DeMiTri :
Références & Conférences intéressantes

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Cette page est là pour recenser les conférences et plus généralement les références qui traitent de sujets pouvant intéresser notre projet (comme la microscopie confocale, la déconvolution, etc.).

Conférence : ISBI 2004

Conférence : Microscopy Conference 2003

Conférence : Focus on Microscopy 2003

Conférence : GENSIP 2002

Conférence : ISBI 2002

Conférence : BIOSIGNAL 2002

Les journaux

Journal of Microscopy http://www.blackwellpublishing.com/journals/jmi/

Les universités

Royal Microscopy Society http://www.rms.org.uk/
Links http://ourworld.compuserve.com/homepages/pvosta/pcrimg.htm
Cours sur le confocal http://www.novaknowledge.nl/biomedisch_clm.htm

Les constructeurs

Voici les liens sur les sites Web des principaux constructeurs de microscopes confocaux. Pour avoir plus de détails concernant les caractéristiques des microscopes, le logo (à gauche) est un lien sur le site du constructeur. Voici donc ces constructeurs par ordre alphabétique :

	Chez Biorad, le Radiance2100 est le seul confocal proposé.
	Leica possède un catalogue bien fourni en ce qui concerne les microscopes confocaux et ils proposent des marqueurs fluorescents dans le orange.
	Nikon propose actuellement le C1 dans son catalogue.
	Olympus proposent 2 confocaux dans leur catalogue : le FLUOVIEW 300 et le FLUOVIEW 500.
	Zeiss fabrique 2 microscopes confocaux : le LSM 5 PASCAL et le LSM 510.

Les softs de déconvolution

Chaque constructeur propose plus ou moins son soft de déconvolution d'images optiques fluorescentes, ou d'images confocales. Nous allons donc en retrouver quelques uns. Mais il y a aussi plusieurs entreprises ou universités qui développent ce genre de produit. En effet, lorsque l'on utilise un microscope confocal avec un large champ (wide-field), il est quasiment toujours nécessaire de déconvoluer l'image obtenue. Nous allons donc présenter quelques logiciels de déconvolution (liste non exhaustive) :

	AmiraDeconv blind and non-blind deconvolution robust maximum likelihood algorithms fast convergence through overrelaxation support for wide-field and confocal microscopes computational PSF estimation PSF extraction from bead measurements correction of intensity attenuation (z-drop) background correction and flat-field correction support for multi-processor systems job queue for batch processing
	AutoDeblur AutoDeblur is a novel deconvolution software application for producing extremely high resolution results through image restoration by removing out-of-focus haze, blur, noise and other problems from both 3D and 2D micrographs. It uses a variety of important and useful deconvolution algorithms, including AutoQuant's proprietary Blind Deconvolution. The Blind Deconvolution algorithm is both iterative and constrained, yet unlike other deconvolution products, it does not require the manual calibration and measurement of the point spread function (PSF). Instead, it constructs the PSF directly from the collected data set. From http://www.aqi.com/
	Bitplane ( http://www.bitplane.com/index_flash.shtml/) distributes Huygens, from SVI. -- N. Dey Huygens makes intelligent use of a microscope's inherent imaging characteristics, which produces higher image resolution and lower noise levels than other deconvolution systems. Depending on the type of image you have and the quality you need, the Huygens system offers three deconvolution options: Maximum Likelihood Estimation (MLE) Iterative Constrained Tikhonov-Miller restoration Non-iterative Tikhonov-Miller algorithm. They distribute also the Autodeblur software (from MediaCybernetics) that permit to deconvolve 2D images. -- N. Dey
	DSP Software: these softwares are toolboxes for Matlab(R). They are available for download at Rice University on http://www-dsp.rice.edu/software/ . There are: Wavelets: Matlab toolbox for filter-bank and wavelet design/analysis Wavelet-based Inverse Halftoning via Deconvolution (WInHD): Matlab code for inverse halftoning using wavelets Fourier-Wavelet Regularized Deconvolution (ForWaRD): Matlab code for image deblurring/deconvolution using wavelets Wavelet-domain Hidden Markov Models: Matlab code for image denoising using wavelet domain hidden Markov models (fast C version now available) etc.
	SharpStack: The Deconvolution Module for Image-Pro Plus & Image-Pro Discovery http://www.mediacy.com/sharpstack.htm The No Neighbor method uses the information from each single slice to construct a 2D PSF. This is the fastest but may not be as representative of the sample as the other methods. Inverse filter, nearest neighbor, and no neighbor algorithm functions are all included in SharpStack. See also: AutoDeblur Gold, wide field only, confocal only or wide field and confocal.
	RealityNET System Solutions propose to power up one's microscope by improving the quality of the images. By sending them raw images and some parameters about the microscope, they will deconvolve them and send it back. For the moment (2004.06), the provided service is FREE, because it is still a testing version of the tools. (Thanks to A. Diaspro for providing us this link!) (For more informations, see http://www.powermicroscope.com )
	MetaMorph The MetaMorph Imaging System can improve experiment performance and image appearance by mathematically removing the out-of-focus effects common to optical light microscopes. In most microscopes, the lens aperture causes light from a point source to spread out or diffract, and light from out-of-focus planes can result in image contamination. This is caused by the optical system's Point Spread Function (PSF) and is most often seen with thick sample preparations. Two deconvolution commands in MetaMorph can be employed to offset these undesirable out-of-focus effects. The first command, called Nearest Neighbors, uses an estimation of the three-dimensional PSF to compute the contributions from adjacent out-of-focus planes, and then removes this data from the original information to create a sharper resulting image. (For more informations, see http://www.image1.com/products/metamorph/deconvolution-3d.cfm )
	XCOSM is an X-Windows interface to Computational Optical Sectioning Microscopy (COSM) algorithms [1-7] for removing out-of-focus light in 3-D volumes collected plane by plane using either widefield or confocal fluorescence microscopy. The interface allows users to view and process multiple 3-D datasets within a simple mouse-driven environment. The software was written for a unix based system. It is possible to compile XCOSM on a PC with linux. Information on COSM can be found in the Tutorial - Image Restoration for 3-D Microscopy and in lectures given by J.-A. Conchello. XCOSM can be dowloaded for free. From http://rayleigh.wustl.edu/~xcosm/
	VayTek Image VayTek Image is an image processing and data acquisition software. It allows scientists to capture images in real time from their microscope and process the images to bring out the relevant features. This free download of VayTek Image provides software that can only use existing images to perform its functions. VayTek Image is designed to capture images from various digital cameras.

Référence : Molecular Expression

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