Marc Allain

Marc Allain
Institut Fresnel · Comix

PhD

About

89
Publications
11,337
Reads
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2,071
Citations
Citations since 2016
48 Research Items
1347 Citations
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2016201720182019202020212022050100150200250
2016201720182019202020212022050100150200250
2016201720182019202020212022050100150200250
Additional affiliations
September 2005 - March 2016
Aix-Marseille Université
Position
  • Professor (Assistant)
February 2005 - September 2005
January 2003 - February 2005
Centre National d’Etudes Spatiales
Position
  • PostDoc Position
Education
September 1999 - December 2002
Université Paris-Sud 11
Field of study
  • Signal processing
May 1998 - September 1999
Polytechnique Montréal
Field of study
  • Biomedical engineering
September 1993 - June 1996
École Supérieure d'Electricité
Field of study
  • Electrical engineering - Signal processing

Publications

Publications (89)
Article
Full-text available
Ptychography is described in the context of polarized light probing anisotropic specimen, i.e., showing properties of birefringence and/or diattenuation. We establish an optimization strategy using a vectorial formalism. A measurement scheme using a set of linearly polarized probes and linear polarization analyzers is proposed, allowing to retrieve...
Preprint
Full-text available
X-ray Bragg coherent diffraction imaging has been demonstrated as a powerful three-dimensional (3D) microscopy approach for the investigation of sub-micrometer-scale crystalline particles. The approach is based on the measurement of a series of coherent Bragg diffraction intensity patterns that are numerically inverted to retrieve an image of the s...
Preprint
The phase retrieval problem, where one aims to recover a complex-valued image from far-field intensity measurements, is a classic problem encountered in a range of imaging applications. Modern phase retrieval approaches usually rely on gradient descent methods in a nonlinear minimization framework. Calculating closed-form gradients for use in these...
Article
Full-text available
Current super-resolution microscopy (SRM) methods suffer from an intrinsic complexity that might curtail their routine use in cell biology. We describe here random illumination microscopy (RIM) for live-cell imaging at super-resolutions matching that of 3D structured illumination microscopy, in a robust fashion. Based on speckled illumination and s...
Preprint
Full-text available
We present a general analytic approach to spatially resolve the nano-scale lattice distortion field of strained and defected compact crystals with Bragg coherent x-ray diffraction imaging (BCDI). Our approach relies on fitting a differentiable forward model simultaneously to multiple BCDI datasets corresponding to independent Bragg reflections from...
Article
Full-text available
New 4th-generation synchrotron sources, with their increased brilliance, promise to greatly improve the performances of coherent X-ray microscopy. This perspective is of major interest for crystal microscopy, which aims at revealing the 3D crystalline structure of matter at the nanoscale, an approach strongly limited by the available coherent flux....
Article
Full-text available
Small ion-irradiation-induced defects can dramatically alter material properties and speed up degradation. Unfortunately, most of the defects irradiation creates are below the visibility limit of state-of-the-art microscopy. As such, our understanding of their impact is largely based on simulations with major unknowns. Here we present an x-ray crys...
Article
We have developed and demonstrated an image super-resolution method-XR-UNLOC: X-Ray UNsupervised particle LOCalization-for hard x-rays measured with fast-frame-rate detectors that is an adaptation of the principle of photo-activated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), which enabled biological flu...
Article
The phase retrieval problem, where one aims to recover a complex-valued image from far-field intensity measurements, is a classic problem encountered in a range of imaging applications. Modern phase retrieval approaches usually rely on gradient descent methods in a nonlinear minimization framework. Calculating closed-form gradients for use in these...
Article
Full-text available
This paper addresses the three-dimensional signal distortion and image reconstruction issues in X-ray Bragg coherent diffraction imaging (BCDI) in the event of a general non-orthogonal orientation of the area detector with respect to the diffracted beam. Growing interest in novel BCDI adaptations at fourth-generation synchrotron light sources has n...
Preprint
Full-text available
In this communication, we discuss how 3D information about the structure of a crystalline sample is encoded in Bragg 3DXCDI measurements. Our analysis brings to light the role of the experimental parameters in the quality of the final reconstruction. One of our salient conclusions is that these parameters can be set prior to the ptychographic 3DXCD...
Article
X-ray Bragg coherent diffraction imaging (BCDI) has been demonstrated as a powerful 3D microscopy approach for the investigation of sub-micrometre-scale crystalline particles. The approach is based on the measurement of a series of coherent Bragg diffraction intensity patterns that are numerically inverted to retrieve an image of the spatial distri...
Article
Full-text available
This two-part article series provides a generalized description of the scattering geometry of Bragg coherent diffraction imaging (BCDI) experiments, the shear distortion effects inherent in the 3D image obtained from presently used methods and strategies to mitigate this distortion. Part I starts from fundamental considerations to present the gener...
Preprint
Full-text available
Super-resolution fluorescence microscopy has been instrumental to progress in biology. Yet, the photo-induced toxicity, the loss of resolution into scattering samples or the complexity of the experimental setups curtail its general use for functional cell imaging. Here, we describe a new technology for tissue imaging reaching a 114nm/8Hz resolution...
Preprint
Full-text available
In this two-part article series we provide a generalized description of the scattering geometry of Bragg coherent diffraction imaging (BCDI) experiments, the shear distortion effects inherent to the resulting three-dimensional (3D) image in currently used phase retrieval methods and strategies to mitigate this distortion. In this Part I, we derive...
Preprint
X-ray Bragg coherent diffraction imaging has been demonstrated as a powerful three-dimensional (3D) microscopy approach for the investigation of sub-micrometer-scale crystalline particles. It is based on the measurement of a series of coherent diffraction intensity patterns that are numerically inverted to retrieve an image of the spatial distribut...
Preprint
In this two-part article series we provide a generalized description of the scattering geometry of Bragg coherent diffraction imaging (BCDI) experiments, the shear distortion effects inherent to the resulting three-dimensional (3D) image from current phase retrieval methods and strategies to mitigate this distortion. In this Part I, we derive in ge...
Article
Full-text available
Coherent diffraction imaging methods enable imaging beyond lens-imposed resolution limits. In these methods, the object can be recovered by minimizing an error metric that quantifies the difference between diffraction patterns as observed, and those calculated from a present guess of the object. Efficient minimization methods require analytical cal...
Article
Full-text available
Coherent x-ray beams with energies ≥50keV can potentially enable three-dimensional imaging of atomic lattice distortion fields within individual crystallites in bulk polycrystalline materials through Bragg coherent diffraction imaging (BCDI). However, the undersampling of the diffraction signal due to Fourier-space compression at high x-ray energie...
Article
Full-text available
Bragg coherent diffraction imaging (BCDI) is a powerful technique to explore the local strain state and morphology of microscale crystals. The method can potentially reach nanometer-scale spatial resolution thanks to the advances in synchrotron design that dramatically increase coherent flux. However, there are experimental bottlenecks that may lim...
Article
Full-text available
Vectorial ptychography has been recently introduced to reconstruct the Jones matrix of an anisotropic object by means of series of ptychographic measurements performed using a set of polarized illumination probes in conjugation with various analyzers. So far, the probes were assumed to be completely known (amplitude, wavefront, state of polarizatio...
Preprint
Full-text available
Coherent diffraction imaging methods enable imaging beyond lens-imposed resolution limits. In these methods, the object can be recovered by minimizing an error metric that quantifies the difference between diffraction patterns as observed, and those calculated from a present guess of the object. Efficient minimization methods require analytical cal...
Preprint
Full-text available
Coherent X-ray beams with energies $\geq 50$ keV can potentially enable three-dimensional imaging of atomic lattice distortion fields within individual crystallites in bulk polycrystalline materials through Bragg coherent diffraction imaging (BCDI). However, the undersampling of the diffraction signal due to Fourier space compression at high X-ray...
Article
Full-text available
We present a numerical study of a microscopy setup in which the sample is illuminated with uncontrolled speckle patterns and the two-photon excitation fluorescence is collected on a camera. We show that, using a simple deconvolution algorithm for processing the speckle low-resolution images, this wide-field imaging technique exhibits resolution sig...
Article
Full-text available
Following the recent establishment of the formalism of vectorial ptychography [Opt. Lett.40, 5144 (2015)OPLEDP0146-959210.1364/OL.40.005144], first measurements, to the best of our knowledge, are reported in the optical range, demonstrating the capability of the proposed method to map the four parameters of the Jones matrix of an anisotropic specim...
Preprint
Full-text available
Following the recent establishment of the formalism of vectorial ptychography [Ferrand et al., Opt. Lett. 40, 5144 (2015)], first measurements are reported in the optical range, demonstrating the capability of the proposed method to map the four parameters of the Jone matrix of an anisotropic specimen, and therefore to quantify a wide range of opti...
Article
Full-text available
Speckle based imaging consists of forming a super- resolved reconstruction of an unknown sample from low- resolution images obtained under random inhomogeneous illu- minations (speckles). In a blind context where the illuminations are unknown, we study the intrinsic capacity of speckle-based imagers to recover spatial frequencies outside the freque...
Article
Full-text available
Biomineralization integrates complex processes leading to an extraordinary diversity of calcareous biomineral crystalline architectures, in intriguing contrast with the consistent presence of a sub-micrometric granular structure. Hence, gaining access to the crystalline architecture at the mesoscale, that is, over a few granules, is key to building...
Article
The blind structured illumination microscopy (SIM) strategy proposed in [1] is fully re-founded in this paper, unveiling the central role of the sparsity of the illumination patterns in the mechanism that drives super-resolution in the method. A numerical analysis shows that the resolving power of the method can be further enhanced with optimized o...
Conference Paper
The Blind-SIM strategy proposed in Mudry, Emeric, et al. "Structured illumination microscopy using unknown speckle patterns." Nature Photonics (2012) is drastically revisited and a Preconditioned Primal-Dual splitting (PPDS) strategy is introduced to provide a very fast reconstruction algorithm.
Article
Full-text available
We present and demonstrate a formalism by which three-dimensional (3D) Bragg x-ray coherent diffraction imaging (BCDI) can be implemented without moving the sample by scanning the energy of the incident x-ray beam. This capability is made possible by introducing a 3D Fourier transform that accounts for x-ray wavelength variability. We demonstrate t...
Article
Full-text available
We present an efficient method of imaging 3D nanoscale lattice behavior and strain fields in crystalline materials with a new methodology -- three dimensional Bragg projection ptychography (3DBPP). In this method, the 2D sample structure information encoded in a coherent high-angle Bragg peak measured at a fixed angle is combined with the real-spac...
Article
Full-text available
Tomographic diffraction microscopy is a three-dimensional quantitative optical imaging technique in which the sample is numerically reconstructed from tens of holograms recorded under different angles of incidence. We show that combining the measurement of the amplitude, the phase, and the polarization of the field scattered by the sample with an a...
Article
Full-text available
We consider a fluorescence microscope in which several three-dimensional images of a sample are recorded for different speckle illuminations. We show, on synthetic data, that by summing the positive deconvolution of each speckle image, one obtains a sample reconstruction with axial and transverse resolutions that compare favorably to that of an ide...
Conference Paper
In deep photoacoustic imaging, resolution is inherently limited by acoustic diffraction, and ultrasonic frequencies cannot be arbitrarily increased because of attenuation in tissue. Here we report on the use of multiple speckle illumination to perform super resolution photoacoustic imaging. We show that the analysis of speckle-induced second-order...
Research
Full-text available
In this communication, a fast reconstruction algorithm is proposed for fluorescence blind structured illumination microscopy (SIM) under the sample positivity constraint. This new algorithm is by far simpler and faster than existing solu- tions, paving the way to 3D and real-time 2D reconstruction.
Article
Full-text available
In this communication, a fast reconstruction algorithm is proposed for fluorescence \textit{blind} structured illumination microscopy (SIM) under the sample positivity constraint. This new algorithm is by far simpler and faster than existing solutions, paving the way to 3D and/or real-time 2D reconstruction.
Conference Paper
This presentation will illustrate how optical speckle patterns, a manifestation of coherent light discarded by the transport theory for energy, may be exploited to enhance photoacoustic imaging, in particular in terms of visibility and super-resolution. Article not available.
Conference Paper
A marginal likelihood estimator is proposed to super-resolution image reconstruction problem in blind structured illumination microscopy. To reduce the computational complexity, we propose an approximation of the likelihood function based on patch models.
Conference Paper
Full-text available
Speckle based imagers provide super-resolved reconstructions techniques from a series of low-resolution acquisitions obtained under speckle illuminations. We demonstrate that, under physically realistic conditions, the correlation of the dataset have a super-resolution power corresponding to the squaring of the imager point spread function.
Article
Full-text available
Speckle based imaging consists in forming a super-resolved reconstruction of an unknown object from low-resolution images obtained under random inhomogeneous illuminations (speckles). However, the origin of this super-resolution is unclear. In this work, we demonstrate that, under physically realistic conditions, the correlation of the data have a...
Article
We report the three-dimensional (3D) mapping of strain and tilts of crystal planes in an extended InP nanostructured layer bonded onto silicon, measured without sample preparation. Our approach takes advantage of 3D x-ray Bragg ptychography combined with an optimized inversion process. The excellent agreement with the sample nominal structure valid...
Article
Full-text available
In deep tissue photoacoustic imaging, the spatial resolution is inherently limited by acoustic diffraction. Moreover, as the ultrasound attenuation increases with frequency, resolution is often traded-off for penetration depth. Here we report on super-resolution photoacoustic imaging by use of multiple speckle illumination. Specifically, we show th...
Article
Full-text available
X-ray Bragg diffraction experiments that utilize tightly focused coherent beams produce complicated Bragg diffraction patterns that depend on scattering geometry, characteristics of the sample, and properties of the x-ray focusing optic. Here, we use a Fourier-transform-based method of modeling the 2D intensity distribution of a Bragg peak and appl...
Article
Full-text available
Progresses in the design of well-defined electronic band structure and dedicated functionalities rely on the high control of complex architectural device nano-scaled structures. This includes the challenging accurate description of strain fields in crystalline structures, which requires non invasive and three-dimensional (3D) imaging methods. Here,...
Article
Full-text available
X-ray coherent diffraction imaging including ptychography provides the nanoscale resolved three-dimensional description of matter. The combination of these approaches to the Bragg geometry case arouses a strong interest for its capability to provide information about strain state in crystals. Among the existing approaches, ptychography is particula...
Article
Full-text available
Coherent diffraction imaging (CDI) is a lens-less microscopy method that extracts the complex-valued exit field from intensity measurements alone. It is of particular importance for microscopy imaging with diffraction set-ups where high quality lenses are not available. The inversion scheme allowing the phase retrieval is based on the use of an ite...
Article
Using spatially non-uniform illumination significantly improves the resolution of light microscopy(1). Indeed, frequency mixing between the object and the illumination permits the recovery of object frequencies beyond the diffraction-limited detection band pass(2-5). However, the image reconstruction process requires a precise knowledge of the illu...
Article
Full-text available
Hard X-ray lens-less microscopy raises hopes for a non-invasive quantitative imaging, capable of achieving the extreme resolving power demands of nanoscience. However, a limit imposed by the partial coherence of third generation synchrotron sources restricts the sample size to the micrometer range. Recently, X-ray ptychography has been demonstrated...
Article
Full-text available
X-ray ptychography is a lensless microscopy method able to provide extended field of view with spatial resolution above the diffraction limit. A series of intensity coherent diffraction patterns measured in the far field is used to obtain the numerical deconvolution between the sample scattering contrast and the illumination function. The measureme...
Article
Full-text available
Hard X-ray lens-less microscopy holds the promise of a resolution power meeting the need of nanoscience, owing to the possibility of circumventing the limits of state-of-the-art X-ray lenses [1]. Beyond the resolution issue, the complex-valued wavefield is imaged, hence ensuring truly quantitative information on the sample scattering contrast. Furt...
Article
Full-text available
Using a Cramer-Rao analysis, we study the theoretical performances of a time and spatially resolved fDOT imaging system for jointly estimating the position and the concentration of a point-wide fluorescent volume in a diffusive sample. We show that the fluorescence lifetime is a critical parameter for the precision of the technique. A time resolved...
Conference Paper
Full-text available
A tomographic procedure is developed for an existing small animal reflectance optical imaging system. Using a simple optimization method and a calibrated set-up, we show that source localization with sub-millimiter precision is achievable.
Conference Paper
Full-text available
In this communication, the intrinsic precision in the localization of a fluorescent source in a turbid medium is analyzed for various fluorescence diffuse optical tomography (fDOT) setups in reflection geometry via a rigorous statistical methodology, the Cramer-Rao bound. Firstly, a spatially and temporally resolved imaging technique (TD) is consid...
Article
We analyze the influence of the contour coding term in segmentation techniques based on active grids and on the minimum description length (MDL) principle. These segmentation techniques have been developed up to now with a contour coding term adapted to polygonal objects. However, this approach can lead to degraded segmentation results for smooth c...