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

Nature Methods volume 9, pages 676–682 (2012)Cite this article

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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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Figure 1: Fiji as a high-powered distribution of ImageJ.
Figure 2: Scripting and ImgLib.
Figure 3: Fiji projects.
Figure 4: Fiji usage.

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Acknowledgements

We thank W. Rasband for developing ImageJ and helping thousands of scientists, those who contributed to the Fiji movement by financing and organizing the hackathons, namely G.M. Rubin for hackathons at Janelia Farm, I. Baines for hackathons at Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, R. Douglas for a hackathon at Institute of Neuroinformatics in Zurich, F. Peri and K. Miura for the hackathon at European Molecular Biology Laboratory, and International Neuroinformatics Coordinating Facility for Fiji image-processing school, W. Pereanu for the confocal image of the larval fly brain, M. Sarov for the confocal scan of C. elegans larva, the scientists who released their code under open-source licenses and made the Fiji project possible. We want to thank Carl Zeiss Microimaging for access to the SPIM demonstrator. K.E. and C.R. were supported by US National Institutes of Health grant RC2GM092519. J.S. and P.T. were funded by Human Frontier Science Program Young Investigator grant RGY0083. P.T. was supported by The European Research Council Community′s Seventh Framework Programme (FP7/2007-2013) grant agreement 260746.

Author information

Author notes

  1. Johannes Schindelin, Stephan Preibisch, Benjamin Schmid & Albert Cardona

    Present address: 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.).,

Authors and Affiliations

  1. Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

    Johannes Schindelin, Tobias Pietzsch, Stephan Preibisch, Stephan Saalfeld, Daniel James White & Pavel Tomancak

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

    Ignacio Arganda-Carreras

  3. Department of Genome Dynamics, Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, California, USA

    Erwin Frise

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

    Verena Kaynig

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

    Mark Longair & Albert Cardona

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

    Curtis Rueden & Kevin Eliceiri

  7. Department of Neurobiology and Genetics, University of Wurzburg, Wurzburg, Germany

    Benjamin Schmid

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

    Jean-Yves Tinevez

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

    Volker Hartenstein

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Corresponding authors

Correspondence to Pavel Tomancak or Albert Cardona.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–3 and Supplementary Table 1 (PDF 1230 kb)

Supplementary Video 1

Visualization of Fiji development. The video, produced using 'gource' tool in Git, visualizes the changes to Fiji source code repository from 15 March 2009 to 16 May 2009. The class hierarchy is visualized as a dynamic tree, the developers are flying pawns that extend rays to classes that they newly created or into which they introduced changes. Between 23 March and 3 April 2009 there was a Fiji hackathon in Dresden, Germany, marked by increased developer activity that carries over the period after the hackathon ended, the 'hackathon effect'. (MOV 10866 kb)

Supplementary Video 2

Visualization of SIFT-mediated stitching of large ssTEM mosaics. The ventral nerve cord of Drosophila first instar larva was sectioned and imaged in electron microscope as a series of overlapping image tiles. The video visualizes the process of reconstruction of such large section series on seven exemplary sections. The corresponding SIFT features that connect images within section and across section are shown as green dots, the residual error of their displacement at a given iteration of the global optimizer is shown as cyan line (iteration number and minimal, average and maximal error are shown in lower left corner). The global optimization proceeds section by section and at each step distributes the registration error equally across the increasing set of tiles. To emphasize the visualization effect all tiles within section are initially placed at the same location discarding their known configuration within section. (MOV 15759 kb)

Supplementary Video 3

Visualization of bead-based registration of multiview microscopy scan of Drosophila embryo. Drosophila embryo expressing His-YFP marker has been imaged in a spinning disc confocal microscope from 18 different angles improvising rotation using custom made sample chamber. The video visualizes the global optimization that is using local geometric bead descriptor matches to recover the shape of the embryo specimen. The bead descriptors (representing constellations of sub-resolution fluorescent beads added to the rigid agarose medium in which the embryo was mounted) are colored according to their displacement at each iteration of the optimizer (red, maximum displacement; green, minimum displacement). The nuclei of the embryo specimen are shown in grey. The displacement at each iteration averaged across all descriptors is shown in the lower left corner. (MOV 6422 kb)

Supplementary Video 4

Segmentation and tracking of nuclei in Drosophila embryo. Cellular blastoderm stage Drosophila embryo expressing His-YFP marker in all cells was imaged from five angles using SPIM throughout gastrulation. The video shows a result of segmentation and tracking algorithm that follows the movements of cells through the gastrulation process. The nuclei are colored according to the angle at which they were detected. (MOV 13736 kb)

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Schindelin, J., Arganda-Carreras, I., Frise, E. et al. Fiji: an open-source platform for biological-image analysis. Nat Methods 9, 676–682 (2012). https://doi.org/10.1038/nmeth.2019

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