers may eventually provide similar rapidity in assaying behavioural phenotypes. However, considerable progress must be made before this can be accomplished. In the case of genome-wide RNAi screens, for example, the presence in the worm genome of some 19,000 genes means that even the minimal user intervention in an automatic phenotyping system will be very costly. Nonetheless, recent advances have shown that drug actions on large numbers of worms can be tracked, raising hopes that high-throughput behavioural screens may soon be available.
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Affiliation(s)
- Steven D Buckingham
- MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK.
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26
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Stephens GJ, Johnson-Kerner B, Bialek W, Ryu WS. Dimensionality and dynamics in the behavior of C. elegans. PLoS Comput Biol 2008; 4:e1000028. [PMID: 18389066 PMCID: PMC2276863 DOI: 10.1371/journal.pcbi.1000028] [Citation(s) in RCA: 279] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Accepted: 02/06/2008] [Indexed: 11/27/2022] Open
Abstract
A major challenge in analyzing animal behavior is to discover some underlying simplicity in complex motor actions. Here, we show that the space of shapes adopted by the nematode Caenorhabditis elegans is low dimensional, with just four dimensions accounting for 95% of the shape variance. These dimensions provide a quantitative description of worm behavior, and we partially reconstruct “equations of motion” for the dynamics in this space. These dynamics have multiple attractors, and we find that the worm visits these in a rapid and almost completely deterministic response to weak thermal stimuli. Stimulus-dependent correlations among the different modes suggest that one can generate more reliable behaviors by synchronizing stimuli to the state of the worm in shape space. We confirm this prediction, effectively “steering” the worm in real time. A great deal of work has been done in characterizing the genes, proteins, neurons, and circuits that are involved in the biology of behavior, but the techniques used to quantify behavior have lagged behind the advancements made in these areas. Here, we address this imbalance in a domain rich enough to allow complex, natural behavior yet simple enough so that movements can be explored exhaustively: the motions of Caenorhabditis elegans freely crawling on an agar plate. From measurements of the worm's curvature, we show that the space of natural worm postures is low dimensional and can be almost completely described by their projections along four principal “eigenworms.” The dynamics along these eigenworms offer both a quantitative characterization of classical worm movement such as forward crawling, reversals, and Omega-turns, and evidence of more subtle behaviors such as pause states at particular postures. We can partially construct equations of motion for this shape space, and within these dynamics we find a set of attractors that can be used as a rigorous definition of behavioral state. Our observations of C. elegans reveal a precise and complete language of motion and new aspects of worm behavior. We believe this is a lesson with promise for other organisms.
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Affiliation(s)
- Greg J Stephens
- Lewis-Sigler Institute for Integrative Genomics, Princeton, New Jersey, United States of America.
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27
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Roussel N, Morton CA, Finger FP, Roysam B. A computational model for C. elegans locomotory behavior: application to multiworm tracking. IEEE Trans Biomed Eng 2007; 54:1786-97. [PMID: 17926677 DOI: 10.1109/tbme.2007.894981] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A computational approach is presented for modeling and quantifying the structure and dynamics of the nematode C. elegans observed by time-lapse microscopy. Worm shape and conformations are expressed in a decoupled manner. Complex worm movements are expressed in terms of three primitive patterns--peristaltic progression, deformation, and translation. The model has been incorporated into algorithms for segmentation and simultaneous tracking of multiple worms in a field, some of which may be interacting in complex ways. A recursive Bayesian filter is used for tracking. Unpredictable behaviors associated with interactions are resolved by multiple-hypothesis tracking. Our algorithm can track worms of diverse sizes and conformations (coiled/uncoiled) in the presence of imaging artifacts and clutter, even when worms are overlapping with others. A two-observer performance assessment was conducted over 16 image sequences representing wild-type and uncoordinated mutants as a function of worm size, conformation, presence of clutter, and worm entanglement. Overall detected tracking failures were 1.41%, undetected tracking failures were 0.41%, and segmentation errors were 1.11% of worm length. When worms overlap, our method reduced undetected failures from 12% to 1.75%, and segmentation error from 11% to 5%. Our method provides the basis for reliable morphometric and locomotory analysis of freely behaving worm populations.
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Affiliation(s)
- Nicolas Roussel
- Electrical and Computer System Engineering Department, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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28
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Tsibidis GD, Tavernarakis N. Nemo: a computational tool for analyzing nematode locomotion. BMC Neurosci 2007; 8:86. [PMID: 17941975 PMCID: PMC2148042 DOI: 10.1186/1471-2202-8-86] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Accepted: 10/17/2007] [Indexed: 11/10/2022] Open
Abstract
Background The nematode Caenorhabditis elegans responds to an impressive range of chemical, mechanical and thermal stimuli and is extensively used to investigate the molecular mechanisms that mediate chemosensation, mechanotransduction and thermosensation. The main behavioral output of these responses is manifested as alterations in animal locomotion. Monitoring and examination of such alterations requires tools to capture and quantify features of nematode movement. Results In this paper, we introduce Nemo (nematode movement), a computationally efficient and robust two-dimensional object tracking algorithm for automated detection and analysis of C. elegans locomotion. This algorithm enables precise measurement and feature extraction of nematode movement components. In addition, we develop a Graphical User Interface designed to facilitate processing and interpretation of movement data. While, in this study, we focus on the simple sinusoidal locomotion of C. elegans, our approach can be readily adapted to handle complicated locomotory behaviour patterns by including additional movement characteristics and parameters subject to quantification. Conclusion Our software tool offers the capacity to extract, analyze and measure nematode locomotion features by processing simple video files. By allowing precise and quantitative assessment of behavioral traits, this tool will assist the genetic dissection and elucidation of the molecular mechanisms underlying specific behavioral responses.
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Affiliation(s)
- George D Tsibidis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology, PO Box 1385, Vasilika Vouton, 71110 Heraklion, Crete, Greece.
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