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
- Nature 482, 485–488 (2012). , &
- Science 336, 159–160 (2012). et al.
- Bioinformatics 24, 1827–1836 (2008).
- Trends Cell Biol. 19, 656–660 (2009). &
- Cell 147, 973–978 (2011).
- Nat. Methods 9, 671–675 (2012). , &
- Genome Biol. 7, R100 (2006). et al.
- Nat. Biotechnol. 28, 348–353 (2010). , , , &
- Nat. Methods 9, 697–710 (2012). et al.
- Nat. Methods 9, 676–682 (2012). et al.
- Time Soc. 13, 129–146 (2004).
- 53–71 (O'Reilly & Associates, 1999). in Open sources. Voices from the open source Revolution (eds., DiBona, C., Ockman, S. & Stone, M.)
- Genome Res. 12, 1611–1618 (2002). et al.
- Genome Biol. 5, R80 (2004). et al.
- 2003). , , & The ITK Software Guide (Kitware Inc.,
- Nat. Methods 9, 683–689 (2012). et al.
- Nat. Methods 9, 690–696 (2012). et al.
- 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.