Automated tracking of whiskers in videos of head fixed rodents.
Identifieur interne : 000B67 ( PubMed/Corpus ); précédent : 000B66; suivant : 000B68Automated 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 [ 1553-7358 ] ; 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.
DOI: 10.1371/journal.pcbi.1002591
PubMed: 22792058
Links to Exploration step
pubmed:22792058Le 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:affiliation>Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America. clackn@janelia.hhmi.org</nlm:affiliation></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">PubMed</idno><date when="2012">2012</date><idno type="doi">10.1371/journal.pcbi.1002591</idno><idno type="RBID">pubmed:22792058</idno><idno type="pmid">22792058</idno><idno type="wicri:Area/PubMed/Corpus">000B67</idno></publicationStmt><sourceDesc><biblStruct><analytic><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:affiliation>Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America. clackn@janelia.hhmi.org</nlm:affiliation></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="eISSN">1553-7358</idno><imprint><date when="2012" type="published">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">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.</div></front></TEI><pubmed><MedlineCitation Owner="NLM" Status="MEDLINE"><PMID Version="1">22792058</PMID><DateCreated><Year>2012</Year><Month>07</Month><Day>13</Day></DateCreated><DateCompleted><Year>2013</Year><Month>01</Month><Day>23</Day></DateCompleted><DateRevised><Year>2015</Year><Month>02</Month><Day>24</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1553-7358</ISSN><JournalIssue CitedMedium="Internet"><Volume>8</Volume><Issue>7</Issue><PubDate><Year>2012</Year></PubDate></JournalIssue><Title>PLoS computational biology</Title><ISOAbbreviation>PLoS Comput. Biol.</ISOAbbreviation></Journal><ArticleTitle>Automated tracking of whiskers in videos of head fixed rodents.</ArticleTitle><Pagination><MedlinePgn>e1002591</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pcbi.1002591</ELocationID><Abstract><AbstractText>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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Clack</LastName><ForeName>Nathan G</ForeName><Initials>NG</Initials><AffiliationInfo><Affiliation>Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America. clackn@janelia.hhmi.org</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>O'Connor</LastName><ForeName>Daniel H</ForeName><Initials>DH</Initials></Author><Author ValidYN="Y"><LastName>Huber</LastName><ForeName>Daniel</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Petreanu</LastName><ForeName>Leopoldo</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Hires</LastName><ForeName>Andrew</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Peron</LastName><ForeName>Simon</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Svoboda</LastName><ForeName>Karel</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Myers</LastName><ForeName>Eugene W</ForeName><Initials>EW</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><Agency>Howard Hughes Medical Institute</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2012</Year><Month>07</Month><Day>05</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS Comput Biol</MedlineTA><NlmUniqueID>101238922</NlmUniqueID><ISSNLinking>1553-734X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Nat Rev Neurosci. 2008 Aug;9(8):601-12</RefSource><PMID Version="1">18641667</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Neurophysiol. 2008 Jul;100(1):504-15</RefSource><PMID Version="1">18463190</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nat Neurosci. 2009 Jun;12(6):792-800</RefSource><PMID Version="1">19430473</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Neurosci. 2010 Feb 3;30(5):1947-67</RefSource><PMID Version="1">20130203</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Neurophysiol. 2011 Apr;105(4):1950-62</RefSource><PMID Version="1">21307326</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nature. 2012 Apr 26;484(7395):473-8</RefSource><PMID Version="1">22538608</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Somatosens Mot Res. 2001;18(3):211-22</RefSource><PMID Version="1">11562084</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Neurosci. 1990 Aug;10(8):2638-48</RefSource><PMID Version="1">2388081</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Neurophysiol. 2005 Apr;93(4):2294-301</RefSource><PMID Version="1">15563552</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>IEEE Trans Pattern Anal Mach Intell. 2005 Oct;27(10):1615-30</RefSource><PMID Version="1">16237996</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Neurosci. 2006 Aug 16;26(33):8451-64</RefSource><PMID Version="1">16914670</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>PLoS Biol. 2007 Feb;5(2):e15</RefSource><PMID Version="1">17227143</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Proc Biol Sci. 2007 Apr 22;274(1613):1035-41</RefSource><PMID Version="1">17331893</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Neurophysiol. 2007 Oct;98(4):2439-55</RefSource><PMID Version="1">17553946</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>PLoS Biol. 2007 Nov;5(11):e305</RefSource><PMID Version="1">18001152</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Neuron. 2008 Feb 28;57(4):599-613</RefSource><PMID Version="1">18304488</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Neurosci. 2008 Mar 26;28(13):3438-55</RefSource><PMID Version="1">18367610</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>IEEE Trans Biomed Eng. 2009 Jan;56(1):15-22</RefSource><PMID Version="1">19224714</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName MajorTopicYN="N" UI="D000818">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D019295">Computational Biology</DescriptorName><QualifierName MajorTopicYN="Y" UI="Q000379">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D005106">Exploratory Behavior</DescriptorName><QualifierName MajorTopicYN="N" UI="Q000502">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D007091">Image Processing, Computer-Assisted</DescriptorName><QualifierName MajorTopicYN="Y" UI="Q000379">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D051379">Mice</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D014738">Vibrissae</DescriptorName><QualifierName MajorTopicYN="Y" UI="Q000502">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D014743">Videotape Recording</DescriptorName><QualifierName MajorTopicYN="Y" UI="Q000379">methods</QualifierName></MeshHeading></MeshHeadingList><OtherID Source="NLM">PMC3390361</OtherID></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2012</Year><Month>1</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2012</Year><Month>5</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="epublish"><Year>2012</Year><Month>7</Month><Day>5</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2012</Year><Month>7</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2012</Year><Month>7</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2013</Year><Month>1</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="doi">10.1371/journal.pcbi.1002591</ArticleId><ArticleId IdType="pii">PCOMPBIOL-D-12-00134</ArticleId><ArticleId IdType="pubmed">22792058</ArticleId><ArticleId IdType="pmc">PMC3390361</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/HapticV1/Data/PubMed/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000B67 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd -nk 000B67 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Ticri/CIDE
|area= HapticV1
|flux= PubMed
|étape= Corpus
|type= RBID
|clé= pubmed:22792058
|texte= Automated tracking of whiskers in videos of head fixed rodents.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/RBID.i -Sk "pubmed:22792058" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd \
| NlmPubMed2Wicri -a HapticV1
| This area was generated with Dilib version V0.6.23. |  |