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A call for bioimaging software usability

Bioimaging software developed in a research setting often is not widely used by the scientific community. We suggest that, to maximize both the public's and researchers' investments, usability should be a more highly valued goal. We describe specific characteristics of usability toward which bioimaging software projects should aim.

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

    Article  CAS  Google Scholar 

  2. Baxter, S.M., Day, S.W., Fetrow, J.S. & Reisinger, S.J. PLoS Comput. Biol. 2, e87 (2006).

    Article  Google Scholar 

  3. Fogel, K. Producing Open Source Software (O'Reilly Media, Inc., 2005).

    Google Scholar 

  4. Bolchini, D., Finkelstein, A., Perrone, V. & Nagl, S. Bioinformatics 25, 406–412 (2009).

    Article  CAS  Google Scholar 

  5. Rimmer, J. J. Audiov. Media Med. 27, 6–10 (2004).

    Article  Google Scholar 

  6. Vandewalle, P., Kovacevic, J. & Vetterli, M. Signal Processing Magazine, IEEE 26, 37–47 (2009).

    Article  Google Scholar 

  7. Mesirov, J.P. Science 327, 415–406 (2010).

    Article  CAS  Google Scholar 

  8. Peng, R.D. Science 334, 1226–1227 (2011).

    Article  CAS  Google Scholar 

  9. Ioannidis, J.P.A. & Khoury, M.J. Science 334, 1230–1232 (2011).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  12. Kamentsky, L. et al. Bioinformatics 27, 1179–1180 (2011).

    Article  CAS  Google Scholar 

  13. Linkert, M. et al. J. Cell Biol. 189, 777–782 (2010).

    Article  CAS  Google Scholar 

  14. Preibisch, S., Tomancak, P. & Saalfeld, S. ImageJ User and Developer Conference 1, 72 (2010).

    Google Scholar 

  15. Sommer, C. et al. Proc. IEEE Int. Symp. Biomed. Imaging 230 (2011).

  16. Goldberg, I.G. et al. Genome Biol. 6, R47 (2005).

    Article  Google Scholar 

  17. Schultheiss, S.J., Münch, M.C., Andreeva, G.D. & Rätsch, G. PLoS ONE 6, e24914 (2011).

    Article  CAS  Google Scholar 

  18. Veretnik, S., Fink, J.L. & Bourne, P.E. PLoS Comput. Biol. 4, e1000136 (2008).

    Article  Google Scholar 

  19. Zhu, H., Hall, P.A.V. & May, J.H.R. ACM Comput. Surv. 29, 366–427 (1997).

    Article  Google Scholar 

  20. Ruusuvuori, P. et al. BMC Bioinformatics 11, 248 (2010).

    Article  Google Scholar 

  21. Ljosa, V., Sokolnicki, K. & Carpenter, A.E. Nat. Methods 9, 637–638 (2012).

    Article  CAS  Google Scholar 

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We thank members of our research groups and our software projects for helpful feedback on the manuscript, in particular CellProfiler cofounder T.R. Jones. This work was supported in part by US National Institutes of Health grants R01 GM089652 (to A.E.C.) and RC2 GM092519 (to K.W.E.), but the opinions expressed are solely those of the authors.

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Correspondence to Anne E Carpenter or Kevin W Eliceiri.

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Carpenter, A., Kamentsky, L. & Eliceiri, K. A call for bioimaging software usability. Nat Methods 9, 666–670 (2012).

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