Sub-diffraction computational imaging via a flexible multicore-multimode fiber.

An ultra-thin multimode fiber is an ideal platform for minimally invasive microscopy with the advantages of a high density of modes, high spatial resolution, and a compact size. In practical applications, the probe needs to be long and flexible, which unfortunately destroys the imaging capabilities of a multimode fiber. In this work, we propose and experimentally demonstrate sub-diffraction imaging through a flexible probe based on a unique multicore-multimode fiber. A multicore part consists of 120 Fermat's spiral distributed single-mode cores. Each of the cores offers stable light delivery to the multimode part, which provides optimal structured light illumination for sub-diffraction imaging. As a result, perturbation-resilient fast sub-diffraction fiber imaging by computational compressive sensing is demonstrated.

Field-position dependent apodization in dark-field digital holographic microscopy for semiconductor metrology.

Measuring overlay between two layers of semiconductor devices is a crucial step during electronic chip fabrication. We present dark-field digital holographic microscopy that addresses various overlay metrology challenges that are encountered in the semiconductor industry. We present measurement results that show that the point-spread function of our microscope depends on the position in the field-of-view. We will show that this novel observation can be explained by a combination of the finite bandwidth of the light source and a wavelength-dependent focal length of the imaging lens. Moreover, we will also present additional experimental data that supports our theoretical understanding. Finally, we will propose solutions that reduce this effect to acceptable levels.

Phosphorylated tau in the retina correlates with tau pathology in the brain in Alzheimer's disease and primary tauopathies.

The retina is a potential source of biomarkers for the detection of neurodegenerative diseases. Accumulation of phosphorylated tau (p-tau) in the brain is a pathological feature characteristic for Alzheimer's disease (AD) and primary tauopathies. In this study the presence of p-tau in the retina in relation to tau pathology in the brain was assessed. Post-mortem eyes and brains were collected through the Netherlands Brain Bank from donors with AD (n = 17), primary tauopathies (n = 8), α-synucleinopathies (n = 13), other neurodegenerative diseases including non-tau frontotemporal lobar degeneration (FTLD) (n = 9), and controls (n = 15). Retina cross-sections were assessed by immunohistochemistry using antibodies directed against total tau (HT7), 3R and 4R tau isoforms (RD3, RD4), and phospho-epitopes Ser202/Thr205 (AT8), Thr217 (anti-T217), Thr212/Ser214 (AT100), Thr181 (AT270), Ser396 (anti-pS396) and Ser422 (anti-pS422). Retinal tau load was compared to p-tau Ser202/Thr205 and p-tau Thr217 load in various brain regions. Total tau, 3R and 4R tau isoforms were most prominently present in the inner plexiform layer (IPL) and outer plexiform layer (OPL) of the retina and were detected in all cases and controls as a diffuse and somatodendritic signal. Total tau, p-tau Ser202/Thr205 and p-tau Thr217 was observed in amacrine and horizontal cells of the inner nuclear layer (INL). Various antibodies directed against phospho-epitopes of tau showed immunoreactivity in the IPL, OPL, and INL. P-tau Ser202/Thr205 and Thr217 showed significant discrimination between AD and other tauopathies, and non-tauopathy cases including controls. Whilst immunopositivity was observed for p-tau Thr212/Ser214, Thr181 and Ser396, there were no group differences. P-tau Ser422 did not show any immunoreactivity in the retina. The presence of retinal p-tau Ser202/Thr205 and Thr217 correlated with Braak stage for NFTs and with the presence of p-tau Ser202/Thr205 in hippocampus and cortical brain regions. Depending on the phospho-epitope, p-tau in the retina is a potential biomarker for AD and primary tauopathies.

Ultimate resolution limits of speckle-based compressive imaging.

Compressive imaging using sparsity constraints is a very promising field of microscopy that provides a dramatic enhancement of the spatial resolution beyond the Abbe diffraction limit. Moreover, it simultaneously overcomes the Nyquist limit by reconstructing an N-pixel image from less than N single-point measurements. Here we present fundamental resolution limits of noiseless compressive imaging via sparsity constraints, speckle illumination and single-pixel detection. We addressed the experimental setup that uses randomly generated speckle patterns (in a scattering media or a multimode fiber). The optimal number of measurements, the ultimate spatial resolution limit and the surprisingly important role of discretization are demonstrated by the theoretical analysis and numerical simulations. We show that, in contrast to conventional microscopy, oversampling may decrease the resolution and reconstruction quality of compressive imaging.

Aberration calibration and correction with nano-scatterers in digital holographic microscopy for semiconductor metrology.

Overlay metrology measures pattern placement between two layers in a semiconductor chip. The continuous shrinking of device dimensions drives the need to explore novel optical overlay metrology concepts that can address many of the existing metrology challenges. We present a compact dark-field digital holographic microscope that uses only a single imaging lens. Our microscope offers several features that are beneficial for overlay metrology, like a large wavelength range. However, imaging with a single lens results in highly aberrated images. In this work, we present an aberration calibration and correction method using nano-sized point scatterers on a silicon substrate. Computational imaging techniques are used to recover the full wavefront error, and we use this to correct for the lens aberrations. We present measured data to verify the calibration method and we discuss potential calibration error sources that must be considered. A comparison with a ZEMAX calculation is also presented to evaluate the performance of the presented method.

Sensitivity analysis of Raman endoscopy with and without wavefront shaping.

Vibrational spectroscopy is a powerful method for the label-free identification of molecules. Spontaneous Raman spectroscopy integrated with an ultra-thin fiber-based endoscope can provide remote, local, and minimally invasive chemical analysis in many fields from biomedical diagnostics to the materials industry. Miniaturization of the probe in combination with a large field of view (FOV) and high sensitivity would be beneficial for a broad class of applications. Here we quantitatively analyze signal-to-noise ratio (SNR) and the sensitivity improvement due to wavefront shaping. We show that wavefront shaping in an ultra-thin single-fiber probe allows to decrease the total measurements time up to several orders of magnitude even without any prior knowledge of the Raman particle location. Such a fiber probe is well suited for minimally-invasive endoscopy in biological and medical applications.

Diffraction-based overlay metrology using angular-multiplexed acquisition of dark-field digital holograms.

In semiconductor device manufacturing, optical overlay metrology measures pattern placement between two layers in a chip with sub-nm precision. Continuous improvements in overlay metrology are needed to keep up with shrinking device dimensions in modern chips. We present first overlay metrology results using a novel off-axis dark-field digital holographic microscopy concept that acquires multiple holograms in parallel by angular multiplexing. We show that this concept reduces the impact of source intensity fluctuations on the noise in the measured overlay. With our setup we achieved an overlay reproducibility of 0.13 nm and measurements on overlay targets with known programmed overlay values showed good linearity of R2= 0.9993. Our data show potential for significant improvement and that digital holographic microscopy is a promising technique for future overlay metrology tools.

The search for a unique Raman signature of amyloid-beta plaques in human brain tissue from Alzheimer's disease patients.

Definite Alzheimer's disease (AD) diagnosis is commonly done on ex vivo brain tissue using immuno-histochemical staining to visualize amyloid-beta (Aß) aggregates, also known as Aß plaques. Raman spectroscopy has shown its potential for non-invasive and label-free determination of bio-molecular compositions, aiding the post-mortem diagnosis of pathological tissue. Here, we investigated whether conventional Raman spectroscopy could be used for the detection of amyloid beta deposits in fixed, ex vivo human brain tissue, taken from the frontal cortex region. We examined the spectra and spectral maps of three severe AD cases and two healthy control cases and compared their spectral outcome among each other as well as to recent results in the literature obtained with various spectroscopic techniques. After hyperspectral Raman mapping, Aß plaques were visualized using Thioflavin-S staining on the exact same tissue sections. As a result, we show that tiny diffuse or tangled-like morphological structures, visible under microscopic conditions on unstained tissue and often but erroneously assumed to be deposits of Aß, are instead usually an aggregation of highly auto-fluorescent lipofuscin granulates without any, or limited, plaque or plaque-like association. The occurrence of these auto-fluorescent particles is equally distributed in both AD and healthy control cases. Therefore, they cannot be used as possible criteria for Alzheimer's disease diagnosis. Furthermore, a unique plaque-specific/Aß spectrum could not be determined even after possible spectral interferences were carefully removed.

Impact of coherence length on the field of view in dark-field holographic microscopy for semiconductor metrology: theoretical and experimental comparisons.

Semiconductor manufacturers continue to increase the component densities on computer chips by reducing the device dimensions to less than 10 nm. This trend requires faster, more precise, and more robust optical metrology tools that contain complex and high-precision optics with challenging imaging requirements. Here, we present dark-field digital holographic microscopy as a promising optical metrology technique that uses optics with acceptable complexity. A theoretical analysis and an experimental demonstration of this technique are presented, showing the impact of the coherence length of the light source on the field of view. Finally, we also present the first holographically obtained images of metrology targets.

Optic axis uniformity as a metric to improve the contrast of birefringent structures and analyze the retinal nerve fiber layer in polarization-sensitive optical coherence tomography.

A new metric is used to improve the contrast of birefringent structures in biological tissue using polarization-sensitive optical coherence tomography. This metric, optic axis uniformity (OAxU), is based on the optic axis of birefringence and quantifies the uniformity of the optic axis direction. OAxU provides surprisingly strong contrast for fibrous structures such as muscle and the retinal nerve fiber layer (RNFL). We used OAxU for automatic segmentation of the RNFL in human eyes. From the segmentation, en face images of RNFL thickness and RNFL birefringence were created. The measured birefringence values are consistent with earlier reports.

Treatment Effects in Retinal Angiomatous Proliferation Imaged with OCT Angiography.

PURPOSE: This prospective case series is aimed at exploring optical coherence tomographic angiography (OCT-A) as a treatment monitoring tool in patients treated for retinal angiomatous proliferation (RAP). METHODS: Twelve treatment-naïve RAP patients were included, with a median age of 79 years (range 65-90). Patients were imaged with an experimental 1,040-nm swept-source phase-resolved OCT-A instrument before and after treatment. Treatment consisted of either intravitreal bevacizumab or triamcinolone injections with or without photodynamic therapy (PDT). Abnormal blood flow after treatment was graded as increased, unchanged, decreased, or resolved. RESULTS: OCT-A images before and after treatment could be obtained in 9 patients. The median follow-up period was 10 weeks (range 5-19). After various treatments, the RAP lesion resolved in 7 patients, in 1 patient the OCT-A depicted decreased flow in the lesion, and 1 patient showed unchanged abnormal blood flow. Monotherapy with intravitreal bevacizumab injections resolved RAP in 1 out of 2 patients. Combined therapy of bevacizumab with PDT resolved RAP in 6 out of 7 patients. CONCLUSIONS: OCT-A visualized resolution of abnormal blood flow in 7 out of 9 RAP patients after various short-term treatment sequences. OCT-A may become an important noninvasive monitoring tool for optimizing treatment strategies in RAP patients.

Compressive imaging through a multimode fiber.

We propose and experimentally demonstrate a new concept of endo-microscopy: compressive multimode (MM) fiber imaging. We show that the speckle patterns generated in a MM fiber represent an excellent basis for compressive sensing. We demonstrate high-resolution compressive imaging through a fiber probe with the total number of measurements 20 times less than what is required for the standard raster scanning approach to endo-microscopy. Moreover, we show that the inherent optical sectioning of a MM fiber can help to overcome the main problem of compressive sensing and can be used for the imaging of bulk structures. Compressive MM fiber imaging does not require complex wavefront shaping and significantly increases the pre-calibration and imaging speed, creating a new approach to endo-microscopy.

Robustness of Light-Transport Processes to Bending Deformations in Graded-Index Multimode Waveguides.

Light transport through a multimode optical waveguide undergoes changes when subjected to bending deformations. We show that optical waveguides with a perfectly parabolic refractive index profile are almost immune to bending, conserving the structure of propagation-invariant modes. Moreover, we show that changes to the transmission matrix of parabolic-index fibers due to bending can be expressed with only two free parameters, regardless of how complex a particular deformation is. We provide detailed analysis of experimentally measured transmission matrices of a commercially available graded-index fiber as well as a gradient-index rod lens featuring a very faithful parabolic refractive index profile. Although parabolic-index fibers with a sufficiently precise refractive index profile are not within our reach, we show that imaging performance with standard commercially available graded-index fibers is significantly less influenced by bending deformations than step-index types under the same conditions. Our work thus predicts that the availability of ultraprecise parabolic-index fibers will make endoscopic applications with flexible probes feasible and free from extremely elaborate computational challenges.

In vivo exploration of retinal nerve fiber layer morphology in Parkinson's disease patients.

Thinning of the retinal nerve fiber layer (RNFL) is a recently discovered feature of Parkinson's disease (PD). Its exact pathological mechanism is yet unknown. We aimed to determine whether morphological changes of the RNFL are limited to RNFL thinning or also comprise an altered internal structure of this layer. Therefore, we investigated RNFL thickness and applied the RNFL attenuation coefficient (RNFL-AC), a novel method derived from optical coherence tomography, in PD patients and healthy controls (HCs). In this pilot study, we included 20 PD patients and 20 HCs matched for age, sex, and ethnicity. An ophthalmologist investigated all participants thoroughly, and we acquired retinal images from both eyes of each participant with a Spectralis optical coherence tomography system. We obtained both the RNFL-AC and RNFL thickness from peripapillary RNFL scans for the entire RNFL, as well as for each quadrant separately. We found no significant differences in the average RNFL-AC or the RNFL-AC of the separate retinal quadrants between PD patients and the HC group. However, compared to the HC group, PD patients had a significantly thinner RNFL in the temporal retinal quadrant. RNFL thinning was found in the temporal quadrant in PD patients without a corresponding change in the RNFL-AC. These findings suggest a reduction in the number of RNFL axons (atrophy) without other major changes in the structural integrity of the remaining RNFL.

Self-interference fluorescence microscopy with three-phase detection for depth-resolved confocal epi-fluorescence imaging.

Three-dimensional confocal fluorescence imaging of in vivo tissues is challenging due to sample motion and limited imaging speeds. In this paper a novel method is therefore presented for scanning confocal epi-fluorescence microscopy with instantaneous depth-sensing based on self-interference fluorescence microscopy (SIFM). A tabletop epi-fluorescence SIFM setup was constructed with an annular phase plate in the emission path to create a spectral self-interference signal that is phase-dependent on the axial position of a fluorescent sample. A Mach-Zehnder interferometer based on a 3 × 3 fiber-coupler was developed for a sensitive phase analysis of the SIFM signal with three photon-counter detectors instead of a spectrometer. The Mach-Zehnder interferometer created three intensity signals that alternately oscillated as a function of the SIFM spectral phase and therefore encoded directly for the axial sample position. Controlled axial translation of fluorescent microsphere layers showed a linear dependence of the SIFM spectral phase with sample depth over axial image ranges of 500 µm and 80 µm (3.9 × Rayleigh range) for 4 × and 10 × microscope objectives respectively. In addition, SIFM was in good agreement with optical coherence tomography depth measurements on a sample with indocyanine green dye filled capillaries placed at multiple depths. High-resolution SIFM imaging applications are demonstrated for fluorescence angiography on a dye-filled capillary blood vessel phantom and for autofluorescence imaging on an ex vivo fly eye.

Altered Adipogenesis in Zebrafish Larvae Following High Fat Diet and Chemical Exposure Is Visualised by Stimulated Raman Scattering Microscopy.

Early life stage exposure to environmental chemicals may play a role in obesity by altering adipogenesis; however, robust in vivo methods to quantify these effects are lacking. The goal of this study was to analyze the effects of developmental exposure to chemicals on adipogenesis in the zebrafish (Danio rerio). We used label-free Stimulated Raman Scattering (SRS) microscopy for the first time to image zebrafish adipogenesis at 15 days post fertilization (dpf) and compared standard feed conditions (StF) to a high fat diet (HFD) or high glucose diet (HGD). We also exposed zebrafish embryos to a non-toxic concentration of tributyltin (TBT, 1 nM) or Tris(1,3-dichloroisopropyl)phosphate (TDCiPP, 0.5 µM) from 0-6 dpf and reared larvae to 15 dpf under StF. Potential molecular mechanisms of altered adipogenesis were examined by qPCR. Diet-dependent modulation of adipogenesis was observed, with HFD resulting in a threefold increase in larvae with adipocytes, compared to StF and HGD. Developmental exposure to TBT but not TDCiPP significantly increased adipocyte differentiation. The expression of adipogenic genes such as pparda, lxr and lepa was altered in response to HFD or chemicals. This study shows that SRS microscopy can be successfully applied to zebrafish to visualize and quantify adipogenesis, and is a powerful approach for identifying obesogenic chemicals in vivo.

Depth-encoded synthetic aperture optical coherence tomography of biological tissues with extended focal depth.

Optical coherence tomography (OCT) has proven to be able to provide three-dimensional (3D) volumetric images of scattering biological tissues for in vivo medical diagnostics. Unlike conventional optical microscopy, its depth-resolving ability (axial resolution) is exclusively determined by the laser source and therefore invariant over the full imaging depth. In contrast, its transverse resolution is determined by the objective's numerical aperture and the wavelength which is only approximately maintained over twice the Rayleigh range. However, the prevailing laser sources for OCT allow image depths of more than 5 mm which is considerably longer than the Rayleigh range. This limits high transverse resolution imaging with OCT. Previously, we reported a novel method to extend the depth-of-focus (DOF) of OCT imaging in Mo et al.Opt. Express 21, 10048 (2013)]. The approach is to create three different optical apertures via pupil segmentation with an annular phase plate. These three optical apertures produce three OCT images from the same sample, which are encoded to different depth positions in a single OCT B-scan. This allows for correcting the defocus-induced curvature of wave front in the pupil so as to improve the focus. As a consequence, the three images originating from those three optical apertures can be used to reconstruct a new image with an extended DOF. In this study, we successfully applied this method for the first time to both an artificial phantom and biological tissues over a four times larger depth range. The results demonstrate a significant DOF improvement, paving the way for 3D high resolution OCT imaging beyond the conventional Rayleigh range.

Polarization sensitive optical frequency domain imaging system for endobronchial imaging.

A polarization sensitive endoscopic optical frequency domain imaging (PS-OFDI) system with a motorized distal scanning catheter is demonstrated. It employs a passive polarization delay unit to multiplex two orthogonal probing polarization states in depth, and a polarization diverse detection unit to detect interference signal in two orthogonal polarization channels. Per depth location four electro-magnetic field components are measured that can be represented in a complex 2x2 field matrix. A Jones matrix of the sample is derived and the sample birefringence is extracted by eigenvalue decomposition. The condition of balanced detection and the polarization mode dispersion are quantified. A complex field averaging method based on the alignment of randomly pointing field phasors is developed to reduce speckle noise. The variation of the polarization states incident on the tissue due to the circular scanning and catheter sheath birefringence is investigated. With this system we demonstrated imaging of ex vivo chicken muscle, in vivo pig lung and ex vivo human lung specimens.