209 research outputs found
Phase control and measurement in digital microscopy
The ongoing merger of the digital and optical components of the modern microscope is creating opportunities for new measurement techniques, along with new challenges for optical modelling. This thesis investigates several such opportunities and challenges which are particularly relevant to biomedical imaging. Fourier optics is used throughout the thesis as the underlying conceptual model, with a particular emphasis on three--dimensional Fourier optics. A new challenge for optical modelling provided by digital microscopy is the relaxation of traditional symmetry constraints on optical design. An extension of optical transfer function theory to deal with arbitrary lens pupil functions is presented in this thesis. This is used to chart the 3D vectorial structure of the spatial frequency spectrum of the intensity in the focal region of a high aperture lens when illuminated by linearly polarised beam. Wavefront coding has been used successfully in paraxial imaging systems to extend the depth of field. This is achieved by controlling the pupil phase with a cubic phase mask, and thereby balancing optical behaviour with digital processing. In this thesis I present a high aperture vectorial model for focusing with a cubic phase mask, and compare it with results calculated using the paraxial approximation. The effect of a refractive index change is also explored. High aperture measurements of the point spread function are reported, along with experimental confirmation of high aperture extended depth of field imaging of a biological specimen. Differential interference contrast is a popular method for imaging phase changes in otherwise transparent biological specimens. In this thesis I report on a new isotropic algorithm for retrieving the phase from differential interference contrast images of the phase gradient, using phase shifting, two directions of shear, and non--iterative Fourier phase integration incorporating a modified spiral phase transform. This method does not assume that the specimen has a constant amplitude. A simulation is presented which demonstrates good agreement between the retrieved phase and the phase of the simulated object, with excellent immunity to imaging noise
Phase control and measurement in digital microscopy
The ongoing merger of the digital and optical components of the modern microscope is creating opportunities for new measurement techniques, along with new challenges for optical modelling. This thesis investigates several such opportunities and challenges which are particularly relevant to biomedical imaging. Fourier optics is used throughout the thesis as the underlying conceptual model, with a particular emphasis on three--dimensional Fourier optics. A new challenge for optical modelling provided by digital microscopy is the relaxation of traditional symmetry constraints on optical design. An extension of optical transfer function theory to deal with arbitrary lens pupil functions is presented in this thesis. This is used to chart the 3D vectorial structure of the spatial frequency spectrum of the intensity in the focal region of a high aperture lens when illuminated by linearly polarised beam. Wavefront coding has been used successfully in paraxial imaging systems to extend the depth of field. This is achieved by controlling the pupil phase with a cubic phase mask, and thereby balancing optical behaviour with digital processing. In this thesis I present a high aperture vectorial model for focusing with a cubic phase mask, and compare it with results calculated using the paraxial approximation. The effect of a refractive index change is also explored. High aperture measurements of the point spread function are reported, along with experimental confirmation of high aperture extended depth of field imaging of a biological specimen. Differential interference contrast is a popular method for imaging phase changes in otherwise transparent biological specimens. In this thesis I report on a new isotropic algorithm for retrieving the phase from differential interference contrast images of the phase gradient, using phase shifting, two directions of shear, and non--iterative Fourier phase integration incorporating a modified spiral phase transform. This method does not assume that the specimen has a constant amplitude. A simulation is presented which demonstrates good agreement between the retrieved phase and the phase of the simulated object, with excellent immunity to imaging noise
Superresolution fluorescence microscopy with structured illumination
The resolution of a conventional fluorescence microscope image is diffraction limited which achieves a spatial resolution of 200nm lateral and 500nm axial. Recently, many superresolution fluorescence microscopy techniques have been developed which allow the observation of many biological structures beyond the diffraction limit. Structured illumination microscopy (SIM) is one of them. The principle of SIM is based on using a harmonic light grid which down modulates the high spatial frequencies of the sample into the observable region of the microscope. The resolution enhancement is highly dependent on the reconstruction technique, which restores the high spatial frequencies of the sample to their original position. Common SIM reconstructions require the perfect knowledge of the illumination pattern. However, to perfectly control the harmonic illumination patterns on the sample plane is not easy in experimental implementations and this makes the experimental setup very technical. Reconstructing SIM images assuming the perfect knowledge of the illumination intensity patterns may, therefore, introduce artifacts on the estimated sample due to the misalignment of the grid that can occur during experimental acquisitions. To tackle this drawback of SIM, in this these, we have developed blind-SIM reconstruction strategies which are independent of the illumination patterns. Using the 3D blind-SIM reconstruction strategies we extended the harmonic SIM to speckle illumination microscopy which uses random unknown speckle patterns that need no control, unlike the harmonic grid patterns. For harmonic-SIM images, since incorporating some information about illumination patterns is valuable, we have developed a 3D positive filtered blind-SIM reconstruction which confines the iterative estimation of the illuminations in the vicinity of the Fourier peaks (using carefully designed Fourier filter masks) in the Fourier space. Using blind-SIM reconstruction techniques a lateral resolution of about 100nm and axial resolution of about 200nm is obtained in both speckle and harmonic SIM. In addition, to reduce the out-of-focus problem in widefield images, a simple computational technique which is based on reconstructing 2D data with 3D PSF is developed based on blind-SIM reconstruction. Moreover, to combine the functionalities of SIM and light sheet microscopy, as a proof of concept, we have developed a simple microscope setup which produces a structured light sheet illumination pattern.La microscopie de fluorescence optique est lâun des outils les plus puissants pour Ă©tudier les structures cellulaires et molĂ©culaires au niveau subcellulaire. La rĂ©solution dâune image de microscope conventionnel Ă fluorescence est limitĂ©e par la diffraction, ce qui permet dâobtenir une
rĂ©solution spatiale latĂ©rale de 200nm et axiale de 500nm. RĂ©cemment, de nombreuses techniques de microscopie de fluorescence de super-rĂ©solution ont Ă©tĂ© dĂ©veloppĂ©es pour permettre dâobserver de
nombreuses structures biologiques au-delĂ de la limite de diffraction. La microscopie dâillumination structurĂ©e (SIM) est lâune de ces technologies. Le principe de la SIM est basĂ© sur lâutilisation dâune grille de lumiĂšre harmonique qui permet de translater les hautes frĂ©quences spatiales de lâĂ©chantillon vers la rĂ©gion dâobservation du microscope. LâamĂ©lioration de la rĂ©solution de cette technologie de microscopie dĂ©pend fortement de la technique de reconstruction, qui rĂ©tablit les hautes frĂ©quences
spatiales de lâĂ©chantillon dans leur position dâorigine. Les mĂ©thodes classiques de reconstruction SIM nĂ©cessitent une connaissance parfaite de lâillumination de lâĂ©chantillon. Cependant, lâimplĂ©mentation dâun contrĂŽle parfait de lâillumination harmonique sur le plan de lâĂ©chantillon
nâest pas facile expĂ©rimentalement et il prĂ©sente un grand dĂ©fi. LâhypothĂšse de la connaissance parfaite de lâintensitĂ© de la lumiĂšre illuminant lâĂ©chantillon en SIM peut donc introduire des artefacts
sur lâimage reconstruite de lâĂ©chantillon, Ă cause des erreurs dâalignement de la grille qui peuvent se prĂ©senter lors de lâacquisition expĂ©rimentale. Afin de surmonter ce dĂ©fi, nous avons dĂ©veloppĂ© dans cette thĂšse des stratĂ©gies de reconstruction «aveugle» qui sont indĂ©pendantes de
dâillumination. Ă lâaide de ces stratĂ©gies de reconstruction dites «blind-SIM», nous avons Ă©tendu la SIM harmonique pour lâappliquer aux cas de «SIM-speckle» qui utilisent des illuminations alĂ©atoires et inconnues qui contrairement Ă lâillumination harmonique, ne nĂ©cessitent pas de controle.
Comme il est utile de rĂ©cupĂ©rer des informations sur lâillumination en SIM harmonique, nous avons dĂ©veloppĂ© une reconstruction blind-SIM tridimensionnel et filtrĂ©e qui confine lâestimation itĂ©rative des illuminations au voisinage des pics dans lâespace de Fourier, en utilisant des masques de filtre de Fourier soigneusement conçus. En utilisant des techniques de reconstruction blind-SIM, une rĂ©solution latĂ©rale dâenviron 100 nm et une rĂ©solution axiale dâenviron 200 nm sont obtenues, Ă la fois en SIM harmonique et en SIM speckle. En outre, pour rĂ©duire le problĂšme de focalisation dans les images de champ large, une technique de calcul simple qui repose sur la reconstruction bidimensionnel de donnĂ©es Ă partir de PSF tridimensionnel est dĂ©veloppĂ©e. En outre, afin de combiner
à la fois les fonctionnalités de la SIM et de la microscopie å nappe de lumiÚre, en tant que preuve de concept, nous avons développé une configuration de microscope simple qui produit une nappe de lumiÚre structuré
Light sheet adaptive optics microscope for 3D live imaging
Optical microscopy is still the main research tool for many biological studies. Indeed with the advent of genetic manipulation and specifically, the use of fluorescent protein expressing in animals and plants it has actually seen a renaissance in the past ten years, in particular with the development of novel techniques such as CARS, PALM, STORM, STED and SPIM. In all of microscopy methods one has to look through the sample at some point. The sample thus adds an additional and uncontrolled optical path, which leads to aberrations in the final image. Adaptive optics (AO) is a way of removing these unwanted aberrations which can cause image degradation and even potentially artifacts within the image. This thesis is concerned with the implementation of AO in non scanning microscopes and presents some novel methods both in wavefront sensored and sensorless configurations. A first implementation of AO on the emission path of a light sheet microscope is also presented
Confocal microscopy of colloidal particles: towards reliable, optimum coordinates
Over the last decade, the light microscope has become increasingly useful as
a quantitative tool for studying colloidal systems. The ability to obtain
particle coordinates in bulk samples from micrographs is particularly
appealing. In this paper we review and extend methods for optimal image
formation of colloidal samples, which is vital for particle coordinates of the
highest accuracy, and for extracting the most reliable coordinates from these
images. We discuss in depth the accuracy of the coordinates, which is sensitive
to the details of the colloidal system and the imaging system. Moreover, this
accuracy can vary between particles, particularly in dense systems. We
introduce a previously unreported error estimate and use it to develop an
iterative method for finding particle coordinates. This individual-particle
accuracy assessment also allows comparison between particle locations obtained
from different experiments. Though aimed primarily at confocal microscopy
studies of colloidal systems, the methods outlined here should transfer readily
to many other feature extraction problems, especially where features may
overlap one another.Comment: Accepted by Advances in Colloid and Interface Scienc
Superresolution fluorescence microscopy with structured illumination
Cotutela Universitat PolitĂšcnica de Catalunya i Aix-Marseille UniversitĂ©The resolution of a conventional fluorescence microscope image is diffraction limited which achieves a spatial resolution of 200nm lateral and 500nm axial. Recently, many superresolution fluorescence microscopy techniques have been developed which allow the observation of many biological structures beyond the diffraction limit. Structured illumination microscopy (SIM) is one of them. The principle of SIM is based on using a harmonic light grid which down modulates the high spatial frequencies of the sample into the observable region of the microscope. The resolution enhancement is highly dependent on the reconstruction technique, which restores the high spatial frequencies of the sample to their original position. Common SIM reconstructions require the perfect knowledge of the illumination pattern. However, to perfectly control the harmonic illumination patterns on the sample plane is not easy in experimental implementations and this makes the experimental setup very technical. Reconstructing SIM images assuming the perfect knowledge of the illumination intensity patterns may, therefore, introduce artifacts on the estimated sample due to the misalignment of the grid that can occur during experimental acquisitions. To tackle this drawback of SIM, in this these, we have developed blind-SIM reconstruction strategies which are independent of the illumination patterns. Using the 3D blind-SIM reconstruction strategies we extended the harmonic SIM to speckle illumination microscopy which uses random unknown speckle patterns that need no control, unlike the harmonic grid patterns. For harmonic-SIM images, since incorporating some information about illumination patterns is valuable, we have developed a 3D positive filtered blind-SIM reconstruction which confines the iterative estimation of the illuminations in the vicinity of the Fourier peaks (using carefully designed Fourier filter masks) in the Fourier space. Using blind-SIM reconstruction techniques a lateral resolution of about 100nm and axial resolution of about 200nm is obtained in both speckle and harmonic SIM. In addition, to reduce the out-of-focus problem in widefield images, a simple computational technique which is based on reconstructing 2D data with 3D PSF is developed based on blind-SIM reconstruction. Moreover, to combine the functionalities of SIM and light sheet microscopy, as a proof of concept, we have developed a simple microscope setup which produces a structured light sheet illumination pattern.La microscopie de fluorescence optique est lâun des outils les plus puissants pour Ă©tudier les structures cellulaires et molĂ©culaires au niveau subcellulaire. La rĂ©solution dâune image de microscope conventionnel Ă fluorescence est limitĂ©e par la diffraction, ce qui permet dâobtenir une
rĂ©solution spatiale latĂ©rale de 200nm et axiale de 500nm. RĂ©cemment, de nombreuses techniques de microscopie de fluorescence de super-rĂ©solution ont Ă©tĂ© dĂ©veloppĂ©es pour permettre dâobserver de
nombreuses structures biologiques au-delĂ de la limite de diffraction. La microscopie dâillumination structurĂ©e (SIM) est lâune de ces technologies. Le principe de la SIM est basĂ© sur lâutilisation dâune grille de lumiĂšre harmonique qui permet de translater les hautes frĂ©quences spatiales de lâĂ©chantillon vers la rĂ©gion dâobservation du microscope. LâamĂ©lioration de la rĂ©solution de cette technologie de microscopie dĂ©pend fortement de la technique de reconstruction, qui rĂ©tablit les hautes frĂ©quences
spatiales de lâĂ©chantillon dans leur position dâorigine. Les mĂ©thodes classiques de reconstruction SIM nĂ©cessitent une connaissance parfaite de lâillumination de lâĂ©chantillon. Cependant, lâimplĂ©mentation dâun contrĂŽle parfait de lâillumination harmonique sur le plan de lâĂ©chantillon
nâest pas facile expĂ©rimentalement et il prĂ©sente un grand dĂ©fi. LâhypothĂšse de la connaissance parfaite de lâintensitĂ© de la lumiĂšre illuminant lâĂ©chantillon en SIM peut donc introduire des artefacts
sur lâimage reconstruite de lâĂ©chantillon, Ă cause des erreurs dâalignement de la grille qui peuvent se prĂ©senter lors de lâacquisition expĂ©rimentale. Afin de surmonter ce dĂ©fi, nous avons dĂ©veloppĂ© dans cette thĂšse des stratĂ©gies de reconstruction «aveugle» qui sont indĂ©pendantes de
dâillumination. Ă lâaide de ces stratĂ©gies de reconstruction dites «blind-SIM», nous avons Ă©tendu la SIM harmonique pour lâappliquer aux cas de «SIM-speckle» qui utilisent des illuminations alĂ©atoires et inconnues qui contrairement Ă lâillumination harmonique, ne nĂ©cessitent pas de controle.
Comme il est utile de rĂ©cupĂ©rer des informations sur lâillumination en SIM harmonique, nous avons dĂ©veloppĂ© une reconstruction blind-SIM tridimensionnel et filtrĂ©e qui confine lâestimation itĂ©rative des illuminations au voisinage des pics dans lâespace de Fourier, en utilisant des masques de filtre de Fourier soigneusement conçus. En utilisant des techniques de reconstruction blind-SIM, une rĂ©solution latĂ©rale dâenviron 100 nm et une rĂ©solution axiale dâenviron 200 nm sont obtenues, Ă la fois en SIM harmonique et en SIM speckle. En outre, pour rĂ©duire le problĂšme de focalisation dans les images de champ large, une technique de calcul simple qui repose sur la reconstruction bidimensionnel de donnĂ©es Ă partir de PSF tridimensionnel est dĂ©veloppĂ©e. En outre, afin de combiner
à la fois les fonctionnalités de la SIM et de la microscopie å nappe de lumiÚre, en tant que preuve de concept, nous avons développé une configuration de microscope simple qui produit une nappe de lumiÚre structuréePostprint (published version
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