Dr. Sophie Morales Profile

Dr. Sophie Morales

at CEA-LETI

SPIE Involvement:

Author

Publications (24)

Proceedings Article | 30 May 2022 Presentation

From phase imaging to CNN-based quantitative representation

Cédric Allier, Lionel Hervé, Chiara Paviolo, Ondrej Mandula, Olivier Cioni, William Pierré, Kiran Padmanabhan, Francesca Andriani, Sophie Morales

Proceedings Volume PC12136, PC121360T (2022) https://doi.org/10.1117/12.2625595

KEYWORDS: Phase imaging, Microscopy, Live cell imaging, Holography, 3D image reconstruction

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Proceedings Article | 30 May 2022 Presentation

Cell cycle analysis from phase and fluorescence images with a simple and compact microscope

Ondrej Mandula, Jean-Philippe Kleman, Francoise LACROIX, Cedric Allier, Lionel Herve, Sophie Morales

Proceedings Volume PC12136, PC1213610 (2022) https://doi.org/10.1117/12.2636853

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Proceedings Article | 30 May 2022 Presentation

3D live cell imaging of whole organoids in time-lapse using intensity diffraction tomography

William Pierré, Lionel Hervé, Cédric Allier, Sophie Morales, Sergei Grudinin, Pierre RAY, Christophe Arnoult, Magali Dhellemmes

Proceedings Volume PC12136, PC1213612 (2022) https://doi.org/10.1117/12.2625734

KEYWORDS: 3D image processing, Tomography, Live cell imaging, Diffraction, 3D modeling, 3D acquisition, Beam propagation method, 3D metrology, Spatial resolution, Scattering

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Proceedings Article | 3 December 2021 Paper

Vascular organ-on-chip imaging: a dedicated single plane illumination fluorescence microscope

Caroline Bissardon, Clément Quintard, Xavier Mermet, Sophie Morales, Jean-Charles Baritaux, Yves Fouillet, Pierre Blandin

Proceedings Volume 11921, 119210F (2021) https://doi.org/10.1117/12.2615633

KEYWORDS: Microfluidics, Microscopes, Luminescence, Capillaries, 3D image processing, Stereoscopy, Image resolution, 3D acquisition, Statistical analysis, Image analysis

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Proceedings Article | 5 March 2021 Poster

Phase imaging of supracellular structures with lens-free microscopy

Romain Alata, Thomas Vourc'h, Lionel Hervé, Sophie Morales, Pascal Silberzan, Cédric Allier

Proceedings Volume 11653, 116531O (2021) https://doi.org/10.1117/12.2579651

KEYWORDS: Reconstruction algorithms, Microscopy, Phase imaging, Inverse problems, Tumors, Inverse optics, Convolutional neural networks, Neural networks, Microscopes, Imaging devices

Proceedings Article | 5 March 2021 Presentation

Deep learning framework applied to optical diffraction tomography (ODT)

William Pierré, Lionel Hervé, Cédric Allier, Sophie Morales, Sergei Grudinin, Shwetadwip Chowdhury, Laura Waller, Christophe ARNOULT, Pierre RAY, Magali Dhellemmes

Proceedings Volume 11649, 116490F (2021) https://doi.org/10.1117/12.2582361

KEYWORDS: Tomography, Optical tomography, Inverse optics, Geometrical optics, Diffraction, Refractive index, Neural networks, Multiple scattering, Physics, Light scattering

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Proceedings Article | 30 March 2020 Presentation

Chromatic aberration-based phase and fluorescence microscope for cell cycle study (Conference Presentation)

Ondrej Mandula, Jean-Philippe Kleman, Francoise Lacroix, Dainel Fiole, Cédric Allier, Lionel Hervé, Sophie Morales

Proceedings Volume 11351, 113510O (2020) https://doi.org/10.1117/12.2555434

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We designed a particularly simple, compact and robust microscope for phase and fluorescent imaging. The phase-contrast image is reconstructed from a single, approximately 100 µm defocused image with an algorithm based on a constrained optimization of Fresnel diffraction model. Fluorescence image is recorded in-focus. No mechanical movement of neither sample nor objective or any other part of the system is needed to change between the phase-contrast and fluorescence modality. The change of focus between phase (out-of-focus) and fluorescence (in-focus) imaging is achieved with chromatic aberration specifically enhanced by the optical design of our system. Our microscope is sufficiently compact (10x10x10 cm^3) to fit into a standard biological incubator. The simple and robust design reduces the vibration and the drift of the sample. The absence of motorized components makes the system robust and resistant to the humid conditions inside the biological incubator. These aspects greatly facilitate the long-time observation of cell cultures. We can observe a thousand of cells in parallel in a single field of view (1mm^2) with resolution down to 2 µm. We show FUCCI marked HeLa cell culture observed over three days directly in the incubator. FUCCI (fluorescence ubiquitination cell-cycle indicator), is a genetically encoded, two-colour (red and green), indicator of the progression through the cell cycle: the cells in G1 phase show red fluorescence nuclei while the cells in S, G2 and M phase display green fluorescence within the nuclei. We use phase images for segmentation and tracking of the individual cells which allows us to determine the level of fluorescence in each cell in the green and red fluorescence channel. We compare the obtained statistics with the data from flow cytometer acquired at the end of the observation. We show that we can produce a statistically relevant time-resolved measurement of a cell population while keeping access to the individual cells.

Proceedings Article | 30 March 2020 Presentation

Alternation of inverse problem and deep learning approaches for phase retrieval with lens-free microscopy (Conference Presentation)

Cédric Allier, Lionel Hervé, Olivier Cioni, Dorothee Kraemer, Ondrej Mandula, Mathilde Menneteau, Sophie Morales

Proceedings Volume 11351, 113510U (2020) https://doi.org/10.1117/12.2555746

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Proceedings Article | 30 March 2020 Presentation

Video lens-free microscopy of human cells: from standard 2D to 3D organoids culture (Conference Presentation)

Cédric Allier, Sophie Morel, Anthony Berdeu, Lionel Hervé, Thomas Bordy, Michel Bornens, Sabine Bardin, Xavier Gidrol, Nathalie Picollet-D'hahan, Sophie Morales

Proceedings Volume 11351, 113510N (2020) https://doi.org/10.1117/12.2555777

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Proceedings Article | 11 March 2020 Presentation

Alternation of inverse problem and deep learning approaches for phase unwrapping in lens-free microscopy (Conference Presentation)

Cédric Allier, Lionel Hervé, Dorothée Kraemer, Olivier Cioni, Mathilde Menneteau, Ondrej Mandula, Sophie Morales

Proceedings Volume 11249, 1124914 (2020) https://doi.org/10.1117/12.2544812

KEYWORDS: Inverse problems, Microscopy, Image restoration, Neural networks, Diffraction, Image processing, Phase retrieval, Data processing

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Proceedings Article | 9 March 2020 Presentation

A simple, compact and robust phase and fluorescence microscope for cell cycle study (Conference Presentation)

Ondrej Mandula, Cedric Allier, Dainel Fiole, Jean-Philippe Kleman, Francoise Lacroix, Lionel Hervé, Sophie Morales

Proceedings Volume 11243, 112430P (2020) https://doi.org/10.1117/12.2543764

KEYWORDS: Luminescence, Microscopes, Image segmentation, Chromatic aberrations

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Proceedings Article | 22 July 2019 Paper

High accuracy platelet counting using lensfree imaging

D. Isèbe, E. Gremion, A. Daynès, B. Thouy, N. Rongeat, S. Bressieux, A. Ali-Cherif, V. Rebuffel, P. Joly, S. Morales, O. Cioni, P. Blandin

Proceedings Volume 11075, 110750O (2019) https://doi.org/10.1117/12.2527008

KEYWORDS: Reconstruction algorithms, Blood, CMOS sensors, Hematology, Holography, Holograms

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Proceedings Article | 22 July 2019 Paper

Results on identification of bacteria aging in complex environmental samples using Raman spectroscopy

V. Rebuffel, J.-C. Baritaux, E. Bergmann, P. Marcoux, I. Espagnon, S. Morales

Proceedings Volume 11075, 110750J (2019) https://doi.org/10.1117/12.2527141

KEYWORDS: Bacteria, Databases, Raman spectroscopy, Pathogens, Microorganisms, Classification systems, Imaging systems, Imaging spectroscopy, Environmental sensing, Confocal microscopy

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Proceedings Article | 22 July 2019 Paper

Design and evaluation of two imaging systems for very wide field fluorescence microscopy

Isaure de Kernier, Nelly Rongeat, Sophie Morales, Serge Monneret, Pierre Blandin

Proceedings Volume 11075, 110750A (2019) https://doi.org/10.1117/12.2526938

KEYWORDS: Blood, Imaging systems, Microscopy, Sensors, Calibration, Microscopes, Optical filters, Signal detection, Hematology

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Proceedings Article | 22 July 2019 Paper

Deep-learning for phase unwrapping in lens-free imaging

L. Hervé, C. Allier, O. Cioni, F. Navarro, M. Menneteau, S. Morales

Proceedings Volume 11076, 1107610 (2019) https://doi.org/10.1117/12.2527004

KEYWORDS: Diffraction, Reconstruction algorithms, Neurons, Video, Inverse optics, Convolutional neural networks, Microscopes, Microscopy, Inverse problems, CMOS sensors

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SPIE Journal Paper | 9 March 2019 Open Access

Large field-of-view phase and fluorescence mesoscope with microscopic resolution

Isaure de Kernier, Anaïs Ali-Cherif, Nelly Rongeat, Olivier Cioni, Sophie Morales, Julien Savatier, Serge Monneret, Pierre Blandin

JBO, Vol. 24, Issue 03, 036501, (March 2019) https://doi.org/10.1117/12.10.1117/1.JBO.24.3.036501

KEYWORDS: Luminescence, Imaging systems, Image resolution, Blood, Sensors, Microscopy, Objectives, Phase contrast, Holograms, Holography

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Proceedings Article | 4 March 2019 Presentation

Surprisingly simple and compact microscope for time-lapse phase and fluorescence imaging based on chromatic aberration (Conference Presentation)

Ondrej Mandula, Cédric Allier, Lionel Herve, Jean-Philippe Kleman, Francoise Lacroix, Anne Fourest-Lieuvin, Angelique Vinit, Sophie Morales

Proceedings Volume 10887, 108870B (2019) https://doi.org/10.1117/12.2509375

KEYWORDS: Luminescence, Microscopes, Chromatic aberrations, Phase imaging, CMOS cameras, Imaging systems, Spatial resolution, Biological research

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Proceedings Article | 4 March 2019 Presentation

Quantitative phase imaging of adherent mammalian cells: a comparison of three different techniques (Conference Presentation)

Cédric Allier, Julien Savatier, Serge Monneret, Yves Usson, Lionel Hervé, Ondrej Mandula, Pierre Blandin, Sophie Morales

Proceedings Volume 10887, 108870C (2019) https://doi.org/10.1117/12.2508421

KEYWORDS: Phase imaging, Image processing, Digital holography, Microscopy, Statistical analysis, Microfluidics, Resonators, Profiling, Holographic interferometry, Holography

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Proceedings Article | 20 February 2019 Presentation + Paper

Statistical study of blood cell populations by very wide-field bimodal phase/fluorescence imaging

Isaure de Kernier, Stéphanie Bressieux, Nelly Rongeat, Anaïs Ali-Chérif, Sophie Morales, Serge Monneret, Pierre Blandin

Proceedings Volume 10885, 108850A (2019) https://doi.org/10.1117/12.2506531

KEYWORDS: Blood, Imaging systems, Image resolution, Flow cytometry, Microscopes, Point spread functions, Sensors, Holography

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Proceedings Article | 23 February 2018 Paper

Dynamic quantitative analysis of adherent cell cultures by means of lens-free video microscopy

C. Allier, R. Vincent, F. Navarro, M. Menneteau, L. Ghenim, X. Gidrol, T. Bordy, L. Hervé, O. Cioni, S. Bardin, M. Bornens, Y. Usson, S. Morales

Proceedings Volume 10503, 105031R (2018) https://doi.org/10.1117/12.2289525

KEYWORDS: Video microscopy, Digital holography, Microscopy, Reconstruction algorithms, Quantitative analysis

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Proceedings Article | 23 February 2018 Paper

3D+time acquisitions of 3D cell culture by means of lens-free tomographic microscopy

Anthony Berdeu, Bastien Laperrousaz, Thomas Bordy, S. Morales, Xavier Gidrol, Nathalie Picollet-D'hahan, Cédric Allier

Proceedings Volume 10499, 1049909 (2018) https://doi.org/10.1117/12.2289474

KEYWORDS: 3D acquisition, Microscopy, Tomography, 3D image processing, Diffraction, Microscopes, Reconstruction algorithms

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Proceedings Article | 23 February 2018 Paper

Phase from defocus

Ondrej Mandula, Cédric Allier, Lionel Hervé, Eric Denarier, Anne Fourest-Lieuvin, Sylvie Gory-Fauré, Angélique Vinit, Sophie Morales

Proceedings Volume 10503, 105031Q (2018) https://doi.org/10.1117/12.2287693

KEYWORDS: Neurons, Microscopes, Video, Phase imaging, Cameras, Data acquisition, Reconstruction algorithms, Image quality standards, Image quality, Image processing

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