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The adoption of emerging imaging technologies in the medical community is often hampered if they provide a new unfamiliar contrast that requires experience to be interpreted. Here, in order to facilitate such integration, we developed two complementary machine learning approaches, respectively based on feature engineering and on convolutional neural networks (CNN), to perform automatic diagnosis of breast biopsies using dynamic full field optical coherence tomography (D-FF-OCT) microscopy. This new technique provides fast, high resolution images of biopsies with a contrast similar to H&E histology, but without any tissue preparation and alteration. We conducted a pilot study on 51 breast biopsies, and more than 1,000 individual images, and performed standard histology to obtain each biopsy diagnosis. Using our automatic diagnosis algorithms, we obtained an accuracy above 88% at the image level, and above 96% at the biopsy level. Finally, we proposed different strategies to narrow down the spatial scale of the automatic segmentation in order to be able to draw the tumor margins by drawing attention maps with the CNN approach, or by performing high resolution precise annotation of the datasets. Altogether, these results demonstrate the high potential of D-FF-OCT coupled to machine learning to provide a rapid, automatic, and accurate histopathology diagnosis.

Viruses can affect all life forms, raising concerns about virus detection and quantification of small nanoparticles. In this paper we use a label-free, full-field, incoherently illuminated common path interferometric method to detect, track, and quantify biotic nanoparticles. The detection consists of amplifying the light scattered by single nanoparticles in the sample solution. Then, the use of single-particle tracking analysis is used to monitor the change in particle diffusive mobility. With this approach, the recognition signature of T5 phages with purified antibodies targeting the major capsid protein is detected in a few minutes. We also tracked the interaction between SPP1 phages and physiological non-purified serum-containing multiples antibodies molecules. The first interactions occur after around one minute, and the recognition signature is detectable after minutes. In addition, we have been able to differentiate two populations of similar size of empty and full (encapsulating DNA) capsids of T5 in a heterogeneous solution demonstrating the robustness of this label-free detection approach. Furthermore, by combining the diffusion coefficient to the number of tracked particles, we were able to estimate the affinity of the virus-antibodies reaction.

Histopathology and microscopic examination of infected tissue are the gold standards to prove the diagnosis of invasive fungal infection (IFI). Yet, they suffer from essential limitations that hamper rapid diagnosis and require the future development of new imaging tools dedicated to fungal diagnostics. To this end, the present work introduces the first use of dynamic full-field optical coherence tomography (D-FF-OCT) for the visualization of microscopic filamentous fungi. Data collected from the observation of three different fungal species (Nannizzia gypsea, Aspergillus fumigatus and Rhizopus arrhizus) confirm the ability of D-FF-OCT to visualize not only the main structures of all selected fungal species (hyphae, spores, conidia, sporulating structures), but also the metabolic activity of the organisms, which could provide additional help in the future to better characterize the signature of each fungal structure. These results demonstrate how D-FF-OCT could serve as potential complementary tool for rapid diagnosis of IFI in both intensive and non-intensive care units.

International audience; Eye movements are commonly seen as an obstacle to high-resolution ophthalmic imaging. In this context we study the natural axial movements of the in vivo human eye and show that they can be used to modulate the optical phase and retrieve tomographic images via time-domain full-field optical coherence tomography (TD-FF-OCT). This approach opens a path to a simplified ophthalmic TD-FF-OCT device, operating without the usual piezo motor-camera synchronization. The device demonstrates in vivo human corneal images under the different image retrieval schemes (2-phase and 4-phase) and different exposure times (3.5 ms, 10 ms, 20 ms). Data on eye movements, acquired with a spectral-domain OCT with axial eye tracking (180 B-scans/s), are used to study the influence of ocular motion on the probability of capturing high-signal tomographic images without phase washout. The optimal combinations of camera acquisition speed and amplitude of piezo modulation are proposed and discussed.

We present a novel method that can assay cellular viability in real-time using supervised machine learning and intracellular dynamic activity data that is acquired in a label-free, non-invasive, and non-destructive manner. Cell viability can be an indicator for cytology, treatment, and diagnosis of diseases. We applied four supervised machine learning models on the observed data and compared the results with a trypan blue assay. The cell death assay performance by the four supervised models had a balanced accuracy of 93.92 ± 0.86%. Unlike staining techniques, where criteria for determining viability of cells is unclear, cell viability assessment using machine learning could be clearly quantified.

Ocular imaging plays an irreplaceable role in the evaluation of eye diseases. Developing cellular-resolution ophthalmic imaging technique for more accurate and effective diagnosis and pathogenesis analysis of ocular diseases is a hot topic in the cross-cutting areas of ophthalmology and imaging. Currently, ocular imaging with traditional optical coherence tomography (OCT) is limited in lateral resolution and thus can hardly resolve cellular structures. Conventional OCT technology obtains ultra-high resolution at the expense of a certain imaging range and cannot achieve full field of view imaging. In the early years, Time-domain full-field OCT (TD-FF-OCT) has been mainly used for ex vivo ophthalmic tissue studies, limited by the low speed and low full-well capacity of existing two-dimensional (2D) cameras. The recent improvements in system design opened new imaging possibilities for in vivo applications thanks to its distinctive optical properties of TD-FF-OCT such as a spatial resolution almost insensitive to aberrations, and the possibility to control the curvature of the optical slice. This review also attempts to look at the future directions of TD-FF-OCT evolution, for example, the potential transfer of the functional-imaging dynamic TD-FF-OCT from the ex vivo into in vivo use and its expected benefit in basic and clinical ophthalmic research. Through non-invasive, wide-field, and cellular-resolution imaging, TD-FF-OCT has great potential to be the next-generation imaging modality to improve our understanding of human eye physiology and pathology.

Retinal degenerative diseases lead to the blindness of millions of people around the world. In case of age-related macular degeneration (AMD), the atrophy of retinal pigment epithelium (RPE) precedes neural dystrophy. But as crucial as understanding both healthy and pathological RPE cell physiology is for those diseases, no current technique allows subcellular in vivo or in vitro live observation of this critical cell layer. To fill this gap, we propose dynamic full-field OCT (D-FFOCT) as a candidate for live observation of in vitro RPE phenotype. In this way, we monitored primary porcine and human stem cell-derived RPE cells in stress model conditions by performing scratch assays. In this study, we quantified wound healing parameters on the stressed RPE, and observed different cell phenotypes, displayed by the D-FFOCT signal. In order to decipher the subcellular contributions to these dynamic profiles, we performed immunohistochemistry to identify which organelles generate the signal and found mitochondria to be the main contributor to D-FFOCT contrast. Altogether, D-FFOCT appears to be an innovative method to follow degenerative disease evolution and could be an appreciated method in the future for live patient diagnostics and to direct treatment choice.

Dynamic full-field optical coherence microscopy (DFFOCM) was used to characterize the intracellular dynamic activities and cytoskeleton of HeLa cells in different viability states. HeLa cell samples were continuously monitored for 24 hours and compared with histological examination to confirm the cell viability states. The averaged mean frequency and magnitude observed in healthy cells were 4.79±0.5 Hz and 2.44±1.06, respectively. In dead cells, the averaged mean frequency was shifted to 8.57±0.71 Hz, whereas the magnitude was significantly decreased to 0.53±0.25. This cell dynamic activity analysis using DFFOCM is expected to replace conventional time-consuming and biopsies-required histological or biochemical methods.

We report on a theoretical model for image formation in full-field optical coherence tomography (FFOCT). Because the spatial incoherence of the illumination acts as a virtual confocal pinhole in FFOCT, its imaging performance is equivalent to a scanning time-gated coherent confocal microscope. In agreement with optical experiments enabling a precise control of aberrations, FFOCT is shown to have nearly twice the resolution of standard imaging at moderate aberration level. Beyond a rigorous study on the sensitivity of FFOCT with respect to aberrations, this theoretical model paves the way towards an optimized design of adaptive optics and \rev{computational tools} for high-resolution and deep imaging of biological tissues., Comment: 23 pages, 10 figures

State-of-the-art adaptive optics optical coherence tomography (AO-OCT) presents important limitations, such as small field-of-view (FOV) and require complex, cumbersome hardware, preventing wide clinical deployment. Here, we introduce adaptive-glasses full-field OCT (FFOCT), a compact retinal imaging system allying high resolution, high frame rate (300Hz) and 5° FOV (footprint: 50 cm × 30 cm).

La tomographie par cohérence optique, plus communément appelée par son acronyme anglais OCT (optical coherence tomography), est une technique d’imagerie non invasive des milieux biologiques, à résolution micrométrique, dont l’impact le plus remarquable concerne l’ophtalmologie. L’OCT « plein champ » est une approche originale de l’OCT, inventée par les auteurs de cet article, qui est désormais disponible commercialement. Après avoir exposé le principe de l’OCT plein champ, nous détaillerons ses performances en soulignant les avantages et les inconvénients par rapport à l’OCT classique. Les potentialités de cette technique seront illustrées par quelques exemples d’applications dans les domaines de l’embryologie, la biologie du développement, l’ophtalmologie et la cancérologie. Enfin, nous présenterons différentes extensions de l'OCT plein champ, exploitant la biréfringence des tissus ainsi que leurs propriétés spectroscopiques et élastiques.Les mouvements des structures intracellulaires dans les tissus fraîchement prélevés peuvent également constituer une source de contraste complémentaire pour l'imagerie par OCT plein champ.

International audience; There is an increasing need for label free methods that could reveal intracellular structures and dynamics. In this context, we develop a new optical tomography method working in transmission - full-field optical transmission tomography (FF-OTT). The method can measure the forward scattering signals and reveals the time-dependent metabolic signals in living cells. FF-OTT is a common path interferometer taking advantage of the Gouy phase shift - a π phase shift that the light wave experiences around the focus. By modulating the position of the focus one can alter the phase of the scattered light. Demodulation of images with different phases rejects the background and enhances the light from the depth-of-field, thus producing an optical section. We test FF-OTT by imaging single-cell diatoms and ex vivo biological samples. In fresh samples, we show that the intracellular motions create visible intensity fluctuations in FF-OTT so that the method is able to reveal a metabolic dynamic contrast. FF-OTT was found to be an efficient label free technique that can be readily implemented thanks to a robust common-path speckle-free interferometer design using an incoherent light source.

International audience; The highest three-dimensional (3D) resolution possible in in-vivo retinal imaging is achieved by combining optical coherence tomography (OCT) and adaptive optics. However, this combination brings important limitations, such as small field-of-view and complex, cumbersome systems, preventing so far the translation of this technology from the research lab to clinics. Here, we mitigate these limitations by combining our compact time-domain full-field OCT (FFOCT) with a multi-actuator adaptive lens positioned just in front of the eye, in a technique we call the adaptive-glasses wavefront sensorless approach. Through this approach, we demonstrate that ocular aberrations can be corrected, increasing the FFOCT signal-to-noise ratio and enabling imaging of different retinal layers with a 2µm × 2µm × 8µm resolution over a 5 o × 5 o field-of-view, without major anisoplanatism influence.; La plus haute résolution tridimensionnelle (3D) possible en imagerie rétinienne in vivo est obtenue en combinant la tomographie par cohérence optique (OCT) et l'optique adaptative. Toutefois, cette combinaison présente des limites importantes, comme un champ de vision réduit et des systèmes complexes et encombrants, ce qui empêche jusqu'à présent la transposition de cette technologie du laboratoire de recherche aux cliniques. Ici, nous atténuons ces limitations en combinant notre OCT compacte à plein champ dans le domaine temporel (FFOCT) avec une lentille adaptative à actionneurs multiples placée juste devant l'œil, dans une technique que nous appelons l'approche des lunettes adaptatives. Grâce à cette approche, nous démontrons que les aberrations oculaires peuvent être corrigées, augmentant le rapport signal/bruit de la FFOCT et permettant l'imagerie de différentes couches de la rétine avec une résolution de 2µm x 2µm x 8µm sur un champ de vision de 5° x 5°, sans influence majeure d'anisoplanatisme.

Eye movements are commonly seen as an obstacle to high-resolution ophthalmic imaging. In this context we study the natural axial movements of in vivo human eye and show that they can be used to modulate the optical phase and retrieve tomographic images via time-domain full-field optical coherence tomography (TD-FF-OCT). This approach opens a path to a simplified ophthalmic TD-FF-OCT device, operating without the usual piezo motor-camera synchronization. The device demonstrates in vivo human corneal images under different image retrieval schemes (2-phase and 4-phase) and different exposure times (3.5 ms, 10 ms, 20 ms).

Dynamic FFOCT allows us to record the intrinsic motion of biological samples in 3D, over hours. We performed scratch assays on primary porcine RPE and human induced pluripotent stem cells derived RPE cell cultures. We plotted motion maps from the optical flow. For wounds

Allying high-resolution with a large field-of-view (FOV) is of great importance in the fields of biology and medicine, but particularly challenging when imaging non-flat living samples such as the retina. Indeed, high-resolution is normally achieved with adaptive optics (AO) and scanning methods, which considerably reduce the useful FOV and increase the system complexity. Here, we introduce coherence gate shaping for FF-OCT, to optically shape the coherence gate geometry to match the retinal curvature, thus achieving a larger FOV than previously possible. Using this instrument, we obtained high-resolution images of photoreceptors close to the foveal center without AO and with a 1x1m² FOV. This novel advance facilitates the extraction of photoreceptor-based biomarkers and 4D monitoring of individual photoreceptors. We compare our findings with AO-assisted ophthalmoscopes, highlighting the potential of FF-OCT, as a compact system, to become a routine clinical imaging technique.

Full Field Optical Transmission Tomography relates to optical tomography, and more precisely to a new type of endogenous cell imaging technique offering structural and metabolic contrasts.

The highest three-dimensional (3D) resolution possible in in vivo retinal imaging is achieved by combining optical coherence tomography (OCT) and adaptive optics. However, this combination brings important limitations, such as small field-of-view and complex, cumbersome systems, preventing so far the translation of this technology from the research lab to clinics. In this Letter, we mitigate these limitations by combining our compact time-domain full-field OCT (FFOCT) with a multi-actuator adaptive lens positioned just in front of the eye, in a technique we call the adaptive-glasses wavefront sensorless approach. Through this approach, we demonstrate that ocular aberrations can be corrected, increasing the FFOCT signal-to-noise ratio (SNR) and enabling imaging of different retinal layers with a 3D cellular resolution over a 5

Optical coherence tomography offers astounding opportunities to image the complex structure of living tissue, but lacks functional information. We present dynamic full-field optical coherence tomography to image living human induced pluripotent stem cell-derived retinal organoids non-invasively. Colored images with an endogenous contrast linked to organelle motility are generated, with sub-micrometer spatial resolution and millisecond temporal resolution, opening an avenue to identify specific cell types in living tissue via their function., Comment: 14 pages, 5 figures, 1 table, 6 videos

International audience; Full-field optical coherence tomography (FFOCT) is an imaging technique of biological tissue based on tissue light reflectance analysis. We evaluated the feasibility of imaging fresh digestive mucosal biopsies after a quick mounting procedure (5 min) using two distinct modalities of FFOCT. In static FFOCT mode, we gained high-resolution images of general gut tissue-specific architecture, such as oesophageal papillae, gastric pits, duodenal villi and colonic crypts. In dynamic FFOCT mode, we imaged individual epithelial cells of the mucosal lining with a cellular or subcellular resolution and identified cellular components of the lamina propria. FFOCT represents a promising dye-free imaging tool for on-site analysis of gut tissue remodelling.

Heterogeneities of biological tissues can strongly affect light propagation at large depths by distorting the initial wavefront. Inspired by previous works in acoustics, we have developed a matrix approach to Full-Field Optical Coherence Tomography (FF-OCT) to push back the fundamental limit of aberrations and multiple scattering. An analysis of the correlations of the matrix allows to correct for aberrations and forward multiple scattering over multiple isoplanatic areas (contrary to classic adaptive optics). Here, we report on the application of this approach to the imaging of the monkey cornea and the quantitative measurement of the corneal transparency.

In this project, we analyzed 30 healthy and tumorous breast samples using static and dynamic full field optical coherence tomography (FF-OCT). We developed an automatic analysis workflow to classify each sample and compared it to an independent standard histological diagnosis. We used a first machine-learning algorithm to obtain cell and fiber segmentation of FF-OCT images and applied a linear support vector machine (SVM) analysis to classify each sample. We could obtain 100% specificity and sensitivity compared to histology. The label-free and non-invasive combination of static and dynamic FF-OCT thus appears very promising to obtain an efficient diagnosis of tumoral samples.