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Current challenges in open-source bioimage informatics

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'.


  1. Ince, D.C., Hatton, L. & Graham-Cumming, J. Nature 482, 485–488 (2012).

    Article  CAS  Google Scholar 

  2. Morin, A. et al. Science 336, 159–160 (2012).

    Article  CAS  Google Scholar 

  3. Peng, H. Bioinformatics 24, 1827–1836 (2008).

    Article  CAS  Google Scholar 

  4. Swedlow, J.R. & Eliceiri, K.W. Trends Cell Biol. 19, 656–660 (2009).

    Article  CAS  Google Scholar 

  5. Danuser, G. Cell 147, 973–978 (2011).

    Article  CAS  Google Scholar 

  6. Schneider, C.A., Rasband, W.S. & Eliceiri, K.W. Nat. Methods 9, 671–675 (2012).

    Article  CAS  Google Scholar 

  7. Carpenter, A.E. et al. Genome Biol. 7, R100 (2006).

    Article  Google Scholar 

  8. Peng, H., Ruan, Z., Long, F., Simpson, J.H. & Myers, E.W. Nat. Biotechnol. 28, 348–353 (2010).

    Article  CAS  Google Scholar 

  9. Eliceiri, K.W. et al. Nat. Methods 9, 697–710 (2012).

    Article  CAS  Google Scholar 

  10. Schindelin, J. et al. Nat. Methods 9, 676–682 (2012).

    Article  CAS  Google Scholar 

  11. Holtgrewe, U. Time Soc. 13, 129–146 (2004).

    Article  Google Scholar 

  12. Stallman, R. in Open sources. Voices from the open source Revolution (eds., DiBona, C., Ockman, S. & Stone, M.) 53–71 (O'Reilly & Associates, 1999).

    Google Scholar 

  13. Stajich, J.E. et al. Genome Res. 12, 1611–1618 (2002).

    Article  CAS  Google Scholar 

  14. Gentleman, R.C.V. et al. Genome Biol. 5, R80 (2004).

    Article  Google Scholar 

  15. Ibanez, L., Schroeder, W., Ng, L. & Cates, J. The ITK Software Guide (Kitware Inc., 2003).

    Google Scholar 

  16. Kankaanpää, P. et al. Nat. Methods 9, 683–689 (2012).

    Article  Google Scholar 

  17. de Chaumont, F. et al. Nat. Methods 9, 690–696 (2012).

    Article  CAS  Google Scholar 

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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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Correspondence to Pavel Tomancak.

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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).

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