Crossref journal-article
Springer Science and Business Media LLC
Nature Methods (297)
Bibliography

de Chaumont, F., Dallongeville, S., Chenouard, N., Hervé, N., Pop, S., Provoost, T., Meas-Yedid, V., Pankajakshan, P., Lecomte, T., Le Montagner, Y., Lagache, T., Dufour, A., & Olivo-Marin, J.-C. (2012). Icy: an open bioimage informatics platform for extended reproducible research. Nature Methods, 9(7), 690–696.

Authors 13
  1. Fabrice de Chaumont (first)
  2. Stéphane Dallongeville (additional)
  3. Nicolas Chenouard (additional)
  4. Nicolas Hervé (additional)
  5. Sorin Pop (additional)
  6. Thomas Provoost (additional)
  7. Vannary Meas-Yedid (additional)
  8. Praveen Pankajakshan (additional)
  9. Timothée Lecomte (additional)
  10. Yoann Le Montagner (additional)
  11. Thibault Lagache (additional)
  12. Alexandre Dufour (additional)
  13. Jean-Christophe Olivo-Marin (additional)
References 29 Referenced 1,394
  1. Swedlow, J.R., Goldberg, I., Brauner, E. & Sorger, P.K. Informatics and quantitative analysis in biological imaging. Science 300, 100–102 (2003). (10.1126/science.1082602) / Science by JR Swedlow (2003)
  2. Peng, H., Ruan, Z., Atasoy, D. & Sternson, S. Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model. Bioinformatics 26, i38–i46 (2010). (10.1093/bioinformatics/btq212) / Bioinformatics by H Peng (2010)
  3. Kalinka, A.T. et al. Gene expression divergence recapitulates the developmental hourglass model. Nature 468, 811–814 (2010). (10.1038/nature09634) / Nature by AT Kalinka (2010)
  4. Meijering, E. et al. Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images. Cytometry A 58, 167–176 (2004). (10.1002/cyto.a.20022) / Cytometry A by E Meijering (2004)
  5. Zimmer, C. et al. On the digital trail of mobile cells. IEEE Signal Process. Mag. 23, 54–62 (2006). (10.1109/MSP.2006.1628878) / IEEE Signal Process. Mag. by C Zimmer (2006)
  6. Chenouard, N., Dufour, A. & Olivo-Marin, J.-C. Tracking algorithms chase down pathogens. Biotechnol. J. 4, 838–845 (2009). (10.1002/biot.200900030) / Biotechnol. J. by N Chenouard (2009)
  7. Fomel, S. & Claerbout, J. Introduction: reproducible research. Comput. Sci. Eng. 11, 5–7 (2009). (10.1109/MCSE.2009.14) / Comput. Sci. Eng. by S Fomel (2009)
  8. Ince, D.C., Hatton, L. & Graham-Cumming, J. The case for open computer programs. Nature 482, 485–488 (2012). (10.1038/nature10836) / Nature by DC Ince (2012)
  9. Vandewalle, P., Kovacevic, J. & Vetterli, M. Reproducible research in signal processing—what, why, and how. IEEE Signal Process. Mag. 26, 37–47 (2009). (10.1109/MSP.2009.932122) / IEEE Signal Process. Mag. by P Vandewalle (2009)
  10. Allan, C. et al. OMERO: flexible, model-driven data management for experimental biology. Nat. Methods 9, 245–253 (2012). (10.1038/nmeth.1896) / Nat. Methods by C Allan (2012)
  11. Abramoff, M.D., Magalhaes, P.J. & Ram, S.J. Image Processing with ImageJ. Biophotonics Int. 11, 36–42 (2004). / Biophotonics Int. by MD Abramoff (2004)
  12. Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012). (10.1038/nmeth.2019) / Nat. Methods by J Schindelin (2012)
  13. Carpenter, A.E. et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 7, R100 (2006). (10.1186/gb-2006-7-10-r100) / Genome Biol. by AE Carpenter (2006)
  14. Kankaanpää, P. et al. BioImageXD: an open, general-purpose and high-throughput image-processing platform. Nat. Methods 9, 683–689 (2012). (10.1038/nmeth.2047) / Nat. Methods by P Kankaanpää (2012)
  15. Olivo-Marin, J.-C. Extraction of spots in biological images using multiscale products. Pattern Recognit. 35, 1989–1996 (2002). (10.1016/S0031-3203(01)00127-3) / Pattern Recognit. by J-C Olivo-Marin (2002)
  16. Cabal, G. et al. SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope. Nature 441, 770–773 (2006). (10.1038/nature04752) / Nature by G Cabal (2006)
  17. Alonso, M. et al. Olfactory discrimination learning increases the survival of adult-born neurons in the olfactory bulb. J. Neurosci. 26, 10508–10513 (2006). (10.1523/JNEUROSCI.2633-06.2006) / J. Neurosci. by M Alonso (2006)
  18. Grassart, A. et al. Pak1 phosphorylation enhances cortactin–N-WASP interaction in clathrin-caveolin-independent endocytosis. Traffic 11, 1079–1091 (2010). (10.1111/j.1600-0854.2010.01075.x) / Traffic by A Grassart (2010)
  19. Genovesio, A. et al. Multiple particle tracking in 3D+t microscopy: method and application to the tracking of endocytozed quantum dots. IEEE Trans. Image Process. 15, 1062–1070 (2006). (10.1109/TIP.2006.872323) / IEEE Trans. Image Process. by A Genovesio (2006)
  20. Arhel, N. et al. Quantitative four-dimensional tracking of cytoplasmic and nuclear HIV-1 complexes. Nat. Methods 3, 817–824 (2006). (10.1038/nmeth928) / Nat. Methods by N Arhel (2006)
  21. Gousset, K. et al. Prions hijack tunneling nanotubes for intercellular spread. Nat. Cell Biol. 11, 328–336 (2009). (10.1038/ncb1841) / Nat. Cell Biol. by K Gousset (2009)
  22. Nicolas, E., Chenouard, N., Olivo-Marin, J.-C. & Guichet, A. A dual role for actin and microtubule cytoskeleton in the transport of golgi units from the nurse cells to the oocyte across ring canals. Mol. Biol. Cell 20, 556–568 (2009). (10.1091/mbc.e08-04-0360) / Mol. Biol. Cell by E Nicolas (2009)
  23. Zimmer, C. & Olivo-Marin, J.-C. Coupled parametric active contours. IEEE Trans. Pattern Anal. Mach. Intell. 27, 1838–1842 (2005). (10.1109/TPAMI.2005.214) / IEEE Trans. Pattern Anal. Mach. Intell. by C Zimmer (2005)
  24. Dufour, A. et al. Segmenting and tracking fluorescent cells in dynamic 3-D microscopy with coupled active surfaces. IEEE Trans. Image Process. 14, 1396–1410 (2005). (10.1109/TIP.2005.852790) / IEEE Trans. Image Process. by A Dufour (2005)
  25. Dufour, A., Thibeaux, R., Labruyère, E., Guillén, N. & Olivo-Marin, J.-C. 3-D active meshes: fast discrete deformable models for cell tracking in 3-D time-lapse microscopy. IEEE Trans. Image Process. 20, 1925–1937 (2011). (10.1109/TIP.2010.2099125) / IEEE Trans. Image Process. by A Dufour (2011)
  26. Melki, M.-T., Saïdi, H., Dufour, A., Olivo-Marin, J.-C. & Gougeon, M.-L. Escape of HIV-1-infected dendritic cells from TRAIL-Mediated NK cell cytotoxicity. A pivotal role of HMGB1. PLoS Pathog. 6, e1000862 (2010). (10.1371/journal.ppat.1000862) / PLoS Pathog. by M-T Melki (2010)
  27. Blazquez, S. et al. Human tumor necrosis factor is a chemoattractant for the parasite Entamoeba histolytica. Infect. Immun. 74, 1407–1411 (2006). (10.1128/IAI.74.2.1407-1411.2006) / Infect. Immun. by S Blazquez (2006)
  28. Thibeaux, R. et al. Newly visualized fibrillar collagen scaffolds dictate Entamoeba histolytica invasion route in the human colon. Cell. Microbiol. 14, 609–621 (2012). (10.1111/j.1462-5822.2012.01752.x) / Cell. Microbiol. by R Thibeaux (2012)
  29. de Chaumont, F. et al. Computerized video analysis of social interactions in mice. Nat. Methods 9, 410–417 (2012). (10.1038/nmeth.1924) / Nat. Methods by F de Chaumont (2012)
Dates
Type When
Created 13 years, 1 month ago (June 28, 2012, 1:26 p.m.)
Deposited 2 years, 3 months ago (May 18, 2023, 6:50 p.m.)
Indexed 44 minutes ago (Aug. 21, 2025, 5:49 a.m.)
Issued 13 years, 1 month ago (June 28, 2012)
Published 13 years, 1 month ago (June 28, 2012)
Published Online 13 years, 1 month ago (June 28, 2012)
Published Print 13 years, 1 month ago (July 1, 2012)
Funders 0

None

@article{de_Chaumont_2012, title={Icy: an open bioimage informatics platform for extended reproducible research}, volume={9}, ISSN={1548-7105}, url={http://dx.doi.org/10.1038/nmeth.2075}, DOI={10.1038/nmeth.2075}, number={7}, journal={Nature Methods}, publisher={Springer Science and Business Media LLC}, author={de Chaumont, Fabrice and Dallongeville, Stéphane and Chenouard, Nicolas and Hervé, Nicolas and Pop, Sorin and Provoost, Thomas and Meas-Yedid, Vannary and Pankajakshan, Praveen and Lecomte, Timothée and Le Montagner, Yoann and Lagache, Thibault and Dufour, Alexandre and Olivo-Marin, Jean-Christophe}, year={2012}, month=jun, pages={690–696} }