Fiji: an open-source platform for biological-image analysis (original) (raw)

References

  1. Turing, A.M. The chemical basis of morphogenesis. 1953. Bull. Math. Biol. 52, 153–197, discussion 119–152 (1990).
    Article CAS Google Scholar
  2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).
    Article CAS Google Scholar
  3. Myers, E.W. et al. A whole-genome assembly of Drosophila. Science 287, 2196–2204 (2000).
    Article CAS Google Scholar
  4. Neumann, B. et al. Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature 464, 721–727 (2010).
    Article CAS Google Scholar
  5. Collinet, C. et al. Systems survey of endocytosis by multiparametric image analysis. Nature 464, 243–249 (2010).
    Article CAS Google Scholar
  6. Shariff, A., Kangas, J., Coelho, L.P., Quinn, S. & Murphy, R.F. Automated image analysis for high-content screening and analysis. J. Biomol. Screen. 15, 726–734 (2010).
    Article Google Scholar
  7. Megason, S.G. & Fraser, S.E. Imaging in systems biology. Cell 130, 784–795 (2007).
    Article CAS Google Scholar
  8. Keller, P.J., Schmidt, A.D., Wittbrodt, J. & Stelzer, E.H. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 322, 1065–1069 (2008).
    Article CAS Google Scholar
  9. Fowlkes, C.C. et al. A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell 133, 364–374 (2008).
    Article CAS Google Scholar
  10. Anderson, J.R. et al. A computational framework for ultrastructural mapping of neural circuitry. PLoS Biol. 7, e1000074 (2009).
    Article Google Scholar
  11. Saalfeld, S., Cardona, A., Hartenstein, V. & Tomancak, P. As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets. Bioinformatics 26, i57–i63 (2010).
    Article CAS Google Scholar
  12. Murray, J.I. et al. Automated analysis of embryonic gene expression with cellular resolution in C. elegans. Nat. Methods 5, 703–709 (2008).
    Article CAS Google Scholar
  13. Fernandez, R. et al. Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution. Nat. Methods 7, 547–553 (2010).
    Article CAS Google Scholar
  14. Bao, Z. et al. Automated cell lineage tracing in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 103, 2707–2712 (2006).
    Article CAS Google Scholar
  15. Long, F., Peng, H., Liu, X., Kim, S.K. & Myers, E. A 3D digital atlas of C. elegans and its application to single-cell analyses. Nat. Methods 6, 667–672 (2009).
    Article CAS Google Scholar
  16. Peng, H. et al. BrainAligner: 3D registration atlases of Drosophila brains. Nat. Methods 8, 493–500 (2011).
    Article CAS Google Scholar
  17. Swedlow, J.R. & Eliceiri, K.W. Open source bioimage informatics for cell biology. Trends Cell Biol. 19, 656–660 (2009).
    Article CAS Google Scholar
  18. Peng, H. Bioimage informatics: a new area of engineering biology. Bioinformatics 24, 1827–1836 (2008).
    Article CAS Google Scholar
  19. Abramoff, M.D., Magalhaes, P.J. & Ram, S.J. Image processing with ImageJ. Biophotonics International 11, 36–42 (2004).
    Google Scholar
  20. Carpenter, A.E. et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 7, R100 (2006).
    Article Google Scholar
  21. Peng, H., Ruan, Z., Long, F., Simpson, J.H. & Myers, E.W. V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Nat. Biotechnol. 28, 348–353 (2010).
    Article CAS Google Scholar
  22. de Chaumont, F., Dallongeville, S. & Olivo-Marin, J.-C. ICY: a new open-source community image processing software in. IEEE Int. Symp. on Biomedical Imaging 234–237 (2011).
  23. Berthold, M.R. et al. KNIME: the Konstanz Information Miner. in Studies in Classification, Data Analysis, and Knowledge Organization (GfKL 2007) 319–326 (Springer, 2007).
  24. Cardona, A. et al. TrakEM2 software for neural circuit reconstruction. PLoS One (in the press).
  25. Schmid, B., Schindelin, J., Cardona, A., Longair, M. & Heisenberg, M. A high-level 3D visualization API for Java and ImageJ. BMC Bioinformatics 11, 274 (2010).
    Article Google Scholar
  26. Preibisch, S., Saalfeld, S., Schindelin, J. & Tomancak, P. Software for bead-based registration of selective plane illumination microscopy data. Nat. Methods 7, 418–419 (2010).
    Article CAS Google Scholar
  27. Preibisch, S., Tomancak, P. & Saalfeld, S. in Proc. ImageJ User and Developer Conf. 1, 72–76 (2010).
    Google Scholar
  28. Matas, J., Chum, O., Urban, M. & Pajdla, T. Robust wide baseline stereo from maximally stable extremal regions. Image Vis. Comput. 22, 761–767 (2004).
    Article Google Scholar
  29. Ibanez, L., Schroeder, W., Ng, L. & Cates, J. The ITK Software Guide (Kitware Inc., 2005).
  30. Köthe, U. Reusable software in computer vision. in Handbook of Computer Vision and Applications Vol. 3 (eds. Jähne, B., Haussecker, H. & Geissler P.) 103–132 (San Diego: Academic Press, 1999).
  31. Preibisch, S., Saalfeld, S. & Tomancak, P. Globally optimal stitching of tiled 3D microscopic image acquisitions. Bioinformatics 25, 1463–1465 (2009).
    Article CAS Google Scholar
  32. Cardona, A. et al. An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy. PLoS Biol. 8, e1000502 (2010).
    Article Google Scholar
  33. Bock, D.D. et al. Network anatomy and in vivo physiology of visual cortical neurons. Nature 471, 177–182 (2011).
    Article CAS Google Scholar
  34. Kaynig, V., Fischer, B., Müller, E. & Buhmann, J.M. Fully automatic stitching and distortion correction of transmission electron microscope images. J. Struct. Biol. 171, 163–173 (2010).
    Article Google Scholar
  35. Saalfeld, S., Fetter, R., Cardona, A. & Tomancak, P. Elastic volume reconstruction from series of ultrathin microscopy sections. Nature Methods advance online publication, doi:10.1038/nmeth.2072 (10 June 2012).
  36. Arganda-Carreras, I. et al. Consistent and elastic registration of histological sections using vector-spline regularization. in Lecture Notes in Computer Science 4241, 85–95 (Springer, 2006).
    Article Google Scholar
  37. Lowe, D.G. Distinctive image features from scale-invariant keypoints. Int. J. Comput. Vis. 60, 91–110 (2004).
    Article Google Scholar
  38. Sethian, J.A. Level Set Methods and Fast Marching Methods: Evolving Interfaces in Computational Geometry, Fluid Mechanics, Computer Vision, and Materials Science (Cambridge University Press, 1999).
  39. Kass, M., Witkin, A. & Terzopoulos, D. Snakes: active contour models. Int. J. Comput. Vis. 1, 321–331 (1988).
    Article Google Scholar
  40. Hall, M. et al. The WEKA data mining software: an update. SIGKDD Explor. 11, 10–18 (2009).
    Article Google Scholar
  41. Kaynig, V., Fuchs, T.J. & Buhmann, J.M. Geometrical consistent 3D tracing of neuronal processes in ssTEM data. Med. Image. Comput. Comput. Assist. Interv. 13, 209–216 (2010).
    PubMed Google Scholar
  42. Cardona, A. et al. Identifying neuronal lineages of Drosophila by sequence analysis of axon tracts. J. Neurosci. 30, 7538–7553 (2010).
    Article CAS Google Scholar
  43. Longair, M.H., Baker, D.A. & Armstrong, J.D. Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes. Bioinformatics 27, 2453–2454 (2011).
    Article CAS Google Scholar
  44. Edelstein, A., Amodaj, N., Hoover, K., Vale, R. & Stuurman, N. Computer control of microscopes using μManager. in Current Protocols in Molecular Biology (John Wiley & Sons, Inc., 2010).

Download references