Opening the black box of traumatic brain injury: a holistic approach combining human 3D neural tissue and an traumatic brain injury induction device.

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 and animal-based 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.

Optical imaging of the small intestine immune compartment across scales.

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.

Artifacts in optical projection tomography due to refractive-index mismatch: model and correction.

Optical projection tomography (OPT) is a powerful tool for three-dimensional (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.

Distributed temperature sensor combining centimeter resolution with hundreds of meters sensing range.

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.

Statistical distortion of supervised learning predictions in optical microscopy induced by image compression.

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.

High resolution optical projection tomography platform for multispectral imaging of the mouse gut.

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 mm after reconstruction of a single acquisition.

Imaging of cortical structures and microvasculature using extended-focus optical coherence tomography at 1.3 μm.

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.

Optical projection tomography for rapid whole mouse brain imaging.

In recent years, three-dimensional mesoscopic imaging has gained significant importance in life sciences for fundamental studies at the whole-organ level. In this manuscript, we present an optical projection tomography (OPT) method designed for imaging of the intact mouse brain. The system features an isotropic resolution of ~50 µm and an acquisition time of four to eight minutes, using a 3-day optimized clearing protocol.

Interferometric synthetic aperture microscopy for extended focus optical coherence microscopy.

Optical coherence microscopy (OCM) is an interferometric technique providing 3D images of biological samples with micrometric resolution and penetration depth of several hundreds of micrometers. OCM differs from optical coherence tomography (OCT) in that it uses a high numerical aperture (NA) objective to achieve high lateral resolution. However, the high NA also reduces the depth-of-field (DOF), scaling with 1/NA.

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

We present a novel extended-focus optical coherence microscope (OCM) attaining 0.7 μm axial and 0.4 μm lateral resolution maintained over a depth of 40 μm, while preserving the advantages of Fourier domain OCM.

NIR-emitting and photo-thermal active nanogold as mitochondria-specific probes.

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.

3D Time-lapse Imaging and Quantification of Mitochondrial Dynamics.

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.

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

Functional magnetic resonance (fMRI) imaging is the current gold-standard in neuroimaging. fMRI exploits local changes in blood oxygenation to map neuronal activity over the entire brain. However, its spatial resolution is currently limited to a few hundreds of microns.

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

In diabetes, pancreatic -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.

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

Aims/hypothesis: 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.

Methods: 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.

Harmonic nanoparticles for regenerative research.

In this visualized experiment, protocol details are provided for in vitro labeling of human embryonic stem cells (hESC) with second harmonic generation nanoparticles (HNPs). The latter are a new family of probes recently introduced for labeling biological samples for multi-photon imaging. HNPs are capable of doubling the frequency of excitation light by the nonlinear optical process of second harmonic generation with no restriction on the excitation wavelength.

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

Potassium niobate nonlinear nanoparticles are used for the first time to monitor the evolution of embryonic stem cells (ESC) by second harmonic microscopy. These particles feature the complete absence of photo-bleaching and unlimited excitation wavelength flexibility. The potential of this approach is made evident for tissue-regeneration studies and applications, by capturing a high-speed movie of ESC-derived cardiomyocytes autonomously beating within a cluster.

Harmonic nanocrystals for biolabeling: a survey of optical properties and biocompatibility.

Nonlinear optical nanocrystals have been recently introduced as a promising alternative to fluorescent probes for multiphoton microscopy. We present for the first time a complete survey of the properties of five nanomaterials (KNbO(3), LiNbO(3), BaTiO(3), KTP, and ZnO), describing their preparation and stabilization and providing quantitative estimations of their nonlinear optical response. In the light of their prospective use as biological and clinical markers, we assess their biocompatibility on human healthy and cancerous cell lines.

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

We present an in-detail description of the design, simulation, fabrication, and packaging of a linear micromirror array specifically designed for temporal pulse shaping of ultrashort laser pulses. The innovative features of this device include a novel comb-drive actuator allowing both piston and tilt motion for phase- and amplitude-shaping, and an X-shaped laterally reinforced spring preventing lateral snap-in while providing high flexibility for both degrees of freedom.

Discriminating biomolecules with coherent control strategies.

The activity of the GAP-Biophotonics research group at the University of Geneva in the field of coherent control for discriminating similar biomolecules, such as flavins, proteins and DNA bases, is presented and future developments are discussed.

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

We describe the performance of a reflective pulse-shaper based on a Micro-ElectroMechanical System (MEMS) linear mirror array. It represents a substantial upgrade of a preceding release [Opt. Lett.

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

We demonstrate the excitation of second harmonic radiation of noncentrosymmetric nanoparticles dispersed on a planar optical waveguide by the evanescent field of the guided mode. Polarization imaging reveals information on the orientation of the crystal axis of individual nanoparticles. Interference patterns generated from adjacent particles at the second harmonic frequency are--to the authors knowledge--observed for the first time.

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

We demonstrate the capabilities of a new optical microelectromechanical systems device that we specifically developed for broadband femtosecond pulse shaping. It consists of a one-dimensional array of 100 independently addressable, high-aspect-ratio micromirrors with up to 3 μm stroke. We apply linear and quadratic phase modulations demonstrating the temporal compression of 800 and 400 nm pulses.

Nanodoublers as deep imaging markers for multi-photon microscopy.

We demonstrate the possibility to excite second-harmonic (SH) active Fe(IO(3))(3) nanocrystals with two distinct laser sources at 800 and 1550 nm, and we show, by a complementary experimental and numerical study, how the wavelength flexibility inherent to non-phase-matched SH nanoparticles can be efficiently exploited to increase imaging penetration depth of markers embedded in biological samples.