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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).

Fast 2D-SAFIR

A fast version of ND-SAFIR in 2 dimensions was also developed in 2008 and 2009 in C++.

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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