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Current challenges in open-source bioimage informatics

Nature Methods volume 9, pages 661–665 (2012)Cite this article

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We discuss the advantages and challenges of the open-source strategy in biological image analysis and argue that its full impact will not be realized without better support and recognition of software engineers' contributions to the biological sciences and more support of this development model from funders and institutions.

The role of open-source development in basic research is best summarized by a quote (written in support for a grant centered on the open-source image-analysis software Fiji) from Andrew C. Oates (personal communication): “The most fundamental element is the openness; if you can't see the code of a piece of commercial software, then you cannot say what the software really does, and this is not scientific.” No one should use PCR to amplify DNA without knowing what causes the band to appear on the gel. Similarly, it is not good scientific practice to press a button in a piece of software and interpret the results without understanding what the software does. Open-source software (Box 1) provides the necessary transparency, giving scientists the opportunity to not only fully understand the computational methods but also to adapt and improve them, building on research of others in the best scientific tradition.

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Figure 1: Informal online self-evaluation of scientists' expertise relevant for bioimage informatics.
Figure 2: Visualization of the 'hackathon effect'.

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Acknowledgements

We thank S. Saalfeld for programming the online survey and plotting the results shown in Figure 1, J. Schindelin for generating the visualization of Fiji development progress shown in Figure 2, J. Schindelin, M. Longair, C. Rueden and D.J. White for insightful discussions about the merits of the open-source strategy, and A.C. Oates for critical reading of the manuscript. P.T. was supported by Human Frontier Science Program Young Investigator grant RGY0083 and the European Research Council Community's Seventh Framework Programme (FP7/2007-2013) grant agreement 260746.

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Authors and Affiliations

  1. Albert Cardona is at the Institute of Neuroinformatics, University of Zurich and ETH Zürich, Zürich, Switzerland.,

    Albert Cardona

  2. Pavel Tomancak is at the Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,

    Pavel Tomancak

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  1. Albert Cardona
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  2. Pavel Tomancak
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Correspondence to Pavel Tomancak.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Video 1

Visualization of the hackathon effect. The video visualizes the changes introduced to the source code of Fiji during the hackathon at EMBL in Heidelberg between 16 March 2010 and 26 March 2010. The Fiji class hierarchy (class is a unit of computer code) is represented as a dynamic hierarchical tree of colored balls. The pawns represent the Fiji developers extending rays to the classes that they change, add or delete. The visualization was generated using the gource tool developed by Andrew Caudwell. (MOV 8468 kb)

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Cardona, A., Tomancak, P. Current challenges in open-source bioimage informatics. Nat Methods 9, 661–665 (2012). https://doi.org/10.1038/nmeth.2082

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