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It is now well established that the movement of the eyes, which occurs constantly even during fixation, tends to “freeze” in response to perceptual events, with a magnitude and time course that depends on the stimulus properties, attention, and anticipation. This “freeze” or oculomotor inhibition (OMI) was found for microsaccades, blinks, smooth-pursuit, and catch-up saccades; yet remains unclear whether it also applies to ocular drift. Since video-based eye-trackers are known to produce positional artifacts, we used here data from a high-speed and precision retinal imaging eye-tracker (FreezEye Tracker, FET). The observers (n = 15) watched a series of flashed Gabor patches, with different spatial frequency and contrast while their eyes were tracked. We analyzed the data by removing the saccades, aligning the traces, and computing four drift measures relative to the stimulus onset: (1) velocity, (2) area, (3) diffusion, and (4) heat map. We found that all measures produced a highly significant modulation over time. The overall drift velocity, area, and diffusion followed the microsaccade inhibition pattern, whereas the heat map peaks showed the opposite pattern. The drift inhibition was also stimulus dependent, showing shorter onset and prolonged release estimates for more salient stimuli, matching the microsaccade OMI for the onset but showing the opposite for the release. Overall, the results confirm that the oculomotor inhibition effect can be generalized for ocular drift, but its opposite stimulus dependency for inhibition release and the shifted time course may suggest a complex interdependency between drift and saccades.

We present a comprehensive computational study on the optimization of the size of gold nanorods for single-molecule plasmonic sensing in terms of optical refractive index sensitivity. We construct an experimentally relevant model of single-molecule–single-nanoparticle sensor based on spherically capped gold nanorods, tip-specific functionalization and passivation layers, and biotin-streptavidin affinity system. We introduce a universal figure of merit for the sensitivity, termed contrast-to-noise ratio (CNR), which relates the change of measurable signal caused by the discrete molecule binding events to the inherent measurement noise. We investigate three distinct sensing modalities relying on direct spectral measurements, monitoring of scattering intensity at fixed wavelength and photothermal effect. By considering a shot-noise-limited performance of an experimental setup, we demonstrate the existence of an optimum nanorod size providing the highest sensitivity for each sensing technique. The optimization at constant illumination intensity (i.e., low-power applications) yields similar values of approximately 20 × 80 nm2 for each considered sensing technique. Second, we investigate the impact of geometrical and material parameters of the molecule and the functionalization layer on the sensitivity. Finally, we discuss the variable illumination intensity for each nanorod size with the steady-state temperature increase as its limiting factor (i.e., high-power applications).

In brief Optical coherence microscopy is a label-free and non-invasive imaging technique capable of 3D subcellular structure visualization. Here we show that this method allows for quality assessment of immature mouse oocytes based on their chromatin conformation and can be a valuable addition to the toolkit used in assisted reproduction procedures. Abstract The success of assisted reproductive technologies, and particularly in vitro maturation, is tightly linked to the quality of oocytes. Therefore, there is a need for robust, reliable, and easy-to-assess biomarkers of oocyte developmental competence. Microscopy techniques visualizing oocyte intracellular structure could provide such biomarkers. However, fluorescence imaging methods, applied frequently in biology and allowing for detailed structural and dynamic studies of single cells, require fluorescent tags to visualize cellular architecture and may cause short- and long-term photo-damage. On the other hand, traditional light microscopy, although relatively non-invasive, does not provide detailed structural information. Optical coherence microscopy (OCM) is a promising alternative, as it does not require sample pre-processing or labelling and can provide 3D images of intracellular structures. Here we applied OCM to assess the chromatin conformation of immature mouse oocytes, a feature that corresponds with their transcriptional status and developmental competence and cannot be examined by traditional light microscopy. We showed that OCM distinguished oocytes with so-called non-surrounded nucleoli (NSN) and surrounded nucleoli (SN) chromatin conformation with very high sensitivity and specificity and that OCM scanning did not decrease the quality of oocytes. Finally, we cross-referenced OCM data with the oocyte ability to undergo normal nuclear and cytoplasmic maturation and proven that indeed oocytes scored with OCM as NSN mature less effectively than oocytes scored as SN. Our results suggest that OCM may be a valuable addition to the imaging toolkit used in assisted reproduction procedures.

The retinal volumetric flow rate contains useful information not only for ophthalmo-logy but also for the diagnosis of common civilization diseases such as diabetes, Alzheimer's disease, or cerebrovascular diseases. Non-invasive optical methods for quantitative flow assessment, such as Doppler optical coherence tomography (OCT), have certain limitations. One is the phase wrapping that makes simultaneous calculations of the flow in all human retinal vessels impossible due to a very large span of flow velocities. We demonstrate that three-dimensional Doppler OCT combined with three-dimensional four Fourier transform fast phase unwrapping (3D 4FT FPU) allows for the calculation of the volumetric blood flow rate in real-time by the implementation of the algorithms in a graphics processing unit (GPU). The additive character of the flow at the furcations is proven using a microfluidic device with controlled flow rates as well as in the retinal veins bifurcations imaged in the optic disc area of five healthy volunteers. We show values of blood flow rates calculated for retinal capillaries and vessels with diameters in the range of 12–150 µm. The potential of quantitative measurement of retinal blood flow volume includes noninvasive detection of carotid artery stenosis or occlusion, measuring vascular reactivity and evaluation of vessel wall stiffness.

Purpose Two-photon vision relies on the perception of pulsed infrared light due to two-photon absorption in visual pigments. This study aimed to measure human pupil reaction caused by a two-photon 1040-nm stimulus and compare it with pupil responses elicited by 520-nm stimuli of similar color. Methods Pupillary light reflex (PLR) was induced on 14 dark-adapted healthy subjects. Three types of fovea-centered stimuli of 3.5° diameter were tested: spirals formed by fast scanning 1040-nm (infrared [IR] laser) or 520-nm (visible [VIS] laser) laser beams and uniformly filled circle created by 520-nm LED (VIS light-emitting diode [LED]). The power of visible stimuli was determined with a dedicated procedure to obtain the same perceived brightness equivalent as for 800 µW used for two-photon stimulation. Results The minimum pupil diameter for IR laser was 88% ± 10% of baseline, significantly larger than for both VIS stimuli: 74% ± 10% (laser) and 69% ± 9% (LED). Mean constriction velocity and time to maximum constriction had significantly smaller values for IR than for both VIS stimuli. Latency times were similar for IR and VIS lasers and slightly smaller for VIS LED. Conclusions The two-photon stimulus caused a considerably weaker pupil reaction than one-photon stimuli of the same shape, brightness, and similar color. The smaller pupil response may be due to weaker two-photon stimulation of rods relative to cones as previously observed for two-photon vision. Contrary to normal vision, in a two-photon process the stray light is not perceived, which might reduce the number of stimulated photoreceptors and further weaken the PLR.

Several specialized retinal optical coherence tomography (OCT) acquisition and processing methods have been recently developed to allow in vivo probing of light-evoked photoreceptors function, focusing on measurements in individual photoreceptors (rods and cones). Recent OCT investigations in humans and experimental animals have shown that the outer segments in dark-adapted rods and cones elongate in response to the visible optical stimuli that bleach fractions of their visual photopigment. We have previously successfully contributed to these developments by implementing OCT intensity-based “optoretinograms” (ORG), the paradigm of using near-infrared OCT (NIR OCT) to measure bleaching-induced back-scattering and/or elongation changes of photoreceptors in the eye in vivo. In parallel, several groups have successfully implemented phase-based ORGs, mainly in human studies, exploiting changes in the phases of back-scattered light. This allowed more sensitive observations of tiny alterations of photoreceptors structures. Applications of the phase-based ORG have been implemented primarily in high speed and cellular resolution AO-OCT systems that can visualize photoreceptor mosaic, allowing phase measurements of path length changes in outer segments of individual photoreceptors. The phase-based ORG in standard resolution OCT systems is much more demanding to implement and has not been explored extensively. This manuscript describes our efforts to implement a phase analysis framework to retinal images acquired with a standard resolution and raster scanning OCT system, which offers much lower phase stability than line-field or full-field OCT detection schemes due to the relatively slower acquisition speed. Our initial results showcase the successful extraction of phase-based ORG signal from the B-scans acquired at ∼100 Hz rate and its favorable comparison with intensity-based ORG signal extracted from the same data sets. We implemented the calculation of phase-based ORG signals using Knox-Thompson paths and modified signal recovery by adding decorrelation weights. The phase-sensitive ORG signal analysis developed here for mouse retinal raster scanning OCT systems could be in principle extended to clinical retinal raster scanning OCT systems, potentially opening doors for clinically friendly ORG probing.

We present a calibration method for finding the coordinates of points in the trajectory of the scanning beam in flying-spot imaging devices. Our method is based on laterally translating the field of view on the imaging object plane by introducing additional beam deflections. We show that laterally translating the field of view provides a series of images whose relative translations are equal to the distances between the points in the scanning pattern to be calibrated. We show how these distances are mapped to the coordinates of the trajectory points. As an example, we demonstrate the calibration of the scanning patterns in an optical system with two independent microelectromechanical system based scanners. Our method profits from a large collection of distance measurements to find the trajectory coordinates, thereby minimizing the effect of random sources of uncertainty in the positions of points in the scanning pattern. We have found that we are capable of finding the coordinates of points in the scanning patterns with accuracy greater than the optical resolution of the imaging system.

In compression optical coherence elastography (OCE), deformation is quantified as the local strain at each pixel in the OCT field-of-view. A range of strain estimation methods have been demonstrated, yet it is unclear which method provides the best performance. Here, we analyze the two most prevalent strain estimation methods used in phase-sensitive compression OCE, i.e., weighted least squares (WLS) and the vector method. We introduce a framework to compare strain imaging metrics, incorporating strain sensitivity, strain signal-to-noise ratio (SNR), strain resolution, and strain accuracy. In addition, we propose a new phase unwrapping algorithm in OCE, fast phase unwrapping (FPU), and combine it with WLS, termed WLSFPU. Using the framework, we compare this new strain estimation method with both a current implementation of WLS that incorporates weighted phase unwrapping (WPU), termed WLSWPU, and the vector method. Our analysis reveals that the three methods provide similar strain sensitivity, strain SNR, and strain resolution, but that WLSFPU extends the dynamic range of accurate, measurable local strain, e.g., measuring a strain of 2.5 mɛ with ∼4% error, that is ×11 and ×15 smaller than the error measured using WLSWPU and the vector method, respectively. We also demonstrate, for the first time, the capability to detect sub-resolution contrast in compression OCE, i.e., changes in strain occurring within the strain axial resolution, and how this contrast varies between the different strain estimation methods. Lastly, we compare the performance of the three strain estimation methods on mouse skeletal muscle and human breast tissue and demonstrate that WLSFPU avoids strain imaging artifacts resulting from phase unwrapping errors in WLSWPU and provides improved contrast over the other two methods.

We present a holographic tomography technique in which the projections are acquired using both wavelength and illumination scanning in the near-infrared region. We show how to process the acquired data to obtain correct values of three-dimensional refractive index distributions in both single-wavelength and multi-wavelength data acquisition schemes and how to properly account for the dispersion of the sample. We perform numerical and experimental comparisons of different illumination scenarios to determine the most efficient measurement protocol. We show that the multi-wavelength protocol is advantageous in terms of signal-to-noise ratio and contrast-to-noise ratio over single-wavelength protocols, even for the same number of projections used for reconstructions. Finally, we show that this approach is suitable for providing high-quality refractive index distributions of relatively thick colon cancer samples.

Quantum Optical Coherence Tomography (Q-OCT) is a non-classical equivalent of Optical Coherence Tomography and is able to provide a twofold axial resolution increase and immunity to resolution-degrading dispersion. The main drawback of Q-OCT are artefacts which are additional elements that clutter an A-scan and lead to a complete loss of structural information for multilayered objects. Whereas there are very practical and successful methods for artefact removal in Time-domain Q-OCT, no such scheme has been devised for Fourier-domain Q-OCT (Fd-Q-OCT), although the latter modality—through joint spectrum detection—outputs a lot of useful information on both the system and the imaged object. Here, we propose two algorithms which process a Fd-Q-OCT joint spectrum into an artefact-free A-scan. We present the theoretical background of these algorithms and show their performance on computer-generated data. The limitations of both algorithms with regards to the experimental system and the imaged object are discussed.

Constructing an image acquired by a non-uniform scanning pattern is a difficult task. The main challenges are:(1) resampling technique (2) discrepancy between demanded (dictated by control signal) and actually performed, empirical scanning path. Here, we show how to calibrate the scanning path of MEMS scanner using Galvanometric Scanner and to what extent the time of acquisition impacts the resulting image.

Limited angle optical diffraction tomography (ODT) is a 3D quantitative phase imaging method that allows to retrieve information about 3D refractive index (RI) distribution of live, unlabeled biosamples. The main limitation of this method is that its common transmission configuration results in very low axial resolution. On the other hand, optical coherence tomography (OCT), working in its most popular reflection configuration retrieves information about the gradient of the RI of investigated samples. However, the results are of qualitative nature. Moreover, due to low numerical aperture of the objective lens typically used in OCT systems, the resolution is high in the axial direction and relatively low in transverse direction. From the point of view of K-space filling, these two imaging modalities are complementary. Here we present a method of combining ODT projections with OCT scans. The combined technique, called optical coherence diffraction tomography (OCDT) operates in transflective mode, where ODT is captured in transmission and OCT in reflection. Theory behind conversion of OCT scans into ODT projections is given. With the use of numerical simulations we show what enhancement can be obtained when OCT and ODT data are combined directly. Also, experimental verification is presented.

The eye motion is broadly considered as a valuable source of information in the fields related to psychology, neuroscience and neurology. Therefore, quantitative characterization of eye tracker data is an important task. Saccades are sigmoidal, ballistic movements that in particular deserve more attention due to their complex shape and natural diversity. We have developed the high accuracy model of saccades and microsaccades of mean absolute error equal to 0.0104 degree on average. We present the methodology for extraction of saccadic features using this model and show the potential of the method in biometric experiments.

Recent OCT based investigations in humans and in experimental animals have shown that rods and cones outer segments elongate in response to light stimuli. In this manuscript we describe our efforts to implement phase-based “optoretinograms” (ORG) analysis framework to retinal images acquired with standard raster scanning FD-OCT system, that offers much lower phase stability compared to full field or line field OCT acquisition schemes. Our initial results, acquired in anesthetized mice in vivo, showcase successful extraction of phase-based ORG signal and its favorable comparison with intensity-based ORG signal extracted from the same data sets.

The optimum size of gold nanorods for single-molecule plasmonic sensing in scattering and absorption modalities is determined by computing ratio of measurable signal to the inherent measurement noise (contrast-to-noise ratio) as a prime figure-of-merit.

We introduce a novel, noninvasive retinal eye-tracking system capable of detecting eye displacements with an angular resolution of 0.039 arcmin and a maximum velocity of 300°/s across an 8° span. Our system is designed based on a confocal retinal imaging module similar to a scanning laser ophthalmoscope. It utilizes a 2D MEMS scanner ensuring high image frame acquisition frequencies up to 1.24 kHz. In contrast with leading eye-tracking technology, we measure the eye displacements via the collection of the observed spatial excursions for all the times corresponding a full acquisition cycle, thus obviating the need for both a baseline reference frame and absolute spatial calibration. Using this approach, we demonstrate the precise measurement of eye movements with magnitudes exceeding the spatial extent of a single frame, which is not possible using existing image-based retinal trackers. We describe our retinal tracker, tracking algorithms and assess the performance of our system by using programmed artificial eye movements. We also demonstrate the clinical capabilities of our system with in vivo subjects by detecting microsaccades with angular extents as small as 0.028°. The rich kinematic ocular data provided by our system with its exquisite degree of accuracy and extended dynamic range opens new and exciting avenues in retinal imaging and clinical neuroscience. Several subtle features of ocular motion such as saccadic dysfunction, fixation instability and abnormal smooth pursuit can be readily extracted and inferred from the measured retinal trajectories thus offering a promising tool for identifying biomarkers of neurodegenerative diseases associated with these ocular symptoms.

Ocular blood flow measurement may have a number of potential applications that explore the relationship between blood flow in the eye and diseases such as: diabetic retinopathy, ocular artery obstruction, hypertensive retinopathy and Alzheimer's disease. Reliable and quantitative method for retinal blood flow estimation is still to be created. Doppler OCT is one of candidates for such a method, but suffers from a number of limitations. Recently we proposed a solution to one of the most prominent artefacts in Doppler OCT, which is the phase wrapping problem. This allows for precise recovery of velocity profile the Doppler OCT technique remains sensitive to temporal dependence of the result on the blood flow velocity changing with the pulse during the OCT measurement. In this report we explore this problem and show that the synchronization of the OCT measurement with heart beats only partially gives control over the acquired blood flows.

Experimental goal of retinal tracker device was to show ability to detect retinal motions caused by eye drifts, saccades and microsaccades with an ultrafast optoelectronic device that provides up to 1240 retinal images per second. Moreover, high speed of the device, related to optical scanning and detection guarantees safe, non-invasive and objective measurements of the living eye.

In recent years, we have witnessed an unprecedented advancement of light microscopy techniques which has allowed us to better understand biological processes occurring during oogenesis and early embryonic development in mammals. In short, two modes of cellular imaging are now available: those involving fluorescent labels and those which are fluorophore-free. Fluorescence microscopy, in its various forms, is used predominantly in research, as it provides detailed information about cellular processes; however, it can involove an increased risk of photodamage. Fluorophore-free techniques provide, on the other hand, a smaller amount of biological data but they are safer for cells and therefore can be potentially used in a clinical setting. Here, we review various fluorescence and fluorophore-free visualisation approaches and discuss their applicability in developmental biology and reproductive medicine.

We propose a novel technique for volumetric spectroscopy of scattering objects. The concept can be considered as a combination of optical coherence tomography (OCT) and Fourier transform spectroscopy. The 3D imaging capability is obtained with the use of coherence gating, but the detection spectrometer is based on 2D CMOS camera that allows for single-shot acquisition of spectral data corresponding to different depths in the object. The latter is possible as the beams from reference and object arms of the OCT interferometer are incident on the diffraction grating at relative angle (α) in the plane determined by the grating lines and the optical axis. In the perpendicular plane the diffraction angles are the same for both beams. The resultant sequence of spectra is subject to 2D Fourier transformation that provides the representation of the OCT signal in form of depth dependent distribution of spectrum of light scattered from sample and the envelope corresponding to the spectrum of the light coming back from particular depth in the object can be extracted and used for calculation of light extinction in the sample. The feasibility of the spectroscopic analysis using acquired 2D interferograms was proved by realization of the differential measurement of the glass cuvette filled with water in one case and with the water solution of the indocyanine green dye in the other. The proposed measurement scheme can show great potential in spectroscopic measurement of biomedical objects, in particular in vivo, due to resistance of the signal on the motion of the object.

Full-field swept-source optical coherence tomography (FF-SS-OCT) provides high-resolution depth-resolved images by parallel Fourier-domain interferometric detection. Traditionally, FF-SS-OCT suffers from the cross-talk-generated noise from spatially coherent lasers. This noise reduces the image quality and limits wide adaptation of FF-SS-OCT for practical and clinical applications. To tackle this problem, we demonstrate and implement the spatiotemporal optical coherence (STOC) manipulation. In STOC, the phase of light in one of the interferometer arm is modulated in time with inhomogeneous phase masks displayed sequentially on the SLM. This modulation is synchronized with light acquisition to effectively control the spatial coherence of the detected light. A term "effectively" means that we do not generate the secondary source with imposed coherence properties (e.g. spatial incoherence). Instead the idea is to tailor the incident light to constrict the region of high fringe visibility to the spatial extents individual detection channels. Hence, SLM pixels are grouped into small blocks of uniform phase shifts. Then, phases are varied in time to modulate the light incident on the sample. By matching the dimensions of the SLM blocks to spatial extents of detection channels, we can de-correlate light from each channel. The unwanted interference between channels is washed-out and the cross-talk-generated noise is suppressed, helping to improve image quality. Here, the STOC approach is validated by imaging 1951 USAF resolution test chart covered by diffuser, scattering phantom and the rat skin ex vivo. Our results show a promising enhancement of the FF-SS-OCT capabilities that can be beneficial for imaging biological samples.

We present a modified Fast Phase Unwrapping (FPU) algorithm and its application for calculation of the axial flow velocity and volumetric flow rate in Doppler optical coherence tomography (DOCT). We outline the FPU method and show that it can be implemented in Fourier-domain optical coherence tomography using Fourier transformations (4FT). We present two-dimensional (2D) and three-dimensional (3D) realizations of the algorithm to reconstruct unwrapped phase in numerical simulations, as well as in data collected from phantom. We demonstrate that the phase unwrapping outcomes of the 2D and 3D 4FT FPU algorithms depend on the phase noise in the input data. For low phase noise data both algorithms generate reliable results. With increasing noise, the 2D algorithm starts generating phase unwrapping errors earlier than the 3D version. With the phase noise larger than a limiting value, none of the algorithms provides error-free results. We demonstrate that within their phase noise applicability limits, the phase unwrapping methods enable calculation of volumetric flow rates in the flow phantom even in the presence of phase wraps. We demonstrate that application of phase unwrapping methods enables extension of the measurable flow velocities beyond the phase range limitation of the Doppler OCT data.

We propose a novel method for spectroscopic optical coherence tomography (OCT). This method uses the dependence of the Doppler frequency spectrum on the wavenumber. Controlled modulation of the light in the spectral OCT interferometer allows for an instantaneous depth-resolved reconstruction of the backscattered light spectrum from all depths. The feasibility of the spectroscopic analysis using the proposed scheme was confirmed experimentally.

We propose a new detection scheme for Spectral Optical Coherence Tomography (SOCT) that allows for a single shot depth-dependent visualization of spectroscopic properties of imaged objects. Compared to commonly used methods based on short time Fourier transformation or recently proposed technique based on Spectral and Time domain Optical Coherence Tomography (STdOCT) [1] it offers increased sensitivity and resistance to motion artefacts. The proposed method, called single shot Spectral and Time domain Optical Coherence Spectroscopy (ssSTdOCS), is based on spectroscopic version of STdOCT, but uses a 2D detector in the spectrometer and thus allows for registration of a complete data set in a single acquisition event. Originally we proposed STdOCS as an alternative for commonly used methods based on short time Fourier transformation. The method utilizes spectral OCT setup with a spectrometer equipped with linescan CCD or CMOS camera as the detector. During the measurement continuous change in optical path difference between the two arms of OCT interferometer is introduced by an optical delay line in the reference arm. Resultant sequence of spectra is subject to 2D Fourier transformation that provides the representation of the OCT signal in “Doppler frequency” – “depth” space. The signal along Doppler frequency axis has envelope corresponding to the spectrum of the light coming back from particular depth in the object. In this aspect it can be regarded as spatially resolved Fourier transform spectroscopy. The measurement scheme required by STdOCS is sensitive to the internal motion of the imaged object, since the resultant 2D data set is built from the interference spectra acquired in time. To avoid this problem we propose here a modification of the measurement instrument. To acquire the whole 2D data set used in STdOCS we propose a spectrometer equipped with 2D array sensor. The broadband light from the superluminescent diode is collimated and brought to the input of Mach-Zehnder interferometer. In the object arm the beam is focused by the objective lens in the object plane and the light scattered within the object is brought to interference with the reference beam in the output beamsplitter. The beams from reference and object arms of the interferometer are incident on the diffraction grating at relative angle in the plane determined by the grating lines and the optical axis. In the perpendicular plane the diffraction angles were the same for both beams. In the reference arm the pair of kinematic mirrors provides the possibility of precise adjustment of the angle between the beams. The first diffraction order is focused on the CCD camera with the use of cylindrical achromatic doublet. In the resulting 2D interferogram each horizontal row contains interferometric spectra with different optical path differences between the optical paths of the reference and object beams resulting from different angles of incidence at the CCD plane. This single-shot exposure event provides data sufficient for STdOCS analysis scheme. We show that the effective quantitative measurement of the depth-dependent absorption spectra of indocyanine green solution placed in glass capillary is possible with the use of our method. 1. Maciej Szkulmowski, Szymon Tamborski, Maciej Wojtkowski, "Spectroscopy by joint spectral and time domain optical coherence tomography," Proc. SPIE 9312, Optical Coherence Tomography and Coherence Domain Optical Methods in Biomedicine XIX, 93122P (2 March 2015)

We present the in-vivo imaging of the global mouse brain ischemia using Bessel beam optical coherence microscopy. This method allows to monitor changes in brain structure with extra control of blood flow during the process of artery occlusion. The results show the capability and sensitivity of OCM system with Bessel beam to analyze brain plasticity after severe injury within a period of 8 days.

Full-field swept-source optical coherence tomography (FF-SS-OCT) provides high-resolution depth-resolved images of the sample by parallel Fourier-domain interferometric detection. Although FF-SS-OCT implements high-speed volumetric imaging, it suffers from the cross-talk-generated noise from spatially coherent lasers. This noise reduces the transversal image resolution, which in turn, limits the wide adaptation of FF-SS-OCT for practical and clinical applications. Here, we introduce the novel spatiotemporal optical coherence (STOC) manipulation. In STOC the time-varying inhomogeneous phase masks are used to modulate the light incident on the sample. By properly adjusting these phase masks, the spatial coherence can be reduced. Consequently, the cross-talk-generated noise is suppressed, the transversal image resolution is improved by the factor of [Formula: see text] , and sample features become visible. STOC approach is validated by imaging 1951 USAF resolution test chart covered by the diffuser, scattering phantom and the rat skin ex vivo. In all these cases STOC suppresses the cross-talk-generated noise, and importantly, do not compromise the transversal resolution. Thus, our method provides an enhancement of FF-SS-OCT that can be beneficial for imaging biological samples.

We propose a simplification for a robust and easy to implement fast phase unwrapping (FPU) algorithm that is used to solve the phase wrapping problem encountered in various fields of optical imaging and metrology. We show that the number of necessary computations using the algorithm can be reduced compared to its original version. FPU can be easily extended from two to three spatial dimensions. We demonstrate the applicability of the two- and three-dimensional FPU algorithm for Doppler optical coherence tomography (DOCT) in numerical simulations, and in the imaging of a flow phantom and blood flow in the human retina in vivo. We introduce an FPU applicability plot for use as a guide in the selection of the most suitable version of the algorithm depending on the phase noise in the acquired data. This plot uses the circular standard deviation of the wrapped phase distribution as a measure of noise and relates it to the root-mean-square error of the recovered, unwrapped phase.

We present a method of OCT angiography (OCTA) data filtering for noise suppression and improved visualization of the retinal vascular networks in en face projection images. In our approach, we use a set of filters applied in three orthogonal axes in the three-dimensional (3-D) data sets. Minimization of artifacts generated in B-scan–wise data processing is accomplished by filtering the cross-sections along the slow scanning axis. A-scans are de-noised by axial filtering. The core of the method is the application of directional filtering to the C-scans, i.e. one-pixel thick sections of the 3-D data set, perpendicular to the direction of the scanning OCT beam. The method uses a concept of structuring, directional kernels of shapes matching the geometry of the image features. We use rotating ellipses to find the most likely local orientation of the vessels and use the best matching ellipses for median filtering of the C-scans. We demonstrate our approach in the imaging of a normal human eye with laboratory-grade spectral-domain OCT setup. The “field performance” is demonstrated in imaging of diabetic retinopathy cases with a commercial OCT device. The absolute complex differences method is used for the generation of OCTA images from the data collected in the most noise-wise unfavorable OCTA scanning regime–two frame scanning.

We present a comprehensive imaging methodology for 3D structural and functional measurements of fertilized mouse oocytes. In contrary to methods used for mouse zygote imaging so far OCT provides 3D data without z axis movement of sample or objective lens. Furthermore, complex scanning protocols used in this study give access to different scales of repetition times and thus may become a tool for investigation of a different dynamic processes. Additionally, proposed scanning approach via variety of statistic operations can be used to enhance the quality of structural images. OCT system capabilities are presented and compared to standard microscopy. With a single 3D measurements one can extract 3D structure of the oocytes as well as en-face images that correspond to both bright and dark field microscopy. As an example of dynamic oocyte imaging pronuclei motion during development is presented. Limitations and possibilities of the new system are discussed.

We used Optical Coherence Microscopy (OCM) to monitor structural and functional changes due to ischemic stroke in small animals brains in vivo. To obtain lateral resolution of 2.2 μm over the range of 600 μm we used extended focus configuration of OCM instrument involving Bessel beam. It provided access to detailed 3D information about the changes in brain vascular system up to the level of capillaries across I and II/III layers of neocortex. We used photothrombotic stroke model involving photoactive application of rose bengal to assure minimal invasiveness of the procedure and precise localization of the clot distribution center. We present the comparative analysis involving structural and angiographic maps of the stroke-affected brain enabling in-depth insight to the process of development of the disorder.

Purpose To investigate whether confluent drusen may be accompanied by fluid accumulation underneath the sensory retina and to determine if the detection of subretinal fluid on spectral-domain optical coherence tomography (OCT) in patients with coalescent drusen is indicative of choroidal neovascularization (CNV). Design Prospective, noncomparative case series. Participants Seventy-four eyes of 57 patients with large, confluent drusen. Methods The retinal structure of patients with coalescent drusen was studied by spectral-domain OCT. Optical coherence tomography reflectivity and outer retina topography maps were created and compared with fluorescein angiography (FA) and indocyanine green angiography (ICGA) images as well as with microperimetry. Main Outcome Measures Optical coherence tomography-derived retinal morphologic features. Results What appears to be fluid beneath the sensory retina was found on spectral-domain OCT in 8 eyes of 7 patients. The outer retina topography maps demonstrated that fluid accumulates only in the concavity between clustering soft drusen, not on their outward slopes. The maps also revealed a reduced distance between the retinal pigment epithelium (RPE) and the photoreceptor inner/outer segment (IS/OS) junction over large drusen and tiny elevations of the IS/OS junction around drusen of all sizes. Microperimetry showed decreased retinal light sensitivity at the site of diminished distance between the RPE and the IS/OS junction. Seven eyes of 6 patients who were followed up were found to have no retinal changes other than confluent drusen along with subretinal fluid during the entire observational period (12–27 months). There was no evidence of CNV on FA or ICGA in any of the patients. Conclusions Large, confluent drusen may be accompanied by subretinal spaces that appear to be filled with fluid. Specific distribution of the fluid limited to the depression between adjacent drusen may indicate that the cluster of coalescent drusen produces mechanical strain to the outer retinal layers that locally pulls the sensory retina away from its normal position. Consequently, the appearance of fluid within subretinal compartment between coalescent drusen in OCT cross-sectional images may not be a reliable marker for the presence of CNV. Financial Disclosure(s) Proprietary or commercial disclosure may be found after the references.

We show that in Fourier domain Optical Coherence Tomography (FdOCT) it is possible to determine the wavelength of light for each point of the detected spectrum using any measurable physical quantity that has linear dependency on wavenumber. The presented approach is robust as the actual values of the measured quantity have no importance for the algorithm. As example we calibrate a SOCT spectrometer using Doppler frequency induced in time-dependent spectral fringes by a mirror moving in one of the arm of the interferometer. The results of calibration are validated using narrow spectral lines generated by optical parametric oscillator.

We present the methodology for spectroscopic examination of absorbing media being the combination of Spectral Optical Coherence Tomography and Fourier Transform Spectroscopy. The method bases on the joint Spectral and Time OCT computational scheme and simplifies data analysis procedure as compared to the mostly used windowing-based Spectroscopic OCT methods. The proposed experimental setup is self-calibrating in terms of wavelength-pixel assignment. The performance of the method in measuring absorption spectrum was checked with the use of the reflecting phantom filled with the absorbing agent (indocyanine green). The results show quantitative accordance with the controlled exact results provided by the reference method.

Purpose: Spectral optical coherence tomography (SOCT) is a new non-invasive, non-contact, high-resolution technique, which provides cross-sectional images of objects that weakly absorb and scatter light. The aim of this article is to demonstrate the application of SOCT to imaging of eyes fitted with contact lenses. Methods: Nine eyes of six different subjects fitted with various contact lenses have been examined with a slit-lamp and a prototype SOCT instrument. Results: Our SOCT system provides high-resolution (4–6 μm longitudinal, 10 μm transversal) tomograms composed of 3000–5000 A-scans with acquisition time of 100–250 ms. The quality of the images is adequate for detailed evaluation of contact lens fit. Design, shape and lens edge position were assessed, and complications of contact lens wear could be visualized. Thickness of the lens, corneal epithelium and stroma as well as the space between the lens and the eye surface have been measured. Conclusions: SOCT allows high-resolution, cross-sectional visualization of the eye fitted with a contact lens. The ability to carry out a detailed evaluation of the fitting relationship between the lens and the ocular surface might be useful in research and optometric practice. SOCT can also be helpful in diagnosis, evaluation and documentation of contact lens complications.

Preliminary results of the application of optical coherence tomography (OCT), in particular in its spectral mode (SOCT), to tracking of deformations in paintings on canvas caused by periodical humidity changes are presented. The setup is able to monitor the position of a chosen point at the surface of a painting with micrometre precision, simultaneously in three dimensions, every 100 seconds. This allows recording of deformations associated with crack formation. For the particular painting model examined, it was shown that the surface moves in-plane towards the corner, and bulges outwards (Z-direction) in response to a rise in humidity. Subsequent to the first humidification/drying cycle, translation in the Z-direction is decreased, whilst in-plane translations increase somewhat. It was also shown that the response of the painting on canvas begins immediately on changing the relative humidity in the surroundings.

In this contribution we examine a methodology to avoid parasitic cross-correlation terms in spectral optical coherence tomography (SOCT) images. The optimal conditions of optical power and exposure time are found theoretically and confirmed experimentally to ensure that parasitic images are hidden under the shot noise. An upper limit on useful exposures may then be estimated. In a case of SOCT imaging of the retina this limit is below the ANSI safety limit.

Complex Spectral domain Optical Coherence Tomography (CSdOCT) increases twice the depth of imaging in comparison with SdOCT by suppressing one of the mirror images. We present a new method of data processing, which further reduces the residual mirror images in CSdOCT. The method takes into account object movements, always present in experiments in vivo, which introduce unpredictable phase shifts. The method is free of polychromatic phase error originating from the wavelength dependence of the phase shift introduced by the reference mirror translation. Tomograms of the anterior chamber of the human eye in vivo are chosen to demonstrate a potential of the technique.