Automated Tracking of Whiskers in Videos of Head Fixed Rodents
Identifieur interne : 002551 ( Main/Exploration ); précédent : 002550; suivant : 002552Automated Tracking of Whiskers in Videos of Head Fixed Rodents
Auteurs : Nathan G. Clack ; Daniel H. O'Connor ; Daniel Huber ; Leopoldo Petreanu ; Andrew Hires ; Simon Peron ; Karel Svoboda ; Eugene W. MyersSource :
- PLoS Computational Biology [ 1553-734X ] ; 2012.
English descriptors
- KwdEn :
- MESH :
- methods : Computational Biology, Image Processing, Computer-Assisted, Videotape Recording.
- physiology : Exploratory Behavior, Vibrissae.
- Animals, Mice.
Abstract
We have developed software for fully automated tracking of vibrissae (whiskers) in high-speed videos (>500 Hz) of head-fixed, behaving rodents trimmed to a single row of whiskers. Performance was assessed against a manually curated dataset consisting of 1.32 million video frames comprising 4.5 million whisker traces. The current implementation detects whiskers with a recall of 99.998% and identifies individual whiskers with 99.997% accuracy. The average processing rate for these images was 8 Mpx/s/cpu (2.6 GHz Intel Core2, 2 GB RAM). This translates to 35 processed frames per second for a 640 px×352 px video of 4 whiskers. The speed and accuracy achieved enables quantitative behavioral studies where the analysis of millions of video frames is required. We used the software to analyze the evolving whisking strategies as mice learned a whisker-based detection task over the course of 6 days (8148 trials, 25 million frames) and measure the forces at the sensory follicle that most underlie haptic perception.
Url:
DOI: 10.1371/journal.pcbi.1002591
PubMed: 22792058
PubMed Central: 3390361
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 002159
- to stream Pmc, to step Curation: 002159
- to stream Pmc, to step Checkpoint: 001844
- to stream PubMed, to step Corpus: 000B67
- to stream PubMed, to step Curation: 000B67
- to stream PubMed, to step Checkpoint: 000B86
- to stream Ncbi, to step Merge: 002135
- to stream Ncbi, to step Curation: 002135
- to stream Ncbi, to step Checkpoint: 002135
- to stream Main, to step Merge: 002578
- to stream Main, to step Curation: 002551
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Automated Tracking of Whiskers in Videos of Head Fixed Rodents</title>
<author><name sortKey="Clack, Nathan G" sort="Clack, Nathan G" uniqKey="Clack N" first="Nathan G." last="Clack">Nathan G. Clack</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="O Connor, Daniel H" sort="O Connor, Daniel H" uniqKey="O Connor D" first="Daniel H." last="O'Connor">Daniel H. O'Connor</name>
</author>
<author><name sortKey="Huber, Daniel" sort="Huber, Daniel" uniqKey="Huber D" first="Daniel" last="Huber">Daniel Huber</name>
</author>
<author><name sortKey="Petreanu, Leopoldo" sort="Petreanu, Leopoldo" uniqKey="Petreanu L" first="Leopoldo" last="Petreanu">Leopoldo Petreanu</name>
</author>
<author><name sortKey="Hires, Andrew" sort="Hires, Andrew" uniqKey="Hires A" first="Andrew" last="Hires">Andrew Hires</name>
</author>
<author><name sortKey="Peron, Simon" sort="Peron, Simon" uniqKey="Peron S" first="Simon" last="Peron">Simon Peron</name>
</author>
<author><name sortKey="Svoboda, Karel" sort="Svoboda, Karel" uniqKey="Svoboda K" first="Karel" last="Svoboda">Karel Svoboda</name>
</author>
<author><name sortKey="Myers, Eugene W" sort="Myers, Eugene W" uniqKey="Myers E" first="Eugene W." last="Myers">Eugene W. Myers</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">22792058</idno>
<idno type="pmc">3390361</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390361</idno>
<idno type="RBID">PMC:3390361</idno>
<idno type="doi">10.1371/journal.pcbi.1002591</idno>
<date when="2012">2012</date>
<idno type="wicri:Area/Pmc/Corpus">002159</idno>
<idno type="wicri:Area/Pmc/Curation">002159</idno>
<idno type="wicri:Area/Pmc/Checkpoint">001844</idno>
<idno type="wicri:source">PubMed</idno>
<idno type="wicri:Area/PubMed/Corpus">000B67</idno>
<idno type="wicri:Area/PubMed/Curation">000B67</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000B86</idno>
<idno type="wicri:Area/Ncbi/Merge">002135</idno>
<idno type="wicri:Area/Ncbi/Curation">002135</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">002135</idno>
<idno type="wicri:doubleKey">1553-734X:2012:Clack N:automated:tracking:of</idno>
<idno type="wicri:Area/Main/Merge">002578</idno>
<idno type="wicri:Area/Main/Curation">002551</idno>
<idno type="wicri:Area/Main/Exploration">002551</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Automated Tracking of Whiskers in Videos of Head Fixed Rodents</title>
<author><name sortKey="Clack, Nathan G" sort="Clack, Nathan G" uniqKey="Clack N" first="Nathan G." last="Clack">Nathan G. Clack</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="O Connor, Daniel H" sort="O Connor, Daniel H" uniqKey="O Connor D" first="Daniel H." last="O'Connor">Daniel H. O'Connor</name>
</author>
<author><name sortKey="Huber, Daniel" sort="Huber, Daniel" uniqKey="Huber D" first="Daniel" last="Huber">Daniel Huber</name>
</author>
<author><name sortKey="Petreanu, Leopoldo" sort="Petreanu, Leopoldo" uniqKey="Petreanu L" first="Leopoldo" last="Petreanu">Leopoldo Petreanu</name>
</author>
<author><name sortKey="Hires, Andrew" sort="Hires, Andrew" uniqKey="Hires A" first="Andrew" last="Hires">Andrew Hires</name>
</author>
<author><name sortKey="Peron, Simon" sort="Peron, Simon" uniqKey="Peron S" first="Simon" last="Peron">Simon Peron</name>
</author>
<author><name sortKey="Svoboda, Karel" sort="Svoboda, Karel" uniqKey="Svoboda K" first="Karel" last="Svoboda">Karel Svoboda</name>
</author>
<author><name sortKey="Myers, Eugene W" sort="Myers, Eugene W" uniqKey="Myers E" first="Eugene W." last="Myers">Eugene W. Myers</name>
</author>
</analytic>
<series><title level="j">PLoS Computational Biology</title>
<idno type="ISSN">1553-734X</idno>
<idno type="eISSN">1553-7358</idno>
<imprint><date when="2012">2012</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term>
<term>Computational Biology (methods)</term>
<term>Exploratory Behavior (physiology)</term>
<term>Image Processing, Computer-Assisted (methods)</term>
<term>Mice</term>
<term>Vibrissae (physiology)</term>
<term>Videotape Recording (methods)</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term>
<term>Image Processing, Computer-Assisted</term>
<term>Videotape Recording</term>
</keywords>
<keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Exploratory Behavior</term>
<term>Vibrissae</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Animals</term>
<term>Mice</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>We have developed software for fully automated tracking of vibrissae (whiskers) in high-speed videos (>500 Hz) of head-fixed, behaving rodents trimmed to a single row of whiskers. Performance was assessed against a manually curated dataset consisting of 1.32 million video frames comprising 4.5 million whisker traces. The current implementation detects whiskers with a recall of 99.998% and identifies individual whiskers with 99.997% accuracy. The average processing rate for these images was 8 Mpx/s/cpu (2.6 GHz Intel Core2, 2 GB RAM). This translates to 35 processed frames per second for a 640 px×352 px video of 4 whiskers. The speed and accuracy achieved enables quantitative behavioral studies where the analysis of millions of video frames is required. We used the software to analyze the evolving whisking strategies as mice learned a whisker-based detection task over the course of 6 days (8148 trials, 25 million frames) and measure the forces at the sensory follicle that most underlie haptic perception.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="O Connor, Dh" uniqKey="O Connor D">DH O'Connor</name>
</author>
<author><name sortKey="Clack, Ng" uniqKey="Clack N">NG Clack</name>
</author>
<author><name sortKey="Huber, D" uniqKey="Huber D">D Huber</name>
</author>
<author><name sortKey="Komiyama, T" uniqKey="Komiyama T">T Komiyama</name>
</author>
<author><name sortKey="Myers, Ew" uniqKey="Myers E">EW Myers</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Knutsen, Pm" uniqKey="Knutsen P">PM Knutsen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Carvell, Ge" uniqKey="Carvell G">GE Carvell</name>
</author>
<author><name sortKey="Simons, Dj" uniqKey="Simons D">DJ Simons</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Heimendahl Von, M" uniqKey="Heimendahl Von M">M Heimendahl von</name>
</author>
<author><name sortKey="Itskov, Pm" uniqKey="Itskov P">PM Itskov</name>
</author>
<author><name sortKey="Arabzadeh, E" uniqKey="Arabzadeh E">E Arabzadeh</name>
</author>
<author><name sortKey="Diamond, Me" uniqKey="Diamond M">ME Diamond</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mitchinson, B" uniqKey="Mitchinson B">B Mitchinson</name>
</author>
<author><name sortKey="Martin, Cj" uniqKey="Martin C">CJ Martin</name>
</author>
<author><name sortKey="Grant, Ra" uniqKey="Grant R">RA Grant</name>
</author>
<author><name sortKey="Prescott, Tj" uniqKey="Prescott T">TJ Prescott</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Diamond, Me" uniqKey="Diamond M">ME Diamond</name>
</author>
<author><name sortKey="Heimendahl Von, M" uniqKey="Heimendahl Von M">M Heimendahl von</name>
</author>
<author><name sortKey="Knutsen, Pm" uniqKey="Knutsen P">PM Knutsen</name>
</author>
<author><name sortKey="Kleinfeld, D" uniqKey="Kleinfeld D">D Kleinfeld</name>
</author>
<author><name sortKey="Ahissar, E" uniqKey="Ahissar E">E Ahissar</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hill, Dn" uniqKey="Hill D">DN Hill</name>
</author>
<author><name sortKey="Bermejo, R" uniqKey="Bermejo R">R Bermejo</name>
</author>
<author><name sortKey="Zeigler, Hp" uniqKey="Zeigler H">HP Zeigler</name>
</author>
<author><name sortKey="Kleinfeld, D" uniqKey="Kleinfeld D">D Kleinfeld</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Venkatraman, S" uniqKey="Venkatraman S">S Venkatraman</name>
</author>
<author><name sortKey="Elkabany, K" uniqKey="Elkabany K">K Elkabany</name>
</author>
<author><name sortKey="Long, Jd" uniqKey="Long J">JD Long</name>
</author>
<author><name sortKey="Yao, Y" uniqKey="Yao Y">Y Yao</name>
</author>
<author><name sortKey="Carmena, Jm" uniqKey="Carmena J">JM Carmena</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jadhav, Sp" uniqKey="Jadhav S">SP Jadhav</name>
</author>
<author><name sortKey="Wolfe, J" uniqKey="Wolfe J">J Wolfe</name>
</author>
<author><name sortKey="Feldman, De" uniqKey="Feldman D">DE Feldman</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Harvey, Ma" uniqKey="Harvey M">MA Harvey</name>
</author>
<author><name sortKey="Bermejo, R" uniqKey="Bermejo R">R Bermejo</name>
</author>
<author><name sortKey="Zeigler, Hp" uniqKey="Zeigler H">HP Zeigler</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Voigts, J" uniqKey="Voigts J">J Voigts</name>
</author>
<author><name sortKey="Sakmann, B" uniqKey="Sakmann B">B Sakmann</name>
</author>
<author><name sortKey="Celikel, T" uniqKey="Celikel T">T Celikel</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ritt, Jt" uniqKey="Ritt J">JT Ritt</name>
</author>
<author><name sortKey="Andermann, Ml" uniqKey="Andermann M">ML Andermann</name>
</author>
<author><name sortKey="Moore, Ci" uniqKey="Moore C">CI Moore</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Knutsen, Pm" uniqKey="Knutsen P">PM Knutsen</name>
</author>
<author><name sortKey="Derdikman, D" uniqKey="Derdikman D">D Derdikman</name>
</author>
<author><name sortKey="Ahissar, E" uniqKey="Ahissar E">E Ahissar</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gyory, G" uniqKey="Gyory G">G Gyory</name>
</author>
<author><name sortKey="Rankov, V" uniqKey="Rankov V">V Rankov</name>
</author>
<author><name sortKey="Gordon, G" uniqKey="Gordon G">G Gordon</name>
</author>
<author><name sortKey="Perkon, I" uniqKey="Perkon I">I Perkon</name>
</author>
<author><name sortKey="Mitchinson, B" uniqKey="Mitchinson B">B Mitchinson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Perkon, I" uniqKey="Perkon I">I Perkon</name>
</author>
<author><name sortKey="Kosir, A" uniqKey="Kosir A">A Kosir</name>
</author>
<author><name sortKey="Itskov, Pm" uniqKey="Itskov P">PM Itskov</name>
</author>
<author><name sortKey="Tasic, J" uniqKey="Tasic J">J Tasic</name>
</author>
<author><name sortKey="Diamond, Me" uniqKey="Diamond M">ME Diamond</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Birdwell, Ja" uniqKey="Birdwell J">JA Birdwell</name>
</author>
<author><name sortKey="Solomon, Jh" uniqKey="Solomon J">JH Solomon</name>
</author>
<author><name sortKey="Thajchayapong, M" uniqKey="Thajchayapong M">M Thajchayapong</name>
</author>
<author><name sortKey="Taylor, Ma" uniqKey="Taylor M">MA Taylor</name>
</author>
<author><name sortKey="Cheely, M" uniqKey="Cheely M">M Cheely</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Huber, D" uniqKey="Huber D">D Huber</name>
</author>
<author><name sortKey="Gutnisky, Da" uniqKey="Gutnisky D">DA Gutnisky</name>
</author>
<author><name sortKey="Peron, S" uniqKey="Peron S">S Peron</name>
</author>
<author><name sortKey="O Connor, Dh" uniqKey="O Connor D">DH O'Connor</name>
</author>
<author><name sortKey="Wiegert, Js" uniqKey="Wiegert J">JS Wiegert</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mehta, Sb" uniqKey="Mehta S">SB Mehta</name>
</author>
<author><name sortKey="Whitmer, D" uniqKey="Whitmer D">D Whitmer</name>
</author>
<author><name sortKey="Figueroa, R" uniqKey="Figueroa R">R Figueroa</name>
</author>
<author><name sortKey="Williams, Ba" uniqKey="Williams B">BA Williams</name>
</author>
<author><name sortKey="Kleinfeld, D" uniqKey="Kleinfeld D">D Kleinfeld</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mikolajczyk, K" uniqKey="Mikolajczyk K">K Mikolajczyk</name>
</author>
<author><name sortKey="Schmid, C" uniqKey="Schmid C">C Schmid</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Torre, V" uniqKey="Torre V">V Torre</name>
</author>
<author><name sortKey="Poggio, Ta" uniqKey="Poggio T">TA Poggio</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rabiner, Lr" uniqKey="Rabiner L">LR Rabiner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gordon, G" uniqKey="Gordon G">G Gordon</name>
</author>
<author><name sortKey="Mitcheson, B" uniqKey="Mitcheson B">B Mitcheson</name>
</author>
<author><name sortKey="Grant, Ra" uniqKey="Grant R">RA Grant</name>
</author>
<author><name sortKey="Diamond, M" uniqKey="Diamond M">M Diamond</name>
</author>
<author><name sortKey="Prescot, T" uniqKey="Prescot T">T Prescot</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<affiliations><list></list>
<tree><noCountry><name sortKey="Clack, Nathan G" sort="Clack, Nathan G" uniqKey="Clack N" first="Nathan G." last="Clack">Nathan G. Clack</name>
<name sortKey="Hires, Andrew" sort="Hires, Andrew" uniqKey="Hires A" first="Andrew" last="Hires">Andrew Hires</name>
<name sortKey="Huber, Daniel" sort="Huber, Daniel" uniqKey="Huber D" first="Daniel" last="Huber">Daniel Huber</name>
<name sortKey="Myers, Eugene W" sort="Myers, Eugene W" uniqKey="Myers E" first="Eugene W." last="Myers">Eugene W. Myers</name>
<name sortKey="O Connor, Daniel H" sort="O Connor, Daniel H" uniqKey="O Connor D" first="Daniel H." last="O'Connor">Daniel H. O'Connor</name>
<name sortKey="Peron, Simon" sort="Peron, Simon" uniqKey="Peron S" first="Simon" last="Peron">Simon Peron</name>
<name sortKey="Petreanu, Leopoldo" sort="Petreanu, Leopoldo" uniqKey="Petreanu L" first="Leopoldo" last="Petreanu">Leopoldo Petreanu</name>
<name sortKey="Svoboda, Karel" sort="Svoboda, Karel" uniqKey="Svoboda K" first="Karel" last="Svoboda">Karel Svoboda</name>
</noCountry>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/HapticV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002551 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 002551 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Ticri/CIDE |area= HapticV1 |flux= Main |étape= Exploration |type= RBID |clé= PMC:3390361 |texte= Automated Tracking of Whiskers in Videos of Head Fixed Rodents }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:22792058" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \ | NlmPubMed2Wicri -a HapticV1
![]() | This area was generated with Dilib version V0.6.23. | ![]() |