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

Johannes Schindelin (1) , Ignacio Arganda-Carreras (2) , Erwin Frise (3) , Verena Kaynig (4) , Mark Longair (5) , Tobias Pietzsch (1) , Stephan Preibisch (1) , Curtis Rueden (6) , Stephan Saalfeld (1) , Benjamin Schmid (7) , Jean-Yves Tinevez (8) , Daniel James White (1) , Volker Hartenstein (9) , Kevin W Eliceiri (6) , Pavel Tomançak (1) , Albert Cardona (5)

1 MPI-CBG - Max Planck Institute of Molecular Cell Biology and Genetics
2 Department of Brain and Cognitive Sciences
3 BDGP - Berkeley Drosophila Genome Project [Berkeley, USA]
4 ETH Zürich - Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich]
5 INI - Institute of Neuroinformatics [Zürich]
6 Laboratory for Optical and Computational Instrumentation [Madison]
7 Department of Genetics and Neurobiology
8 PFID - Imagerie Dynamique (Plate-Forme)
9 Department of Molecular, Cell and Developmental Biology [Los Angeles]

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.

Keywords: Imaging; Software

Domains: Life Sciences [q-bio]

Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, et al.. Fiji: an open-source platform for biological-image analysis. Nature Methods, 2012, 9 (7), pp.676-682. ⟨10.1038/nmeth.2019⟩. ⟨pasteur-02616466⟩