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Extermann Jérôme

Extermann Jérôme

Maître d'enseignement HES

Main skills

Optics

Applied Physics

Experimental physics

Imagerie Biomédicale

Lasers

Remote sensing applications

  • Contact

  • Teaching

  • Research

  • Publications

  • Conferences

Main contract

Maître d'enseignement HES

Desktop: A206A

Haute école du paysage, d'ingénierie et d'architecture de Genève
Rue de la Prairie 4, 1202 Genève, CH
hepia
Faculty
Technique et IT
Main Degree Programme
Microtechniques
BSc HES-SO en Génie mécanique - Haute école du paysage, d'ingénierie et d'architecture de Genève
  • Mathematics
BSc HES-SO en Technique des bâtiments - Haute école du paysage, d'ingénierie et d'architecture de Genève
  • Physique Avancée
  • Physique Appliquée pour étudiant-e-s en systèmes énergétiques
  • Thermodynamique appliquée
  • Dynamique des fluides 2
BSc HES-SO en Microtechniques - Haute école du paysage, d'ingénierie et d'architecture de Genève
  • Physique Avancée
  • Microscopie
  • optique
  • Spectroscopie optique
MSc HES-SO en Engineering - HES-SO Master
  • Bio-capteurs et instrumentation

Completed

REMOTE

Role: Co-applicant

Financement: Innosuisse

Description du projet :

Real-timE Monitoring of biO-contamination based on cosT- Effective optical device

Research team within HES-SO: Extermann Jérôme , Schmidt Cédric

Partenaires professionnels: Kiselev, Denis, Plair SA

Durée du projet: 01.01.2022 - 31.03.2024

Montant global du projet: 549'000 CHF

Statut: Completed

ICARO

Role: Main Applicant

Financement: Innosuisse

Description du projet :

Quantum-inspired image compression for optical microcopy

Research team within HES-SO: Extermann Jérôme , Pomarico Enrico

Partenaires professionnels: Sanguinetti Bruno, Dotphoton SA

Durée du projet: 04.01.2019 - 03.01.2021

Montant global du projet: 559'000 CHF

Statut: Completed

2024

Cryogenic temperature 3D mapping via a distributed temperature sensor with centimeter resolution
Scientific paper ArODES

Luca Corradin, Gabriel Thiebaut, Gaëtan Gras, Félix Bussières, Jérôme Extermann, Enrico Pomarico

Optics Express,  2024, 32, 14, 24889

Link to the publication

Summary:

We conduct 3D mapping of cryogenic temperatures via a Raman-based distributed temperature sensor, employing standard telecom single-mode fibers and polarization-independent superconducting nanowire single photon detectors (SNSPDs). By coiling a test fiber around various stages of a liquid helium cooled cryostat, our device demonstrates a lower temperature sensing limit of (48 ± 2) K, below the nitrogen boiling point. This achievement is made possible by the low dark count rates of SNSPDs, as validated by theoretical simulations. Furthermore, we utilize our device to map cryogenic temperatures on the 350 cm2 surface of a specially designed hollow cylindrical aluminum sample, accommodating approximately 2 m of standard single-mode optical fiber. During nitrogen cooling, we monitor the temporal evolution of the spatially dependent temperature gradient on the metallic sample with a temporal sampling down to one minute. Fiber-based distributed temperature sensing with centimetric spatial resolution can be effectively applied for 3D mapping at cryogenic temperatures of superconducting, quantum computing and aerospace instrumentation.

2023

Opening the black box of traumatic brain injury :
Scientific paper ArODES
a holistic approach combining human 3D neural tissue and an in vitro traumatic brain injury induction device

Céline Loussert-Fonta, Luc Stoppini, Yoan Neuenschwander, Ophélie Righini, Denis Prim, Cédric Schmidt, Marc O. Heuschkel, Loris Gomez Baisac, Milica Jovic, Marc E. Pfeifer, Jérôme Extermann, Adrien Roux

Frontiers in Neuroscience,  2023, vol. 17, article no. 1189615

Link to the publication

Summary:

Traumatic brain injury (TBI) is caused by a wide range of physical events and can induce an even larger spectrum of short- to long-term pathophysiologies. Neuroscientists have relied on animal models to understand the relationship between mechanical damages and functional alterations of neural cells. These in vivo and animal-based in vitro models represent important approaches to mimic traumas on whole brains or organized brain structures but are not fully representative of pathologies occurring after traumas on human brain parenchyma. To overcome these limitations and to establish a more accurate and comprehensive model of human TBI, we engineered an in vitro platform to induce injuries via the controlled projection of a small drop of liquid onto a 3D neural tissue engineered from human iPS cells. With this platform, biological mechanisms involved in neural cellular injury are recorded through electrophysiology measurements, quantification of biomarkers released, and two imaging methods [confocal laser scanning microscope (CLSM) and optical projection tomography (OPT)]. The results showed drastic changes in tissue electrophysiological activities and significant releases of glial and neuronal biomarkers. Tissue imaging allowed us to reconstruct the injured area spatially in 3D after staining it with specific nuclear dyes and to determine TBI resulting in cell death. In future experiments, we seek to monitor the effects of TBI-induced injuries over a prolonged time and at a higher temporal resolution to better understand the subtleties of the biomarker release kinetics and the cell recovery phases.

Data models for dataset drift controls in machine learning with optical images
Scientific paper ArODES

Luis Oala, Marco Aversa, Gabriel Nobis, Kurt Willis, Yoan Neuenschwander, Michèle Buck, Christian Matek, Jérôme Extermann, Enrico Pomarico, Wojciech Samek, Roderick Murray-Smith, Christoph Clausen, Bruno Sanguinetti

Transactions on machine learning research,

Link to the publication

Summary:

Camera images are ubiquitous in machine learning research. They also play a central role in the delivery of important services spanning medicine and environmental surveying. However, the application of machine learning models in these domains has been limited because of robustness concerns. A primary failure mode are performance drops due to differences between the training and deployment data. While there are methods to prospectively validate the robustness of machine learning models to such dataset drifts, existing approaches do not account for explicit models of the primary object of interest: the data. This limits our ability to study and understand the relationship between data generation and downstream machine learning model performance in a physically accurate manner. In this study, we demonstrate how to overcome this limitation by pairing traditional machine learning with physical optics to obtain explicit and differentiable data models. We demonstrate how such data models can be constructed for image data and used to control downstream machine learning model performance related to dataset drift. The findings are distilled into three applications. First, drift synthesis enables the controlled generation of physically faithful drift test cases to power model selection and targeted generalization. Second, the gradient connection between machine learning task model and data model allows advanced, precise tolerancing of task model sensitivity to changes in the data generation. These drift forensics can be used to precisely specify the acceptable data environments in which a task model may be run. Third, drift optimization opens up the possibility to create drifts that can help the task model learn better faster, effectively optimizing the data generating process itself. A guide to access the open code and datasets is available at https://github.com/aiaudit-org/raw2logit.

Optical imaging of the small intestine immune compartment across scales
Scientific paper ArODES

Arielle Louise Planchette, Cédric Schmidt, Olivier Burri, Mercedes Gomez de Agüero, Aleksandra Radenovic, Alessio Mylonas, Jérôme Extermann

Communications Biology,  2023, vol. 6, article no. 352

Link to the publication

Summary:

The limitations of 2D microscopy constrain our ability to observe and understand tissue-wide networks that are, by nature, 3-dimensional. Optical projection tomography (OPT) enables the acquisition of large volumes (ranging from micrometres to centimetres) in various tissues. We present a multi-modal workflow for the characterization of both structural and quantitative parameters of the mouse small intestine. As proof of principle, we evidence its applicability for imaging the mouse intestinal immune compartment and surrounding mucosal structures. We quantify the volumetric size and spatial distribution of Isolated Lymphoid Follicles (ILFs) and quantify the density of villi throughout centimetre-long segments of intestine. Furthermore, we exhibit the age and microbiota dependence for ILF development, and leverage a technique that we call reverse-OPT for identifying and homing in on regions of interest. Several quantification capabilities are displayed, including villous density in the autofluorescent channel and the size and spatial distribution of the signal of interest at millimetre-scale volumes. The concatenation of 3D imaging with reverse-OPT and high-resolution 2D imaging allows accurate localisation of ROIs and adds value to interpretations made in 3D. Importantly, OPT may be used to identify sparsely-distributed regions of interest in large volumes whilst retaining compatibility with high-resolution microscopy modalities, including confocal microscopy. We believe this pipeline to be approachable for a wide-range of specialties, and to provide a new method for characterisation of the mouse intestinal immune compartment.

2022

Artifacts in optical projection tomography due to refractive index mismatch :
Scientific paper ArODES
model and correction

Yan Liu, Jonathan Dong, Cédric Schmidt, Aleix Boquet-Pujadas, Jérôme Extermann, Michael Unser

Optics letters,  vol. 47, issue 11

Link to the publication

Summary:

Optical projection tomography (OPT) is a powerful tool for 3D imaging of mesoscopic samples. While it is able to achieve resolution of a few tens of microns over a sample volume of several cubic centimeters, the reconstructed images often suffer from artifacts caused by inaccurate calibration. In this work, we focus on the refractive-index mismatch between the sample and the surrounding medium. We derive a 3D cone-beam forward model of OPT that approximates the effect of refractiveindex mismatch. We then implement a fast and efficient reconstruction method to correct for the induced seagull-shaped artifacts on experimental images of fluorescent beads.

Statistical distortion of supervised learning predictions in optical microscopy induced by image compression
Scientific paper ArODES

Enrico Pomarico, Cédric Schmidt, Florian Chays, David Nguyen, Arielle Planchette, Audrey Tissot, Adrien Roux, Stéphane Pagès, Laura Batti, Christoph Clausen, Theo Lasser, Aleksandra Radenovic, Bruno Sanguinetti, Jérôme Extermann

Scientific Reports,  2022, vol. 12, article no. 3464

Link to the publication

Summary:

The growth of data throughput in optical microscopy has triggered the extensive use of supervised learning (SL) models on compressed datasets for automated analysis. Investigating the effects of image compression on SL predictions is therefore pivotal to assess their reliability, especially for clinical use. We quantify the statistical distortions induced by compression through the comparison of predictions on compressed data to the raw predictive uncertainty, numerically estimated from the raw noise statistics measured via sensor calibration. Predictions on cell segmentation parameters are altered by up to 15% and more than 10 standard deviations after 16-to-8 bits pixel depth reduction and 10:1 JPEG compression. JPEG formats with higher compression ratios show significantly larger distortions. Interestingly, a recent metrologically accurate algorithm, offering up to 10:1 compression ratio, provides a prediction spread equivalent to that stemming from raw noise. The method described here allows to set a lower bound to the predictive uncertainty of a SL task and can be generalized to determine the statistical distortions originated from a variety of processing pipelines in AI-assisted fields.

Distributed temperature sensor combining centimeter resolution with hundreds of meters sensing range
Scientific paper ArODES

Julien Gasser, Daryl Warpelin, Félix Bussières, Jérôme Extermann, Enrico Pomarico

Optics Express,  2022, vol. 30, no. 5, pp. 6768-6777

Link to the publication

Summary:

We present a Raman distributed temperature sensor based on standard telecom single mode fibers and efficient polarization-independent superconducting nanowire single photon detectors. Our device shows 3 cm and 1.5 °C resolution on a 5 m fiber upon one minute integration. We show that spatial resolution is limited by the laser pulse width and not by the detection system. Moreover, for long fibers the minimum distance for a measurable temperature step change increases of around 4 cm per km length, because of chromatic dispersion at the Stokes and Anti-Stokes wavelengths. Temperature resolution is mainly affected by the drop in the laser repetition rate when long fibers are tested. On a 500 m fiber, a trade-off of 10 cm and 8 °C resolution is achieved with 3 minutes integration. Fiber-based distributed temperature sensing, combining centimetric spatial resolution with hundreds of meters sensing range, could pave the way for a new kind of applications, such as 2D and 3D temperature mapping of complex electronic devices, particles detectors, cryogenic and aerospace instrumentation.

2021

High resolution optical projection tomography platform for multispectral imaging of the mouse gut
Scientific paper ArODES

Cédric Schmidt, Arielle L. Planchette, David Nguyen, Gabriel Giardina, Yoan Neuenschwander, Mathieu Di Franco, Alessio Mylonas, Adrien C. Descloux, Enrico Pomarico, Aleksandra Radenovic, Jérôme Extermann

Biomedical Optics Express,  2021, vol. 12, no. 6, pp. 3619-3629

Link to the publication

Summary:

Optical projection tomography (OPT) is a powerful tool for three-dimensional imaging of mesoscopic biological samples with great use for biomedical phenotyping studies. We present a fluorescent OPT platform that enables direct visualization of biological specimens and processes at a centimeter scale with high spatial resolution, as well as fast data throughput and reconstruction. We demonstrate nearly isotropic sub-28 μm resolution over more than 60 mm3 after reconstruction of a single acquisition. Our setup is optimized for imaging the mouse gut at multiple wavelengths. Thanks to a new sample preparation protocol specifically developed for gut specimens, we can observe the spatial arrangement of the intestinal villi and the vasculature network of a 3-cm long healthy mouse gut. Besides the blood vessel network surrounding the gastrointestinal tract, we observe traces of vasculature at the villi ends close to the lumen. The combination of rapid acquisition and a large field of view with high spatial resolution in 3D mesoscopic imaging holds an invaluable potential for gastrointestinal pathology research.

2018

Imaging of cortical structures and microvasculature using extended-focus optical coherence tomography at 13??µm
Scientific paper ArODES

Paul J. Marchand, DanielLaboratoire d'Optique Biomédicale, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzer Szlag, Jérôme Extermann, Arno Bouwens, David Nguyen, Markus Rudin, Theo Lasser

Optics Letters,  2018, vol. 43, no. 8, pp. 1782-1785

Link to the publication

Summary:

Extended-focus optical coherence tomography (xf-OCT) is a variant of optical coherence tomography (OCT) wherein the illumination and/or detection modes are engineered to provide a constant diffractionless lateral resolution over an extended depth of field (typically 3 to 10× the Rayleigh range). xf-OCT systems operating at 800 nm have been devised and used in the past to image brain structures at high-resolution in vivo, but are limited to ∼500  μm in penetration depth due to their short illumination wavelength. Here we present an xf-OCT system optimized to an image deeper within the cortex by using a longer illumination central wavelength of 1310 nm. The system offers a lateral resolution of 3 and 6.5 μm, over a depth of 900 μm and >1.5  mm using a 10× and 5× objective, respectively, in air. We characterize the system’s resolution using microbeads embedded in PDMS and demonstrate its capabilities by imaging the cortical structure and microvasculature in anesthetized mice to a depth of ∼0.8  mm. Finally, we illustrate the difference in penetration depths obtainable with the new system and an xf-OCT system operating at 800 nm.

2017

3D time-lapse imaging and quantification of mitochondrial dynamics
Scientific paper ArODES

Miguel Sison, Sabyasachi Chakrabortty, Jérôme Extermann, Amir Nahas, james Paul Marchand, Antonio Lopez, Tanja Weil, Theo Lasser

Scientific Reports,  2017, vol. 7, article no. 43275

Link to the publication

Summary:

We present a 3D time-lapse imaging method for monitoring mitochondrial dynamics in living HeLa cells based on photothermal optical coherence microscopy and using novel surface functionalization of gold nanoparticles. The biocompatible protein-based biopolymer coating contains multiple functional groups which impart better cellular uptake and mitochondria targeting efficiency. The high stability of the gold nanoparticles allows continuous imaging over an extended time up to 3000 seconds without significant cell damage. By combining temporal autocorrelation analysis with a classical diffusion model, we quantify mitochondrial dynamics and cast these results into 3D maps showing the heterogeneity of diffusion parameters across the whole cell volume.

NIR-emitting and photo-thermal active nanogold as mitochondria-specific probes
Scientific paper ArODES

Sabyasachi Chakrabortty, Miguel Sison, Yuzhou Wu, Anita Ladenburger, Goutam Pramanik, Johannes Biskupek, Jérôme Extermann, Ute Kaiser, Theo Lasser, Tanja Weil

Biomaterials Science,  2017, vol. 5, no. 5, article no. 966-971

Link to the publication

Summary:

We report a bioinspired multifunctional albumin derived polypeptide coating comprising grafted poly(ethylene oxide) chains, multiple copies of the HIV TAT derived peptide enabling cellular uptake as well as mitochondria targeting triphenyl-phosphonium (TPP) groups. Exploring these polypeptide copolymers for passivating gold nanoparticles (Au NPs) yielded (i) NIR-emitting markers in confocal microscopy and (ii) photo-thermal active probes in optical coherence microscopy. We demonstrate the great potential of such multifunctional protein-derived biopolymer coatings for efficiently directing Au NP into cells and to subcellular targets to ultimately probe important cellular processes such as mitochondria dynamics and vitality inside living cells.

Optical projection tomography for rapid whole mouse brain imaging
Scientific paper

David Nguyen, Paul James Marchand, Arielle Planchette, Julia Nilsson, Miguel Sison, Extermann Jérôme, Antonio Lopez, Marcin Sylwestrzak, Jessica Sordet-Dessimoz, Anja Schmidt-Christensen, Dan Holmberg, Dimitri Van de Ville, Theo Lasser

Biomedical Optics Express, 2017 , vol.  8, pp.  5637-5650

Link to the publication

Interferometric synthetic aperture microscopy for extended focus optical coherence microscopy
Scientific paper

Séverine Coquoz, Arno Bouwens, Paul James Marchand, Extermann Jérôme, Theo Lasser

Optics Express, 2017 , vol.  25, no  30807-30819

Link to the publication

Visible spectrum extended-focus optical coherence microscopy for label-free sub-cellular tomography
Scientific paper

Paul James Marchand, Arno Bouwens, Daniel Szlag, David Nguyen, Adrien Descloux, Miguel Sison, Séverine Coquoz, Extermann Jérôme, Theo Lasser

Biomedical Optics Express, 2017 , vol.  8, pp.  3343-3359

Link to the publication

3D Time-lapse Imaging and Quantification of Mitochondrial Dynamics
Scientific paper

Miguel Sison, Sabyasachi Chakrabortty, Extermann Jérôme, Amir Nahas, Paul James Marchand, Antonio Lopez, Tanja Weil, Theo Lasser

Scientific Reports, 2017 , vol.  7, no  43275

Link to the publication

Statistical parametric mapping of stimuli evoked changes in total blood flow velocity in the mouse cortex obtained with extended-focus optical coherence microscopy
Scientific paper

Paul James Marchand, Arno Bouwens, Tristan Bolmont, Vincent Shamaei, David Nguyen, Daniel Szlag, Extermann Jérôme, Theo Lasser

Biomedical Optics Express, 2017 , vol.  8, pp.  1-15

Link to the publication

2016

Label-free fast 3D coherent imaging reveals pancreatic islet micro-vascularization and dynamic blood flow
Scientific paper ArODES

Corinne Berclaz, Daniel Szlag, David Nguyen, Jérôme Extermann, Arno Bouwens, Paul J. Marchand, Julia Nilsson, Anja Schmidt-Christensen, Dan Holmberg, Anne Grapin-Botton, Théo Lasser

Biomedical Optics Express,  2016, vol. 7, no. 11, pp. 4569-4580

Link to the publication

Summary:

In diabetes, pancreatic β-cells play a key role. These cells are clustered within structures called islets of Langerhans inside the pancreas and produce insulin, which is directly secreted into the blood stream. The dense vascularization of islets of Langerhans is critical for maintaining a proper regulation of blood glucose homeostasis and is known to be affected from the early stage of diabetes. The deep localization of these islets inside the pancreas in the abdominal cavity renders their in vivo visualization a challenging task. A fast label-free imaging method with high spatial resolution is required to study the vascular network of islets of Langerhans. Based on these requirements, we developed a label-free and three-dimensional imaging method for observing islets of Langerhans using extended-focus Fourier domain Optical Coherence Microscopy (xfOCM). In addition to structural imaging, this system provides three-dimensional vascular network imaging and dynamic blood flow information within islets of Langerhans. We propose our method to deepen the understanding of the interconnection between diabetes and the evolution of the islet vascular network.

Longitudinal three-dimensional visualisation of autoimmune diabetes by functional optical coherence imaging
Scientific paper

Corinne Berclaz, Anja Schmidt-Christensen, Daniel Szlag, Extermann Jérôme, Lisbeth Hansen, Arno Bouwens, Martin Villiger, Joan Goulley, Frans Schuit, Anne Grapin-Botton, Theo Lasser, Dan Holmberg

Diabetologia, 2016 , vol.  59, pp.  550-559

Link to the publication

Label-free fast 3d coherent imaging reveals pancreatic islet micro-vascularization and dynamic blood flow.
Scientific paper

Corinne Berclaz, Daniel Szlag, David Nguyen, Extermann Jérôme, Arno Bouwens, Paul James Marchand, Julia Nilsson, Anja Schmidt-Christiensen, Dan Holmberg, Anne Grapin-Botton, Theo Lasser

Biomedical Optics Express, 2016 , vol.  7, pp.  4569-4580

Link to the publication

2015

Longitudinal three-dimensional visualisation of autoimmune diabetes by functional optical coherence imaging
Scientific paper ArODES

Corinne Berclaz, Anja Schmidt-Christensen, Daniel Szlag, Jérôme Extermann, Lisbeth Hansen, Arno Bouwens, Martin Villiger, Joan Goulley, Frans Schuit, Anne Grapin-Botton, Theo Lasser, Dan Holmberg

Diabetologia,  2016, vol. 59, pp. 550-559

Link to the publication

Summary:

It is generally accepted that structural and functional quantitative imaging of individual islets would be beneficial to elucidate the pathogenesis of type 1 diabetes. We here introduce functional optical coherence imaging (FOCI) for fast, label-free monitoring of beta cell destruction and associated alterations of islet vascularisation. NOD mouse and human islets transplanted into the anterior chamber of the eye (ACE) were imaged with FOCI, in which the optical contrast of FOCI is based on intrinsic variations of the index of refraction resulting in a faster tomographic acquisition. In addition, the phase sensitivity allows simultaneous label-free acquisition of vascularisation. We demonstrate that FOCI allows longitudinal quantification of progressive autoimmune insulitis, including the three-dimensional quantification of beta cell volume, inflammation and vascularisation. The substantially increased backscattering of islets is dominated by the insulin–zinc nanocrystals in the beta cell granules. This translates into a high specificity for the functional beta cell volume of islets. Applying FOCI to a spontaneous mouse model of type 1 diabetes, we quantify the modifications of the pancreatic microvasculature accompanying the progression of diabetes and reveal a strong correlation between increasing insulitis and density of the vascular network of the islet. FOCI provides a novel imaging technique for investigating functional and structural diabetes-induced alterations of the islets. The label-free detection of beta cell volume and infiltration together with vascularisation offers a unique extension to study ACE-transplanted human islets. These results are contributing to a deeper understanding of human islet transplant rejection and label-free in vivo monitoring of drug efficacy.

2014

Harmonic nanoparticles for regenerative research
Scientific paper

Flavio Ronzoni, Thibaud Magouroux, Rémi Vernet, Extermann Jérôme, Darragh Crotty, Adriele Prina-Mello, Daniel Ciepielewski, Yuri Volkov, Luigi Bonacina, Jean-Pierre Wolf, Marisa Jaconi

Jove-Journal of Visualized Experiments, 2014 , vol.  87

Link to the publication

2013

Discriminability of tryptophan containing dipeptides using quantum control
Scientific paper

Svetlana Afonina, Ondrej Nenadl, Ariana Rondi, Luigi Bonacina, Extermann Jérôme, Denis Kiselev, Igor Dolamic, Thomas Burgi, Jean-Pierre Wolf

Applied Physics B, 2013 , vol.  111, pp.  541-549

Link to the publication

2012

Harmonic nanocrystals for biolabeling: A survey of optical properties and biocompatibility.
Scientific paper

Davide Staedler, Thibaud Magouroux, Rachid Hadji, Cécile Joulaud, Extermann Jérôme, Sébastien Schwung, Solène Passemard, Christelle Kasparian, Gareth Clarke, Matthias Gerrmann, Ronan Le Dantec, Yannick Mugnier, Daniel Rytz, Daniel Ciepielewski, Christine Galez, Sandrine Gerber-Lemaire, Lucienne Juillerat-Jeanneret, Luigi Bonacina, Jean-Pierre Wolf

Acs Nano, 2012 , vol.  6, pp.  2542-2549

Link to the publication

High-speed tracking of murine cardiac stem cells by harmonic nanodoublers
Scientific paper

Thibaud Magouroux, Extermann Jérôme, Pernilla Hoffmann, Yannick Mugnier, Ronan Le Dantec, Marisa Jaconi, Christelle Kasparian, Daniel Ciepielewski, Luigi Bonacina, Jean-Pierre Wolf

Small, 2012 , vol.  8, pp.  2752-2756

Link to the publication

2011

Spectral phase, amplitude, and spatial modulation from ultraviolet to infrared with a reflective MEMS pulse shaper
Scientific paper

Extermann Jérôme, Stefan Martin Weber, Denis Kiselev, Luigi Bonacina, Sébastien Lani, Fabio Jutzi, Wilfried Noell, Nico de Rooij, Jean-Pierre Wolf

Optics Express, 2011 , vol.  19, pp.  7580-7586

Link to the publication

Design, simulation, fabrication, packaging, and characterization of a mems-based mirror array for femtosecond pulse-shaping in phase and amplitude
Scientific paper

Stefan Martin Weber, Luigi Bonacina, Wilfried Noell, Denis Kiselev, Extermann Jérôme, Fabio Jutzi, Sébastien Lani, Ondrej Nenadl, Jean-Pierre Wolf, Nico de Rooij

Review of Scientific Instruments, 2011 , vol.  82, no  075106

Link to the publication

Ensemble and individual characterization of the nonlinear optical properties of zno and batio3 nanocrystals.
Scientific paper

Ronan Le Dantec, Yannick Mugnier, Gnon Djanta, Luigi Bonacina, Extermann Jérôme, Laurent Badie, Cécile Joulaud, Matthias Gerrmann, Daniel Rytz, Jean-Pierre Wolf, Christine Galez

J. Phys. Chem. C, 2011 , vol.  115, no  15140-15146

Link to the publication

Discriminating biomolecules with coherent control strategies
Scientific paper

Ariana Rondi, Denis Kiselev, Sarah Machado, Extermann Jérôme, Stefan Martin Weber, Luigi Bonacina, Jean-Pierre Wolf, Jonathan Roslund, Matthias Roth, Herschel Rabitz

Chimia, 2011 , vol.  65, pp.  346-349

Link to the publication

2010

Ultraviolet and near-infrared femtosecond temporal pulse shaping with a new high-aspect-ratio one-dimensional micromirror array
Scientific paper

Stefan Martin Weber, Extermann Jérôme, Luigi Bonacina, Wilfried Noell, Denis Kiselev, Severin Waldis, Nico de Rooij, Jean-Pierre Wolf

Optics Letters, 2010 , vol.  35, no  3102–3104

Link to the publication

Evanescent-field-induced second harmonic generation by noncentrosymmetric nanoparticles.
Scientific paper

Ronja Baumer, Luigi Bonacina, Jörg Enderlein, Extermann Jérôme, Thomas Fricke-Begemann, Gerd Marowsky, Jean-Pierre Wolf

Optics Express, 2010 , vol.  18, no  23218–23225

Link to the publication

2009

Nanodoublers as deep imaging markers for multi-photon microscopy
Scientific paper

Extermann Jérôme, Luigi Bonacina, Enrique Cuna, Christelle Kasparian, Yannick Mugnier, Thomas Feurer, Jean-Pierre Wolf

Optics Express, 2009 , vol.  17, no  15342–15349

Link to the publication

An inexpensive nonlinear medium for intense ultrabroadband pulse characterization
Scientific paper

Extermann Jérôme, Pierre Bejot, Luigi Bonacina, Yannick Mugnier, Ronan Le Dantec, Thomas Mazingue, Christine Galez, Jean-Pierre Wolf

Applied Physics B, 2009 , vol.  97, pp.  537-540

Link to the publication

Characterization of a mems-based pulse-shaping device in the deep ultraviolet
Scientific paper

Ariana Rondi, Extermann Jérôme, Luigi Bonacina, Stefan Martin Weber, Jean-Pierre Wolf

Applied Physics B, 2009 , vol.  96, pp.  537-540

Link to the publication

2008

Identification of biological microparticles using ultrafast depletion spectroscopy.
Scientific paper

François Courvoisier, Luigi Bonacina, Véronique Boutou, Vincent Guyon, Christophe Bonnet, Benoît Thuillier, Extermann Jérôme, Matthias Roth, Herschel Rabitz, Jean-Pierre Wolf

Faraday Discussions, 2008 , vol.  137, pp.  37-49

Link to the publication

Effects of atmospheric turbulence on remote optimal control experiments
Scientific paper

Extermann Jérôme, Pierre Béjot, Luigi Bonacina, Pierre Billaud, Jérôme Kasparian, Jean-Pierre Wolf

Applied Physics Letters, 2008 , vol.  92, no  041103

Link to the publication

Nano-FROG: Frequency resolved optical gating by a nanometric object
Scientific paper

Extermann Jérôme, Luigi Bonacina, François Courvoisier, Denis Kiselev, Yanninck Mugnier, Ronan Le Dantec, Christine Galez, Jean-Pierre Wolf

Optics Express, 2008 , vol.  16, no  10405-10411

Link to the publication

2007

32 TW atmospheric white-light laser
Scientific paper

Pierre Béjot, Luigi Bonacina, Extermann Jérôme, Michel Moret, Jean-Pierre Wolf, Roland Ackermann, Noelle Lascoux, Rami Salamé, Estelle Salmon, Jérôme Kasparian, Luc Bergé, Stéphanie Champeaux, Claude Guet

Applied Physics Letters, 2007 , vol.  90, no  151106, pp.  1-3

Link to the publication

Polar Fe(IO3)(3) nanocrystals as local probes for nonlinear microscopy
Scientific paper

Luigi Bonacina, Yannick Mugnier, François Courvoisier, Ronan Le Dantec, Extermann Jérôme, Yannick Lambert, Véronique Boutou, Christine Galez, Jean-Pierre Wolf

Applied Physics B-Lasers and Optics, 2007 , vol.  87, no  3, pp.  399-403

Link to the publication

Multiobjective genetic approach for optimal control of photoinduced processes
Scientific paper

Luigi Bonacina, Extermann Jérôme, Ariana Rondi, Véronique Boutou, Jean-Pierre Wolf

Physical Review A, 2007 , vol.  76, no  023408

Link to the publication

2021

Quantifying the effect of image compression on upervised learning tasks in microscopy
Conference ArODES

Enrico Pomarico, Cédric Schmidt, D. Nguyen, A. Planchette, Adrien Roux, S. Pagès, L. Batti, C. Clausen, T, Lasser, A. Radenovic, B. Sanguinetti, Jérôme Extermann

Proceedings of Focus on Microscopy 2021, Online Conference, 28-31 March 2021

Link to the conference

Optical projection tomography platform optimized for the gastrointestinal research
Conference ArODES

Cédric Schmidt, Arielle L. Planchette, David Nguyen, Gabriel Giardina, Yoan Neuenschwander, Alessio Mylonas, Adrien Descloux, Enrico Pomarico, Aleksandra Radenovic, Jérôme Extermann

Proceedings of Focus on Microscopy 2021, 28-31 March 2021, Online Conference

Link to the conference

Optical Projection Tomography Platform Optimized for the Gastrointestinal Research
Conference

Schmidt Cédric, Arielle L Planchette, David Nguyen, Gabriel Giardina, Neuenschwander Yoan, Alessio Mylonas, Adrien Descloux, Pomarico Enrico, Aleksandra Radenovic, Extermann Jérôme

Focus on Microscopy, 28.02.2021 - 31.03.2021, Online

Summary:

We present a fluorescent OPT platform optimized for the mesoscale imaging of the mouse gut at multiple wavelengths. In particular, we demonstrate a sub-30 μm resolution along the 3 dimensions and over more than 60 mm3 in a single acquisition. Here, we observe the spatial arrangement of the intestinal villi and the vasculature network penetrating until the extremity of the villi. We believe our approach to be of high potential for gastrointestinal pathology research.

2020

Unchaining hyperspectral imaging with quantum-inspired compression (UHIQIC)
Conference ArODES

Christoph Clausen, Bruno Sanguinetto, Yosef Akhtman, Enrico Pomarico, Jérôme Extermann

Proceedings of ATTRACT Online Conference "Igniting the Deep Tech Revolution", 22 September 2020, Online

Link to the conference

Summary:

With hyperspectral imaging, image content can be identified based on fine spectral details related to chemical composition. Immediate applications in smart agriculture and environmental monitoring have the potential for strong societal benefits. However, the technology struggles with the vast amount of data that it produces, in particular when deployed on satellites. The current movement towards increased use of lossy compression is highly risky, because even careful and tedious parameter tuning cannot guarantee that no applications are compromised. We implemented and validated a compression method that simultaneously provides a strong data reduction and preserves analysis results for all possible applications.

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