Open Access

Nature Methods, volume 9, issue 7, pages 676-682

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

Johannes Schindelin ^{1, 2}

Ignacio Arganda Carreras ³

Erwin Frise ⁴

Verena Kaynig ⁵

Mark Longair ⁶

Pietzsch Tobias ¹

Stephan Preibisch ^{1, 2}

Curtis Rueden ⁷

Saalfeld Stephan ¹

Benjamin Schmid ^{2, 8}

Jean-Yves Tinevez ⁹

Daniel James White ¹

Volker Hartenstein ¹⁰

Kevin Eliceiri ⁷

Pavel Tomancak ¹

Albert Cardona ^{2, 6}

Show full list: 16 authors

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Max Planck institute of Molecular Cell Biology and Genetics, Dresden, Germany |

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.).,

Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, USA |

⁴

Department of Genome Dynamics, Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, USA |

⁵

Department of Computer Science of the Swiss Federal Institute of Technology Zurich, Zurich, Switzerland |

⁶

Institute of Neuroinformatics of the University of Zurich and Swiss Federal Institute of Technology Zurich, Zurich, Switzerland

⁷

Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, USA |

⁸

Department of Neurobiology and Genetics, University of Wurzburg, Wurzburg, Germany |

⁹

Institut Pasteur, Imagopole, La plate-forme d'imagerie dynamique, Paris, France |

¹⁰

Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, USA |

Publication type: Journal Article

Publication date: 2012-06-28

Springer Nature

Journal: Nature Methods

scimago Q1

SJR: 14.796

CiteScore: 58.7

Impact factor: 36.1

ISSN: 15487091, 15487105

DOI: 10.1038/nmeth.2019

Copy DOI

PubMed ID: 22743772

Biochemistry

Molecular Biology

Cell Biology

Biotechnology

Abstract

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.

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