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International audience; Context. Extreme adaptive optics systems, such as the Spectro-Polarimetric High-contrast Exoplanet REsearch facility (SPHERE), push forward the limits in high contrast and high resolution in direct imaging. The main objectives of these instruments are exoplanet detection and characterisation. Aims: We aim to increase the contrast limits to detect new satellites orbiting known asteroids. We use cutting-edge data reduction techniques and data processing algorithms that are essential to best analyse the raw data provided by the instruments and increase their performances. Doing so, the unequalled performances of SPHERE also make it a unique tool to resolve and study asteroids in the solar system, expanding the domain of its main science targets. Methods: We applied a newly developed data reduction pipeline for integral field spectrographs on archival SPHERE data of a resolved asteroid, (130) Elektra. It was coupled with a dedicated point spread function reconstruction algorithm to model the asteroid halo. Following the halo removal, the moon signal could be extracted more accurately. The moon positions were fitted at three epochs and were used to derive the orbital parameters via a genetic-based algorithm. Results: We announce the discovery of S/2014 (130) 2, a third moon orbiting (130) Elektra, making it the first quadruple asteroid ever found. It is identified in three different epochs, 9, 30, and 31 Dec. 2014, at a respective angular separation of 258 mas (333 km), 229 mas (327 km), and 319 mas (457 km). We estimate that this moon has a period of 0.679 ± 0.001 day and a semi-major axis of 344 ± 5 km, with an eccentricity of 0.33 ± 0.05 and an inclination of 38° ±19° compared to the primary rotation axis. With a relative magnitude to the primary of 10.5 ± 0.5, its size is estimated to be 1.6 ± 0.4 km. Conclusions: The orbital parameters of S/2014 (130) 2 are poorly constrained due to the unfavourable configurations of the available fragmentary data. Additional observations are needed to better estimate its orbit and to suggest a formation model. This new detection nonetheless shows that dedicated data reduction and processing algorithms modelling the physics of the instruments can push their contrast limits further. Visualisations are available at https://www.aanda.org Based on publicly available archival data provided by the ESO Science Archive Facility under programme ID 60.A-9362(A) (Yang et al.).

In-line digital holography is a simple yet powerful tool to image absorbing and/or phase objects. However, the holograms of interest are corrupted by the background signal due to unwanted scattering elements located in the optical path. Using only two holograms of the same object, shifted to different locations, an inverse problems approach is applied to jointly estimate the complex transmittance of the sample and the contribution of the interferent background signal at the sensor plane. Experimental results with stained bacteria are presented and show improved reconstructions of the sample while also accounting for the background contribution.

International audience; The Center for Optics and Photonics of the National Astronomical Research Institute of Thailand, together with the Institut d'Optique Graduate School and the Centre de Recherche Astrohpysique de Lyon (CRAL), is currently developing the Evanescent Wave Coronagraph (EvWaCo). The coronagraph relies on the tunneling effect to produce a fully achromatic focal plane mask (FPM) with an adjustable size. The full instrument comprises a coronagraph and adaptive optics system that will be mounted on the Thai National Telescope and is specified to reach a raw contrast of 10−4 at an inner working angle of 3 Airy radii. The coronagraph will be used to perform high contrast observations of stellar systems during on-sky observations over the spectral domain [600 nm, 900 nm]. In this paper, we present the opto-mechanical design of the EvWaCo prototype and the performance measured in laboratory conditions. We also discuss the potential applications for space-based observations and the development plan under this project in the next five years.

The evanescent wave coronagraph uses the principle of frustrated total internal reflection (FTIR) to suppress the light coming from the star and study its close environment. Its focal plane mask is composed of a lens and a prism placed in contact with each other to produce the coronagraphic effect. In this paper, we present the experimental results obtained using an upgraded focal plane mask of the Evanescent Wave Coronagraph (EvWaCo). These experimental results are also compared to the theoretical performance of the coronagraph obtained through simulations. Experimentally, we reach a raw contrast equal to a few $10^{-4}$ at a distance equal to 3 ${\lambda}/D$ over the full I-band (${\lambda}_c =$ $800$ $nm$, ${\Delta}{\lambda}/{\lambda} \approx 20\%$) and equal to 4 ${\lambda}/D$ over the full R-band (${\lambda}_c =$ $650$ $nm$, ${\Delta}{\lambda}/{\lambda} \approx 23\%$) in unpolarized light. However, our simulations show a raw contrast close to $10^{-4}$ over the full I-band and R-band at the same distance, thus, confirming the theoretical achromatic advantage of the coronagraph. We also verify the stability of the mask through a series of contrast measurements over a period of 8 months. Furthermore, we measure the sensitivity of the coronagraph to the lateral and longitudinal misalignment of the focal plane mask, and to the lateral misalignment of the Lyot stop., Comment: 27 pages, 19 figures, accepted by AJ

We propose to reconstruct biological samples using calibration beads to perform numerical autofocusing in in-line holographic microscopy. The approach is based on a joint inversion using both a parametric and a regularized inversion method.

Research is continuously developing imaging methods to better understand the structure and function of biological systems. In this paper, we describe our work to develop lens-free microscopy as a novel mean to observe and quantify cells in 2D and 3D cell culture conditions. At first, we developed a lens-free video microscope based on multiple wavelength acquisitions to perform time-lapse 2D imaging of dense cell culture inside the incubator. We demonstrated that novel phase retrieval techniques enable imaging thin cell samples with high concentration (~15000 cells over a large field of view of 29.4 mm2). The experimental data can next be further analyzed with existing cell profiling and tracking algorithms. As an example, we showed that a 7 days acquisition of a culture of HeLa cells leads to a dataset featuring 2.106 cell point measurements and 104 cell cycle tracks. Recently, we extended our work to the video-microscopy of 3D organoids culture. We showed the capability of lens-free microscopy to perform 3D+time acquisitions of 3D organoids culture. To our knowledge, our technique is the only one able to reconstruct very large volumes of 3D cell culture (~5 mm3) by phase contrast imaging. This new mean of microscopy allowed us to observe a broad range of phenomena present in 3D environments, e.g. self-organizations, displacement of large clusters, merging and interconnection over long distances (>1 mm). In addition, this 3D microscope can capture the interactions of single cells and organoids with their 3D environment, e.g. traction forces generated by large cell aggregates over long distances, up to 1.5 mm. Overall, lens-free microscopy techniques favor ease of use and label-free experimentations as well as time-lapse acquisitions of large datasets. Importantly, we consider that these lens-free microscopy technique can thus expand the repertoire of phenomena that can be studied within 2D and 3D organoids cultures.

Context. The improvement of large size detectors permitted the development of integral field spectrographs (IFSs) in astronomy. Spectral information for each spatial element of a two-dimensional field of view is obtained thanks to integral field units that spread the spectra on the 2D grid of the sensor. Aims. Here we aim to solve the inherent issues raised by standard data-reduction algorithms based on direct mapping of the 2D + λ data cube: the spectral cross-talk due to the overlap of neighbouring spectra, the spatial correlations of the noise due to the re-interpolation of the cube on a Cartesian grid, and the artefacts due to the influence of defective pixels. Methods. The proposed method, Projection, Interpolation, and Convolution (PIC), is based on an “inverse-problems” approach. By accounting for the overlap of neighbouring spectra as well as the spatial extension in a spectrum of a given wavelength, the model inversion reduces the spectral cross-talk while deconvolving the spectral dispersion. Considered as missing data, defective pixels undetected during the calibration are discarded on-the-fly via a robust penalisation of the data fidelity term. Results. The calibration of the proposed model is presented for the Spectro-Polarimetric High-contrast Exoplanet REsearch instrument (SPHERE). This calibration was applied to extended objects as well as coronagraphic acquisitions dedicated to exoplanet detection or disc imaging. Artefacts due to badly corrected defective pixels or artificial background structures observed in the cube reduced by the SPHERE data reduction pipeline are suppressed while the reconstructed spectra are sharper. This reduces the false detections by the standard exoplanet detection algorithms. Conclusions. These results show the pertinence of the inverse-problems approach to reduce the raw data produced by IFSs and to compensate for some of their imperfections. Our modelling forms an initial building block necessary to develop methods that can reconstruct and/or detect sources directly from the raw data.

We developed 2D and 3D lens-free microscopes, based on the data processing of raw diffraction images. By nature, these systems allows imaging large field of view of unlabeled samples and easily provide time-lapses.

National audience; The Very Large Telescope instrument SPHERE is equipped with an integral field spectrograph. The sensor field is composed of thousands of spectra produced by a hexagonal lenslet array. We propose a new data reduction algorithm based on an inverse problem approach whose data fidelity is enforced by robust penalization to automatically identify the defective pixels. Our reconstructions by inversion of the forward model represent a notable improvement with respect to reconstructions obtained with the current data reduction pipeline (reconstructions based on data interpolation).

Thanks to a novel three-dimensional imaging platform based on lens-free microscopy, it is possible to perform multi-angle acquisitions and holographic reconstructions of 3D cell cultures directly into the incubator. Being able of reconstructing volumes as large as ~5 mm3 over a period of time covering several days, allows us to observe a broad range of migration strategies only present in 3D environment, whether it is single cell migration, collective migrations of cells and dispersal of cells. In addition we are able to distinguish new interesting phenomena, e.g. large-scale cell-to-matrix interactions (>1 mm), fusion of cell clusters into large aggregate (~10,000 µm2) and conversely, total dissociation of cell clusters into clumps of migrating cells. This work on a novel 3D + time lens-free microscopy technique thus expands the repertoire of phenomena that can be studied within 3D cell cultures.

International audience; In-line digital holography is a simple and powerful tool to image absorbing and/or phase objects in numerous fields such as crystallography, biology or fluid mechanics. Nevertheless, this kind of interference imaging technique leads to a loss of the phase of the complex wave front on the sensor. This lack of phase information can be critical in the reconstruction process. Thus, the simplicity of the setup must be balanced by dedicated reconstruction algorithm to retrieve the object from its hologram, such as inverse approaches. In the case of simple objects for which an analytical model of propagation is known, parametric algorithms are very effective. But these approaches fail at reconstructing more complex objects, where non-parametric solutions must be involved. This may lead to a loss in precision or specificity. In this work we propose a new approach combining these two methods to take benefits from their own advantages. The object to reconstruction is split in two subparts. A part is described by a parametric model. The other part of the object is simulated via a non-parametric model. These two parts which interfere are jointly considered in the reconstruction algorithm by alternating parametric and non-parametric procedures. We apply this new technique to evaporating droplets where the high contrast fringes produced by the droplets tend to mask the fringes produced by the plume. With our method, both the droplet and the plume are jointly reconstructed.

Editors: Thomas G. Brown, Carol J. Cogswell, Tony Wilson; We propose a three-dimensional (3D) imaging platform based on lens-free microscopy to perform multi-angle acquisitions on 3D cell cultures embedded in extracellular matrix (ECM). We developed algorithms based on the Fourier diffraction theorem to perform fully 3D reconstructions of biological samples and we adapted the lens-free microscope to incubator conditions. Here we demonstrate for the first time, 3D+time lens-free acquisitions of 3D cell culture over 8 days directly into the incubator. The 3D reconstructed volume is as large as ~5 mm3 and provides a unique way to observe in the same 3D cell culture experiment multiple cell migration strategies. Namely, in a 3D cell culture of prostate epithelial cells embedded within a Matrigel® matrix, we are able to distinguish single cell ’leaders’, migration of cell clusters, migration of large aggregates of cells, and also close-gap and large-scale branching. In addition, we observe long-scale 3D deformations of the ECM that modify the geometry of the 3D cell culture. Interestingly, we also observed the opposite, i.e. we found that large aggregates of cells may deform the ECM by generating traction forces over very long distances. In sum we put forward a novel 3D lens-free microscopy tomographic technique to study the single and collective cell migrations, the cell-to-cell interactions and the cell-to-matrix interactions.

International audience; We propose a new imaging platform based on lens-free time-lapse microscopy for 3D cell culture and its dedicated algorithm lying on a fully 3D regularized inverse problem approach. First 3D + t results are presented.

International audience; We propose a three-dimensional (3D) imaging platform based on lens-free microscopy to perform multiangle acquisitions on 3D cell cultures embedded in extracellular matrices. Lens-free microscopy acquisitions present some inherent issues such as the lack of phase information on the sensor plane and a limited angular coverage. We developed and compared three different algorithms based on the Fourier diffraction theorem to obtain fully 3D reconstructions. These algorithms present an increasing complexity associated with a better reconstruction quality. Two of them are based on a regularized inverse problem approach. To compare the reconstruction methods in terms of artefact reduction, signal-to-noise ratio, and computation time, we tested them on two experimental datasets: an endothelial cell culture and a prostate cell culture grown in a 3D extracellular matrix with large reconstructed volumes up to ∼5 mm3∼5 mm3 with a resolution sufficient to resolve isolated single cells. The lens-free reconstructions compare well with standard microscopy.

In-line digital holography is a simple yet powerful tool to image absorbing and/or phase objects. Nevertheless, the loss of the phase of the complex wavefront on the sensor can be critical in the reconstruction process. The simplicity of the setup must thus be counterbalanced by dedicated reconstruction algorithms, such as inverse approaches, in order to retrieve the object from its hologram. In the case of simple objects for which the diffraction pattern produced in the hologram plane can be modeled using few parameters, a model fitting algorithm is very effective. However, such an approach fails to reconstruct objects with more complex shapes, and an image reconstruction technique is then needed. The improved flexibility of these methods comes at the cost of a possible loss of reconstruction accuracy. In this work, we combine the two approaches (model fitting and regularized reconstruction) to benefit from their respective advantages. The sample to be reconstructed is modeled as the sum of simple parameterized objects and a complex-valued pixelated transmittance plane. These two components jointly scatter the incident illumination, and the resulting interferences contribute to the intensity on the sensor. The proposed hologram reconstruction algorithm is based on alternating a model fitting step and a regularized inversion step. We apply this algorithm in the context of fluid mechanics, where holograms of evaporating droplets are analyzed. In these holograms, the high contrast fringes produced by each droplet tend to mask the diffraction pattern produced by the surrounding vapor wake. With our method, the droplet and the vapor wake can be jointly reconstructed.

International audience; New microscopes are needed to help realize the full potential of 3D organoid culture studies bygathering large quantitative and systematic data over extended period of time while preserving the integrityof the living sample. On another hand, lensfree video microscopy is addressing these needs in the context of2D cell culture, providing label-free and non-phototoxic acquisition of large datasets. As scientistsroutinely adopt 3D culture techniques, the new challenging task is to extend lensfree microscopy techniquesto 3D structures.In order to image such large volume while preserving the ability to catch every single cell, we proposenew imaging platforms based on lensfree microscopy. We have built lensfree diffractive tomography setupsperforming multi-angle acquisitions of 3D organoid culture embedded in Matrigel® and developed adedicated 3D holographic reconstruction algorithm based on the Fourier diffraction theorem.With a first prototype we have been able to reconstruct a 3D volume as large as 21.5 mm^3 of a 3Dorganoid culture of prostatic RWPE1 cells in Matrigel® showing the ability of these cells to assemble in 3Dintricate cellular network at the mesoscopic scale. Comparisons with 2D images showed that it ispossible to detect single cells isolated from the main cellular structure.From results of the first prototype and numerical simulations, a second prototype wasdesigned to improve the reconstructions quality, especially on the vertical axis. First results on dust andbubbles lying at the bottom of a Petri® dish are promising.The adaptation of lensfree microscopy techniques to 3D organoid cultures imaging and thepresentation of the associated algorithms are the scopes of the present communication.

National audience; New microscopes are needed to help realize the full potential of 3D organoid culture studies by gathering large quantitative and systematic data over extended period of time while preserving the integrity of the living sample. In order to reconstruct large volume while keeping the ability to catch every single cell, we propose new imaging platforms based on lensfree microscopy, a technic which is addressing these needs in the context of 2D cell culture, providing label-free and non-phototoxic acquisition of large datasets. We have built lensfree diffractive tomography setups performing multi-angle acquisitions of 3D organoid culture embedded in Matrigel ® and developed dedicated 3D holographic reconstruction algorithms based on the Fourier diffraction theorem. Nonetheless, holographic setups do not record the phase of the incident wavefront and the biological samples in Petri dish strongly limit the angular coverage. These limitations introduces numerous artefacts in the sample reconstruction. We developed several methods to overcome them, such as multi wavelength imaging or iterative phase retrieval. The most promising technic currently developed is based on a regularized inverse problem approach directly performed on the 3D volume to reconstruct. 3D reconstructions were realized on several complex samples such as 3D networks or spheroids embedded in capsules with large reconstructed volumes up to ~25 mm^3 while still being able to identify single cells. To our knowledge, this is the first time that such an inverse problem approach is implemented in the context of lensfree diffractive tomography enabling to reconstruct large volume of unstained biological samples.

Lensfree imaging is an emerging microscopy technique based on in-line holography as invented by Gabor in 1948. Albeit the existence of the method since decades, the recent development of digital sensors, helped the realization of its full potential. Over the recent years, innovations and improvements in CMOS imaging technology design and fabrication have allowed to decrease the pixel pitch down to ∼1μm and the number of pixels has dramatically increased up to 250 million of pixels. As a result, the performance of lensfree microscopy, which features a bare CMOS sensor without any magnification optics, have tremendously increased while keeping the design simple, robust, and at a reasonable low cost. The detection ability improved from 10 μm (cell) in 2009, to 1 μm (bacteria) in 2010, down to 100 nm beads in 2012, paving the way to the detection of viruses in 2013.

National audience; The study of in vitro cell populations is a major concern for biologists in the realms of drug screening and oncology for example. With standard microscopy techniques, crucial information at the mesoscopic scale is still difficult to reach due to reduced field of view and complexity to monitor cell behaviors in real time over large periods of time. Lensfree video microscopy has already overcome these difficulties in the context of 2D cell biology. Based on the in-line holography principle, it puts cells directly between a coherent light source and a sensor allowing large field of view, e.g. 30 mm 2. With the growth of 3D cell cultures, the new challenging task is to extend this imaging technique to acquisitions and 3D reconstructions of cellular culture. For this purpose, we have developed an experimental optical bench dedicated to lensfree diffractive tomography and studied several 3D reconstruction algorithms on acquisitions of 3D prostatic cell cultures.