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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.

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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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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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