Insight into the fundamental trade-offs of diffusion MRI from polarization-sensitive optical coherence tomography in ex vivo human brain

In the first study comparing high angular resolution diffusion MRI (dMRI) in the human brain to axonal orientation measurements from polarization-sensitive optical coherence tomography (PSOCT), we compare the accuracy of orientation estimates from various dMRI sampling schemes and reconstruction methods. We find that, if the reconstruction approach is chosen carefully, single-shell dMRI data can yield the same accuracy as multi-shell data, and only moderately lower accuracy than a full Cartesian-grid sampling scheme. Our results suggest that current dMRI reconstruction approaches do not benefit substantially from ultra-high b-values or from very large numbers of diffusion-encoding directions. We also show that accuracy remains stable across dMRI voxel sizes of 1 ​mm or smaller but degrades at 2 ​mm, particularly in areas of complex white-matter architecture. We also show that, as the spatial resolution is reduced, axonal configurations in a dMRI voxel can no longer be modeled as a small set of distinct axon populations, violating an assumption that is sometimes made by dMRI reconstruction techniques. Our findings have implications for in vivo studies and illustrate the value of PSOCT as a source of ground-truth measurements of white-matter organization that does not suffer from the distortions typical of histological techniques.Published versio

Colocalization of neurons in optical coherence microscopy and Nissl-stained histology in Brodmann’s area 32 and area 21

Published in final edited form as: Brain Struct Funct. 2019 January ; 224(1): 351–362. doi:10.1007/s00429-018-1777-z.Optical coherence tomography is an optical technique that uses backscattered light to highlight intrinsic structure, and when applied to brain tissue, it can resolve cortical layers and fiber bundles. Optical coherence microscopy (OCM) is higher resolution (i.e., 1.25 µm) and is capable of detecting neurons. In a previous report, we compared the correspondence of OCM acquired imaging of neurons with traditional Nissl stained histology in entorhinal cortex layer II. In the current method-oriented study, we aimed to determine the colocalization success rate between OCM and Nissl in other brain cortical areas with different laminar arrangements and cell packing density. We focused on two additional cortical areas: medial prefrontal, pre-genual Brodmann area (BA) 32 and lateral temporal BA 21. We present the data as colocalization matrices and as quantitative percentages. The overall average colocalization in OCM compared to Nissl was 67% for BA 32 (47% for Nissl colocalization) and 60% for BA 21 (52% for Nissl colocalization), but with a large variability across cases and layers. One source of variability and confounds could be ascribed to an obscuring effect from large and dense intracortical fiber bundles. Other technical challenges, including obstacles inherent to human brain tissue, are discussed. Despite limitations, OCM is a promising semi-high throughput tool for demonstrating detail at the neuronal level, and, with further development, has distinct potential for the automatic acquisition of large databases as are required for the human brain.Accepted manuscrip

Modélisation de la couleur de la peau et sa représentation dans les œuvres d'art

In a first step, we are interested in the skin color modeling. The skin is a multilayer structure, containing various scatterers. The interaction of light in such a matter is modeled by the radiative transfer equation, solved by the auxiliary function method. The necessary optical properties of the scatterers are either determined by Mie theory or found in the literature. An optical model is developed and validated by diffuse reflection spectra measured on real skin. The influence of the physiological parameters is then studied. Finally, the problem is inversed and these physiological parameters are determined from a measured spectrum. In a second step, we are interested in complexion in the western easel paintings. A literature review and experimental works on real paintings reveals similarities between complexion in art and real skin. They also show that the pigments have changed little over the centuries, unlike the pictorial techniques (characterized primarily by the binder). The influence of the binders on the visual appearance of paintings, meaning the gloss (surface scattering) and the color (volume scattering), is studied experimentally on samples made with 5 binders and 4 pigments. We discriminate three types of binders: aqueous binders, egg tempera and safflower oil. The gloss comes primarily from the evaporation rate of the solvent and the color comes mainly from the refractive indices of the binders. These findings may be slightly modified according to the pigments.Dans un premier temps, nous nous intéressons à la modélisation de la couleur de la peau. Cette dernière est une structure multicouche, chacune contenant des centres diffuseurs de différentes tailles. L'interaction lumière/matière dans un tel milieu est modélisée par l'équation de transfert radiatif, résolue par la méthode de la fonction auxiliaire. Les propriétés optiques des centres diffuseurs sont soient déterminées par la théorie de Mie, soient trouvées dans la littérature. Un modèle optique est développé et validé par des spectres de réflexion diffuse mesurés sur des peaux réelles. L'influence des paramètres physiologiques est ensuite étudiée. Enfin, le problème est inversé et ces paramètres physiologiques sont déterminés à partir d'un spectre mesuré. Dans un second temps, nous nous intéressons aux carnations dans les peintures de chevalet occidentales. Une étude bibliographique et expérimentale sur de vraies œuvres révèle des similitudes entre les carnations et la peau réelle. Il en ressort aussi que les pigments ont peu changé au cours des siècles, contrairement aux techniques picturales (caractérisées principalement par le liant). L'influence des liants sur l'aspect visuel des peintures, c'est-à-dire la brillance (diffusion de surface) et la couleur (diffusion de volume), est étudiée expérimentalement sur des échantillons, réalisés avec 5 liants et 4 pigments. On discrimine trois types de liants: les liants aqueux, la tempera à l'œuf et l'huile de carthame. La brillance vient principalement du taux d'évaporation du solvant des liants et la couleur provient principalement des indices de réfraction des liants. Ces conclusions peuvent être légèrement modifiées selon les pigments

Modélisation de la couleur de la peau et sa représentation dans les œuvres d'art

Tout d abord, nous nous intéressons à la modélisation de la couleur de la peau, structure multicouche contenant des centres diffuseurs de différentes tailles. L'interaction lumière/matière dans un tel milieu est modélisée par l'équation de transfert radiatif, résolue par la méthode de la fonction auxiliaire. Les propriétés optiques des centres diffuseurs sont déterminées par la théorie de Mie ou trouvées dans la littérature. Un modèle est développé et validé par des spectres de réflexion mesurés sur des peaux réelles. L'influence des paramètres physiologiques est ensuite étudiée. Enfin, le problème est inversé et ces paramètres sont déterminés à partir d'un spectre mesuré. Puis, nous nous intéressons aux carnations des œuvres d art. Une étude bibliographique et expérimentale sur de vraies œuvres révèle des similitudes entre les carnations et la peau réelle. Les pigments ont peu changé au cours des siècles, contrairement aux techniques picturales. L'influence des liants sur la brillance et la couleur des peintures est étudiée expérimentalement sur des échantillons tests. On discrimine 3 types de liants: les liants aqueux, la tempera à l'œuf et l'huile de carthame. Ces différences proviennent du taux d'évaporation du solvant et des indices de réfraction des liants.PARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

Characterizing the optical properties of human brain tissue with high numerical aperture optical coherence tomography

Quantification of tissue optical properties with optical coherence tomography (OCT) has proven to be useful in evaluating structural characteristics and pathological changes. Previous studies primarily used an exponential model to analyze low numerical aperture (NA) OCT measurements and obtain the total attenuation coefficient for biological tissue. In this study, we develop a systematic method that includes the confocal parameter for modeling the depth profiles of high NA OCT, when the confocal parameter cannot be ignored. This approach enables us to quantify tissue optical properties with higher lateral resolution. The model parameter predictions for the scattering coefficients were tested with calibrated microsphere phantoms. The application of the model to human brain tissue demonstrates that the scattering and back-scattering coefficients each provide unique information, allowing us to differentially identify laminar structures in primary visual cortex and distinguish various nuclei in the midbrain. The combination of the two optical properties greatly enhances the power of OCT to distinguish intricate structures in the human brain beyond what is achievable with measured OCT intensity information alone, and therefore has the potential to enable objective evaluation of normal brain structure as well as pathological conditions in brain diseases. These results represent a promising step for enabling the quantification of tissue optical properties from high NA OCT.P01 NS055104 - NINDS NIH HHS; R01 NS091230 - NINDS NIH HHS; S10 RR029050 - NCRR NIH HHShttps://www.ncbi.nlm.nih.gov/pubmed/29296492Published versio

Holographic laser Doppler ophthalmoscopy

International audienceWe report laser Doppler ophthalmoscopic fundus imaging in the rat eye with near-IR heterodyne holography. Sequential sampling of the beat of the reflected radiation against a frequency-shifted optical local oscillator is made onto an array detector. Wide-field maps of fluctuation spectra in the 10 Hz to 25 kHz band exhibit angiographic contrasts in the retinal vascular tree without requirement of an exogenous marker

Colocalization of neurons in optical coherence microscopy and Nissl-stained histology in Brodmann’s area 32 and area 21

Optical coherence tomography is an optical technique that uses backscattered light to highlight intrinsic structure, and when applied to brain tissue, it can resolve cortical layers and fiber bundles. Optical coherence microscopy (OCM) is higher resolution (i.e., 1.25 µm) and is capable of detecting neurons. In a previous report, we compared the correspondence of OCM acquired imaging of neurons with traditional Nissl stained histology in entorhinal cortex layer II. In the current method-oriented study, we aimed to determine the colocalization success rate between OCM and Nissl in other brain cortical areas with different laminar arrangements and cell packing density. We focused on two additional cortical areas: medial prefrontal, pre-genual Brodmann area (BA) 32 and lateral temporal BA 21. We present the data as colocalization matrices and as quantitative percentages. The overall average colocalization in OCM compared to Nissl was 67% for BA 32 (47% for Nissl colocalization) and 60% for BA 21 (52% for Nissl colocalization), but with a large variability across cases and layers. One source of variability and confounds could be ascribed to an obscuring effect from large and dense intracortical fiber bundles. Other technical challenges, including obstacles inherent to human brain tissue, are discussed. Despite limitations, OCM is a promising semi-high throughput tool for demonstrating detail at the neuronal level, and, with further development, has distinct potential for the automatic acquisition of large databases as are required for the human brain.National Institute of Mental Health (Grant MH107456)National Institute for Biomedical Imaging and Bioengineering (Grant P41EB015896, 1R01EB023281, R01EB006758, R21EB018907, R01EB019956)National Institute on Aging (Grant 5R01AG008122, R01AG016495)National Institute of Diabetes and Digestive and Kidney Diseases (Grant 1-R21-DK-108277-01)National Institute for Neurological Disorders and Stroke (Grant R01NS0525851, R21NS072652, R01NS070963, R01NS083534, 5U01NS086625)NIH Blueprint for Neuroscience Research (Grant 5U01-MH093765)NIH Shared Instrumentation (Grants 1S10RR023401, 1S10RR019307, 1S10RR023043

as-PSOCT: Volumetric microscopic imaging of human brain architecture and connectivity.

Published in final edited form as: Neuroimage. 2018 January 15; 165: 56–68. doi:10.1016/j.neuroimage.2017.10.012.Polarization sensitive optical coherence tomography (PSOCT) with serial sectioning has enabled the investigation of 3D structures in mouse and human brain tissue samples. By using intrinsic optical properties of back-scattering and birefringence, PSOCT reliably images cytoarchitecture, myeloarchitecture and fiber orientations. In this study, we developed a fully automatic serial sectioning polarization sensitive optical coherence tomography (as-PSOCT) system to enable volumetric reconstruction of human brain samples with unprecedented sample size and resolution. The 3.5 μm in-plane resolution and 50 μm through-plane voxel size allow inspection of cortical layers that are a single-cell in width, as well as small crossing fibers. We show the abilities of as-PSOCT in quantifying layer thicknesses of the cerebellar cortex and creating microscopic tractography of intricate fiber networks in the subcortical nuclei and internal capsule regions, all based on volumetric reconstructions. as-PSOCT provides a viable tool for studying quantitative cytoarchitecture and myeloarchitecture and mapping connectivity with microscopic resolution in the human brain.U01 MH093765 - NIMH NIH HHS; R01 NS070963 - NINDS NIH HHS; U01 NS086625 - NINDS NIH HHS; R21 EB018907 - NIBIB NIH HHS; R01 AG016495 - NIA NIH HHS; S10 RR019307 - NCRR NIH HHS; R01 NS052585 - NINDS NIH HHS; R01 AG008122 - NIA NIH HHS; R01 AG049899 - NIA NIH HHS; R01 EB019956 - NIBIB NIH HHS; R21 NS072652 - NINDS NIH HHS; P01 NS055104 - NINDS NIH HHS; S10 RR023043 - NCRR NIH HHS; K01 DK101631 - NIDDK NIH HHS; R01 EB006758 - NIBIB NIH HHS; P41 EB015896 - NIBIB NIH HHS; R01 NS083534 - NINDS NIH HHS; S10 RR023401 - NCRR NIH HHShttps://www.ncbi.nlm.nih.gov/pubmed/29017866https://www.ncbi.nlm.nih.gov/pubmed/29017866Accepted manuscrip

Holographic laser Doppler imaging of microvascular blood flow

International audienceWe report on local superficial blood flow monitoring in biological tissue from laser Doppler holographic imaging. In time-averaging recording conditions, holography acts as a narrowband bandpass filter, which, combined with a frequency-shifted reference beam, permits frequency-selective imaging in the radiofrequency range. These Doppler images are acquired with an off-axis Mach–Zehnder interferometer. Microvascular hemodynamic components mapping is performed in the cerebral cortex of the mouse and the eye fundus of the rat with near-infrared laser light without any exogenous marker. These measures are made from a basic inverse-method analysis of local first-order optical fluctuation spectra at low radiofrequencies, from 0 Hz to 100 kHz. Local quadratic velocity is derived from Doppler broadenings induced by fluid flows, with elementary diffusing wave spectroscopy formalism in backscattering configuration. We demonstrate quadratic mean velocity assessment in the 0.1-10 mm/s range in vitro and imaging of superficial blood perfusion with a spatial resolution of about 10 micrometers in rodent models of cortical and retinal blood flow

Improving the characterization of ex vivo human brain optical properties using high numerical aperture optical coherence tomography by spatially constraining the confocal parameters

SIGNIFICANCE: The optical properties of biological samples provide information about the structural characteristics of the tissue and any changes arising from pathological conditions. Optical coherence tomography (OCT) has proven to be capable of extracting tissue's optical properties using a model that combines the exponential decay due to tissue scattering and the axial point spread function that arises from the confocal nature of the detection system, particularly for higher numerical aperture (NA) measurements. A weakness in estimating the optical properties is the inter-parameter cross-talk between tissue scattering and the confocal parameters defined by the Rayleigh range and the focus depth. AIM: In this study, we develop a systematic method to improve the characterization of optical properties with high-NA OCT. APPROACH: We developed a method that spatially parameterizes the confocal parameters in a previously established model for estimating the optical properties from the depth profiles of high-NA OCT. RESULTS: The proposed parametrization model was first evaluated on a set of intralipid phantoms and then validated using a low-NA objective in which cross-talk from the confocal parameters is negligible. We then utilize our spatially parameterized model to characterize optical property changes introduced by a tissue index matching process using a simple immersion agent, 2,2'-thiodiethonal. CONCLUSIONS: Our approach improves the confidence of parameter estimation by reducing the degrees of freedom in the non-linear fitting model.Published versio