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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Bibliographic Details
Published in:Nature methods Vol. 9; no. 7; pp. 676 - 682
Main Authors: 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
Format: Journal Article
Language:English
Published: New York Nature Publishing Group US 01.07.2012
Nature Publishing Group
Subjects:
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
Online Access:Get full text
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Summary: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.
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PMCID: PMC3855844
present address University of Wisconsin at Madison, LOCI, Madison, WI, USA
ISSN:1548-7091
1548-7105
1548-7105
DOI:10.1038/nmeth.2019