Signal extraction from movies of honeybee brain activity : the ImageBee plugin for KNIME

Strauch, Martin; Rein, Julia; Lutz, Christian; Galizia, C. Giovanni

Signal extraction from movies of honeybee brain activity : the ImageBee plugin for KNIME

Dateien

Strauch_217008.pdfGröße: 1.78 MBDownloads: 378

Datum

2013

Autor:innen

Strauch, Martin

Rein, Julia

Lutz, Christian

Galizia, C. Giovanni

Open Access-Veröffentlichung

Open Access Gold

Sammlungen

Biologie

Publikationstyp

Zeitschriftenartikel

Publikationsstatus

Published

Erschienen in

BMC Bioinformatics. 2013, 14(Suppl 18), S4. eISSN 1471-2105. Available under: doi: 10.1186/1471-2105-14-S18-S4

Zusammenfassung

Background

In the antennal lobe, a dedicated olfactory center of the honeybee brain, odours are encoded as activity patterns of coding units, the so-called glomeruli. Optical imaging with calcium-sensitive dyes allows us to record these activity patterns and to gain insight into olfactory information processing in the brain.

Method

We introduce ImageBee, a plugin for the data analysis platform KNIME. ImageBee provides a variety of tools for processing optical imaging data. The main algorithm behind ImageBee is a matrix factorisation approach. Motivated by a data-specific, non-negative mixture model, the algorithm aims to select the generating extreme vectors of a convex cone that contains the data. It approximates the movie matrix by non-negative combinations of the extreme vectors. These correspond to pure glomerular signals that are not mixed with neighbour signals.

Results

Evaluation shows that the proposed algorithm can identify the relevant biological signals on imaging data from the honeybee AL, as well as it can recover implanted source signals from artificial data.

Conclusions

ImageBee enables automated data processing and visualisation for optical imaging data from the insect AL. The modular implementation for KNIME offers a flexible platform for data analysis projects, where modules can be rearranged or added depending on the particular application.

Fachgebiet (DDC)

570 Biowissenschaften, Biologie

Zitieren

ISO 690

STRAUCH, Martin, Julia REIN, Christian LUTZ, C. Giovanni GALIZIA, 2013. Signal extraction from movies of honeybee brain activity : the ImageBee plugin for KNIME. In: BMC Bioinformatics. 2013, 14(Suppl 18), S4. eISSN 1471-2105. Available under: doi: 10.1186/1471-2105-14-S18-S4

BibTex

@article{Strauch2013Signa-21700,
  year={2013},
  doi={10.1186/1471-2105-14-S18-S4},
  title={Signal extraction from movies of honeybee brain activity : the ImageBee plugin for KNIME},
  number={Suppl 18},
  volume={14},
  journal={BMC Bioinformatics},
  author={Strauch, Martin and Rein, Julia and Lutz, Christian and Galizia, C. Giovanni},
  note={Article Number: S4}
}

RDF

<rdf:RDF
    xmlns:dcterms="http://purl.org/dc/terms/"
    xmlns:dc="http://purl.org/dc/elements/1.1/"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:bibo="http://purl.org/ontology/bibo/"
    xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#"
    xmlns:foaf="http://xmlns.com/foaf/0.1/"
    xmlns:void="http://rdfs.org/ns/void#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > 
  <rdf:Description rdf:about="https://kops.uni-konstanz.de/server/rdf/resource/123456789/21700">
    <dc:contributor>Strauch, Martin</dc:contributor>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2013-11-08T10:24:08Z</dc:date>
    <dc:creator>Lutz, Christian</dc:creator>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/21700/2/Strauch_217008.pdf"/>
    <dcterms:rights rdf:resource="http://creativecommons.org/licenses/by/2.0/"/>
    <dc:language>eng</dc:language>
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dc:contributor>Lutz, Christian</dc:contributor>
    <dcterms:bibliographicCitation>BMC Bioinformatics ; 14 (2013), suppl. 18. - S4</dcterms:bibliographicCitation>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2013-11-08T10:24:08Z</dcterms:available>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
    <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/21700/2/Strauch_217008.pdf"/>
    <dcterms:abstract xml:lang="eng">Background&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;In the antennal lobe, a dedicated olfactory center of the honeybee brain, odours are encoded as activity patterns of coding units, the so-called glomeruli. Optical imaging with calcium-sensitive dyes allows us to record these activity patterns and to gain insight into olfactory information processing in the brain.&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;Method&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;We introduce ImageBee, a plugin for the data analysis platform KNIME. ImageBee provides a variety of tools for processing optical imaging data. The main algorithm behind ImageBee is a matrix factorisation approach. Motivated by a data-specific, non-negative mixture model, the algorithm aims to select the generating extreme vectors of a convex cone that contains the data. It approximates the movie matrix by non-negative combinations of the extreme vectors. These correspond to pure glomerular signals that are not mixed with neighbour signals.&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;Results&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;Evaluation shows that the proposed algorithm can identify the relevant biological signals on imaging data from the honeybee AL, as well as it can recover implanted source signals from artificial data.&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;Conclusions&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;ImageBee enables automated data processing and visualisation for optical imaging data from the insect AL. The modular implementation for KNIME offers a flexible platform for data analysis projects, where modules can be rearranged or added depending on the particular application.</dcterms:abstract>
    <dc:creator>Galizia, C. Giovanni</dc:creator>
    <dc:rights>Attribution 2.0 Generic</dc:rights>
    <dcterms:title>Signal extraction from movies of honeybee brain activity : the ImageBee plugin for KNIME</dcterms:title>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dcterms:issued>2013</dcterms:issued>
    <dc:creator>Strauch, Martin</dc:creator>
    <dc:contributor>Rein, Julia</dc:contributor>
    <dc:creator>Rein, Julia</dc:creator>
    <dc:contributor>Galizia, C. Giovanni</dc:contributor>
    <bibo:uri rdf:resource="http://kops.uni-konstanz.de/handle/123456789/21700"/>
  </rdf:Description>
</rdf:RDF>

Universitätsbibliographie

Ja