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Space TimE RePresentation, Imaging

and cellular dynamics of molecular

COmplexes




ND-SAFIR software

Overview

ND-SAFIR is a software for denoising n-dimentionnal images especially dedicated to microscopy image sequence analysis. It is able to deal with 2D, 3D, 2D+time, 3D+time images have one or more color channel. It is adapted to Gaussian and Poisson-Gaussian noise which are usually encountered in photonic imaging. Several papers describe the detail of the method used in ndsafir to recover noise free images (see references).

Involved people and institutions

ND-SAFIR is the result of a collaboration between Inria, Rennes, INRA, Jouy-en-Josas and Institut Curie, Paris. It has been mostly developped during the PhD thesis of J. Boulanger with INRA, MIA 78352 Jouy-and-Josas, France and Inria Rennes Bretagne Atlantique, VISTA 35042 Rennes, France under the supervision of P. Bouthemy and C. Kervrann. It has been rewriten during his stay as a post-doctoral fellow with J. Salamero and J.-B. Sibarita at the UMR-144 Institut Curie/CNRS, Cell and Tissue Image Facility PICT-IBISA 75000 Paris. Finally, several contributions have been added by the team of J. Sedat at UCSF.

Commercial software distribution

Roper Scientific France has integrated ND-Safir (within Meatamorph interface) into a easy to use GUI named Safir: http://www.roperscientific.fr/new/brochures/denoising_brochure.pdf

Contacts: jeremy.thiblet@roperscientific.fr or info@roperscientific.fr

Free academic software distribution

ND-Safir demonstration

You can try ND-Safir on our mobyle web portal: Try ND-Safir

see also demonstration on still images

Free download binaries

Binaries of the software ndsafir is freely and electronically ditributed. Developped in standard C/C++ under Linux using the CImg library, it has been tested over several plateform such as Linux/Unix, Windows XP and Mac OS.

Free distribution of sources

To get for free the ND-SAFIR sources please complete and return 2 signed copies of the english form (license_agreement_ENG.pdf) and 2 copies of the french form (license_agreement_FRA.pdf) by regular mail to the following address:

Charles KERVRANN
Inria Rennes - Bretagne Atlantique
Campus Universitaire de Beaulieu
35042 Rennes Cedex - France


References

  • J. Boulanger. Non-parametric estimation and contributions to image sequence analysis: Modeling, simulation and estimation of the intracellular traffic in video-microscopy image sequences. Université de Rennes 1, Mention Traitement du Signal et des Télécommunications, Jan 2007. (pdf)
  • J. Boulanger, C. Kervrann, P. Bouthemy, P. Elbau, J.-B. Sibarita, J. Salamero Patch-based non-local functional for denoising fluorescence microscopy image sequences. IEEE Trans. on Medical Imaging, 29(2): 442-454, 2010 (pdf)
  • J. Boulanger, J.-B. Sibarita, C. Kervrann, P. Bouthemy. Non-parametric regression for patch-based fluorescence microscopy image sequence denoising. In Proc. IEEE Int. Symp. on Biomedical Imaging: from nano to macro (ISBI'08), Paris, May 2008 (pdf)
  • C. Kervrann, J. Boulanger. Local adaptivity to variable smoothness for exemplar-based image regularization and representation. Int. J. Computer Vision, 79(1): 45-69, 2008. (pdf) (see demonstration on still images)
  • J. Boulanger, C. Kervrann, P. Bouthemy. Space-time adaptation for patch based image sequence restoration. IEEE Trans. on Pattern Analysis and Machine Intelligence 28(6): 1096-1102, 2007. (pdf)
  • C. Kervrann, J. Boulanger. Optimal spatial adaptation for patch-based image denoising. IEEE Trans. on Image Processing, 15(10): 2866-2878, 2006. (pdf)

See also:

  1. P.M. Carlton, J. Boulanger, Ch. Kervrann, J.-B. Sibarita, J. Salamero, S. Gordon-Messer, J.E. Haber, S. Haase, L. Shao, L. Winoto, A. Matsuda,, P. Kner, S. Usawa, Y. Strukov, M. Gustafsson, Z. Kam, D. Agard, J. Sedat. Fast live simultaneous multi-wavelength 4-dimensional optical microscopy . Proc Natl Acad Sci USA, 107(37): 16016-16022, 2010
  2. J.R. Swedlow. Advanced hardware and software tols for fast multidimensional imaging of living cells. Proc Natl Acad Sci USA, 107(37): 16005-16006, 2010
  3. M. Baker. Seeing more with less. Nature Methods (Research highlights), 7(10): 782, 2010
  4. A. Matsuda, L.Shao, J. Boulanger, Ch. Kervrann, P.M. Carlton, P. Kner, E. Brandlund, D. Agard, J.W. Sedat. <b>Condensed mitotic chromosome structure at nanometer resolution using PALM and EGFP-histones. PloS One, (9): e12768, 2010 (see “http://hal.inria.fr/inria-00541020/en/”, HAL-INRIA-00541020)

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