Fiji: an Open-source Platform for Biological-image Analysis

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2012 Jun 30

PMID 22743772

Citations 26696

Authors

Johannes Schindelin

Ignacio Arganda-Carreras

Erwin Frise

Verena Kaynig

Mark Longair

Tobias Pietzsch

Stephan Preibisch

Curtis Rueden

Stephan Saalfeld

Benjamin Schmid

Jean-Yves Tinevez

Daniel James White

Volker Hartenstein

Kevin Eliceiri

Pavel Tomancak

Albert Cardona

Affiliations

Soon will be listed here.

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.

Citing Articles

Eccentric training effects on hamstring muscles in oral contraceptive users and naturally menstruating women.

Seynnes O, Nordez A, Lacourpaille L, Hesseberg E, Vesterhus I, Fjeldberg K Eur J Appl Physiol. 2025; .

PMID: 40088271 DOI: 10.1007/s00421-025-05753-x.

Chronic intermittent hypoxia disrupts protective microgliosis in ischemic proliferative retinopathy.

Yang T, Ronning K, Augustin S, Blond F, Nous C, Argyriou F J Neuroinflammation. 2025; 22(1):82.

PMID: 40087728 DOI: 10.1186/s12974-025-03392-9.

Force transmission is a master regulator of mechanical cell competition.

Schoenit A, Monfared S, Anger L, Rosse C, Venkatesh V, Balasubramaniam L Nat Mater. 2025; .

PMID: 40087537 DOI: 10.1038/s41563-025-02150-9.

Phototropin connects blue light perception to starch metabolism in green algae.

Yuan Y, Iannetta A, Kim M, Sadecki P, Arend M, Tsichla A Nat Commun. 2025; 16(1):2545.

PMID: 40087266 DOI: 10.1038/s41467-025-57809-3.

Bacterial Supplements Significantly Improve the Growth Rate of Cultured Asparagopsis armata.

Li J, Alperstein L, Tatsumi M, de Nys R, Nappi J, Egan S Mar Biotechnol (NY). 2025; 27(2):65.

PMID: 40085266 DOI: 10.1007/s10126-025-10440-1.

References

Shariff A, Kangas J, Coelho L, Quinn S, Murphy R . Automated image analysis for high-content screening and analysis. J Biomol Screen. 2010; 15(7):726-34. DOI: 10.1177/1087057110370894. View

Anderson J, Jones B, Yang J, Shaw M, Watt C, Koshevoy P . A computational framework for ultrastructural mapping of neural circuitry. PLoS Biol. 2009; 7(3):e1000074. PMC: 2661966. DOI: 10.1371/journal.pbio.1000074. View

Preibisch S, Saalfeld S, Schindelin J, Tomancak P . Software for bead-based registration of selective plane illumination microscopy data. Nat Methods. 2010; 7(6):418-9. DOI: 10.1038/nmeth0610-418. View

Peng H, Ruan Z, Long F, Simpson J, Myers E . V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Nat Biotechnol. 2010; 28(4):348-53. PMC: 2857929. DOI: 10.1038/nbt.1612. View

Kaynig V, Fischer B, Muller E, Buhmann J . Fully automatic stitching and distortion correction of transmission electron microscope images. J Struct Biol. 2010; 171(2):163-73. DOI: 10.1016/j.jsb.2010.04.012. View

Collinet C, Stoter M, Bradshaw C, Samusik N, Rink J, Kenski D . Systems survey of endocytosis by multiparametric image analysis. Nature. 2010; 464(7286):243-9. DOI: 10.1038/nature08779. View

Long F, Peng H, Liu X, Kim S, Myers E . A 3D digital atlas of C. elegans and its application to single-cell analyses. Nat Methods. 2009; 6(9):667-72. PMC: 2882208. DOI: 10.1038/nmeth.1366. View

Schmid B, Schindelin J, Cardona A, Longair M, Heisenberg M . A high-level 3D visualization API for Java and ImageJ. BMC Bioinformatics. 2010; 11:274. PMC: 2896381. DOI: 10.1186/1471-2105-11-274. View

Fernandez R, Das P, Mirabet V, Moscardi E, Traas J, Verdeil J . Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution. Nat Methods. 2010; 7(7):547-53. DOI: 10.1038/nmeth.1472. View

10.

Saalfeld S, Cardona A, Hartenstein V, Tomancak P . As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets. Bioinformatics. 2010; 26(12):i57-63. PMC: 2881403. DOI: 10.1093/bioinformatics/btq219. View

11.

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

12.

Turing A . The chemical basis of morphogenesis. 1953. Bull Math Biol. 1990; 52(1-2):153-97; discussion 119-52. DOI: 10.1007/BF02459572. View

13.

Fowlkes C, Luengo Hendriks C, Keranen S, Weber G, Rubel O, Huang M . A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell. 2008; 133(2):364-74. DOI: 10.1016/j.cell.2008.01.053. View

14.

Preibisch S, Saalfeld S, Tomancak P . Globally optimal stitching of tiled 3D microscopic image acquisitions. Bioinformatics. 2009; 25(11):1463-5. PMC: 2682522. DOI: 10.1093/bioinformatics/btp184. View

15.

Bock D, Lee W, Kerlin A, Andermann M, Hood G, Wetzel A . Network anatomy and in vivo physiology of visual cortical neurons. Nature. 2011; 471(7337):177-82. PMC: 3095821. DOI: 10.1038/nature09802. View

16.

Kaynig V, Fuchs T, Buhmann J . Geometrical consistent 3D tracing of neuronal processes in ssTEM data. Med Image Comput Comput Assist Interv. 2010; 13(Pt 2):209-16. DOI: 10.1007/978-3-642-15745-5_26. View

17.

Neumann B, Walter T, Heriche J, Bulkescher J, Erfle H, Conrad C . Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature. 2010; 464(7289):721-7. PMC: 3108885. DOI: 10.1038/nature08869. View

18.

Bao Z, Murray J, Boyle T, Ooi S, Sandel M, Waterston R . Automated cell lineage tracing in Caenorhabditis elegans. Proc Natl Acad Sci U S A. 2006; 103(8):2707-12. PMC: 1413828. DOI: 10.1073/pnas.0511111103. View

19.

Cardona A, Saalfeld S, Arganda I, Pereanu W, Schindelin J, Hartenstein V . Identifying neuronal lineages of Drosophila by sequence analysis of axon tracts. J Neurosci. 2010; 30(22):7538-53. PMC: 2905806. DOI: 10.1523/JNEUROSCI.0186-10.2010. View

20.

Peng H . Bioimage informatics: a new area of engineering biology. Bioinformatics. 2008; 24(17):1827-36. PMC: 2519164. DOI: 10.1093/bioinformatics/btn346. View