Fiji: an open-source platform for biological-image analysis

Presented is an overview of the image-analysis software platform Fiji, a distribution of ImageJ that updates the underlying ImageJ architecture and adds modern software design elements to expand the capabilities of the platform and facilitate collaboration between biologists and computer scientists....

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Vydáno v:	Nature methods Ročník 9; číslo 7; s. 676 - 682
Hlavní autoři:	Schindelin, Johannes, Arganda-Carreras, Ignacio, Frise, Erwin, Kaynig, Verena, Longair, Mark, Pietzsch, Tobias, Preibisch, Stephan, Rueden, Curtis, Saalfeld, Stephan, Schmid, Benjamin, Tinevez, Jean-Yves, White, Daniel James, Hartenstein, Volker, Eliceiri, Kevin, Tomancak, Pavel, Cardona, Albert
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	New York Nature Publishing Group US 01.07.2012 Nature Publishing Group
Témata:	631/1647/245 631/1647/794 Algorithms Animals Bioinformatics Biological Microscopy Biological Techniques Biology Biomedical and Life Sciences Biomedical Engineering/Biotechnology Brain - ultrastructure Computational Biology - methods Drosophila melanogaster - ultrastructure Image Enhancement - methods Image processing Image Processing, Computer-Assisted - methods Image retrieval Imaging, Three-Dimensional - methods Information Dissemination Life Sciences Methods Microscope and microscopy Open source software perspective Proteomics Public software Software Software Design Technology application United States Switzerland Fiji Imaging Software
ISSN:	1548-7091, 1548-7105, 1548-7105
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Abstract	Presented is an overview of the image-analysis software platform Fiji, a distribution of ImageJ that updates the underlying ImageJ architecture and adds modern software design elements to expand the capabilities of the platform and facilitate collaboration between biologists and computer scientists. Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
AbstractList	Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities. Fiji is a distribution of the popular Open Source software ImageJ focused on biological image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image processing algorithms. Fiji facilitates the transformation of novel algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities. Presented is an overview of the image-analysis software platform Fiji, a distribution of ImageJ that updates the underlying ImageJ architecture and adds modern software design elements to expand the capabilities of the platform and facilitate collaboration between biologists and computer scientists. Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities. Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
Audience	Academic
Author	Eliceiri, Kevin Schindelin, Johannes Frise, Erwin Saalfeld, Stephan Longair, Mark Pietzsch, Tobias Preibisch, Stephan Cardona, Albert Hartenstein, Volker White, Daniel James Rueden, Curtis Schmid, Benjamin Tinevez, Jean-Yves Arganda-Carreras, Ignacio Kaynig, Verena Tomancak, Pavel
AuthorAffiliation	7 University of Wisconsin at Madison, LOCI, Madison, WI, USA 1 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany 3 Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA 9 Institute Pasteur, La plate-forme d’imagerie dynamique - imagopole, Paris, France 8 University of Würzburg, Department of Neurobiology and Genetics, Würzburg, Germany 10 Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, USA 5 Department of Computer Science, of the Swiss Federal Institute of Technology Zürich, Switzerland 6 Institute of Neuroinformatics of the University of Zürich and Swiss Federal Institute of Technology Zürich, Switzerland 4 Berkeley Drosophila Genome Project, Department of Genome Dynamics, Lawrence Berkeley National Labs, Berkeley, CA, USA
AuthorAffiliation_xml	– name: 5 Department of Computer Science, of the Swiss Federal Institute of Technology Zürich, Switzerland – name: 6 Institute of Neuroinformatics of the University of Zürich and Swiss Federal Institute of Technology Zürich, Switzerland – name: 9 Institute Pasteur, La plate-forme d’imagerie dynamique - imagopole, Paris, France – name: 3 Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA – name: 7 University of Wisconsin at Madison, LOCI, Madison, WI, USA – name: 1 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany – name: 10 Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, USA – name: 4 Berkeley Drosophila Genome Project, Department of Genome Dynamics, Lawrence Berkeley National Labs, Berkeley, CA, USA – name: 8 University of Würzburg, Department of Neurobiology and Genetics, Würzburg, Germany
Author_xml	– sequence: 1 givenname: Johannes surname: Schindelin fullname: Schindelin, Johannes organization: Max Planck Institute of Molecular Cell Biology and Genetics, Present addresses: Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA (J.S.), Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany (B.S.) and Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA (S.P. and A.C.) – sequence: 2 givenname: Ignacio surname: Arganda-Carreras fullname: Arganda-Carreras, Ignacio organization: Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology – sequence: 3 givenname: Erwin surname: Frise fullname: Frise, Erwin organization: Department of Genome Dynamics, Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory – sequence: 4 givenname: Verena surname: Kaynig fullname: Kaynig, Verena organization: Department of Computer Science of the Swiss Federal Institute of Technology Zurich – sequence: 5 givenname: Mark surname: Longair fullname: Longair, Mark organization: Institute of Neuroinformatics of the University of Zurich and Swiss Federal Institute of Technology Zurich – sequence: 6 givenname: Tobias surname: Pietzsch fullname: Pietzsch, Tobias organization: Max Planck Institute of Molecular Cell Biology and Genetics – sequence: 7 givenname: Stephan surname: Preibisch fullname: Preibisch, Stephan organization: Max Planck Institute of Molecular Cell Biology and Genetics, Present addresses: Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA (J.S.), Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany (B.S.) and Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA (S.P. and A.C.) – sequence: 8 givenname: Curtis surname: Rueden fullname: Rueden, Curtis organization: Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison – sequence: 9 givenname: Stephan surname: Saalfeld fullname: Saalfeld, Stephan organization: Max Planck Institute of Molecular Cell Biology and Genetics – sequence: 10 givenname: Benjamin surname: Schmid fullname: Schmid, Benjamin organization: Department of Neurobiology and Genetics, University of Wurzburg, Present addresses: Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA (J.S.), Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany (B.S.) and Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA (S.P. and A.C.) – sequence: 11 givenname: Jean-Yves surname: Tinevez fullname: Tinevez, Jean-Yves organization: Institut Pasteur, Imagopole, La plate-forme d'imagerie dynamique – sequence: 12 givenname: Daniel James surname: White fullname: White, Daniel James organization: Max Planck Institute of Molecular Cell Biology and Genetics – sequence: 13 givenname: Volker surname: Hartenstein fullname: Hartenstein, Volker organization: Department of Molecular, Cell and Developmental Biology, University of California – sequence: 14 givenname: Kevin surname: Eliceiri fullname: Eliceiri, Kevin organization: Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison – sequence: 15 givenname: Pavel surname: Tomancak fullname: Tomancak, Pavel email: tomancak@mpi-cbg.de organization: Max Planck Institute of Molecular Cell Biology and Genetics – sequence: 16 givenname: Albert surname: Cardona fullname: Cardona, Albert email: acardona@ini.phys.ethz.ch organization: Institute of Neuroinformatics of the University of Zurich and Swiss Federal Institute of Technology Zurich, Present addresses: Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA (J.S.), Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany (B.S.) and Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA (S.P. and A.C.)
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/22743772$$D View this record in MEDLINE/PubMed https://pasteur.hal.science/pasteur-02616466$$DView record in HAL
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Snippet	Presented is an overview of the image-analysis software platform Fiji, a distribution of ImageJ that updates the underlying ImageJ architecture and adds modern... Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to... Fiji is a distribution of the popular Open Source software ImageJ focused on biological image analysis. Fiji uses modern software engineering practices to...
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SubjectTerms	631/1647/245 631/1647/794 Algorithms Animals Bioinformatics Biological Microscopy Biological Techniques Biology Biomedical and Life Sciences Biomedical Engineering/Biotechnology Brain - ultrastructure Computational Biology - methods Drosophila melanogaster - ultrastructure Image Enhancement - methods Image processing Image Processing, Computer-Assisted - methods Image retrieval Imaging, Three-Dimensional - methods Information Dissemination Life Sciences Methods Microscope and microscopy Open source software perspective Proteomics Public software Software Software Design Technology application
Title	Fiji: an open-source platform for biological-image analysis
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