Current challenges in open-source bioimage informatics

Journal name:
Nature Methods
Year published:
Published online

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.

At a glance


  1. Informal online self-evaluation of scientists' expertise relevant for bioimage informatics.
    Figure 1: Informal online self-evaluation of scientists' expertise relevant for bioimage informatics.

    (a,b) Results for image analysis versus programming (a) and biology versus programming (b). Size of plotted circles is proportional to the percentage of responders selecting a given combination of categories, and data are color-coded by the reported primary expertise.

  2. Visualization of the 'hackathon effect'.
    Figure 2: Visualization of the 'hackathon effect'.

    (a) Situation at the beginning of the Fiji Hackathon at the European Molecular Biology Laboratory (16–26 March 2010). (b,c) Developer activity during the hackathon. (d) Overview of the code generated during the 10-day coding spree. Shown are screenshots from a video generated by the 'gource' tool. Modifications to files of the Fiji project are depicted as rays from the symbols for developers (pawns) to the files represented by a tree of colored balls.


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Author information


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

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

Competing financial interests

The authors declare no competing financial interests.

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Supplementary information


  1. Supplementary Video 1 (8.7M)

    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.

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