Multiplexed imaging in live cells using pulsed interleaved excitation spectral FLIM.

Multiplexed fluorescence detection has become increasingly important in the fields of biosensing and bioimaging. Although a variety of excitation/detection optical designs and fluorescence unmixing schemes have been proposed to allow for multiplexed imaging, rapid and reliable differentiation and quantification of multiple fluorescent species at each imaging pixel is still challenging. Here we present a pulsed interleaved excitation spectral fluorescence lifetime microscopic (PIE-sFLIM) system that can simultaneously image six fluorescent tags in live cells in a single hyperspectral snapshot. Using an alternating pulsed laser excitation scheme at two different wavelengths and a synchronized 16-channel time-resolved spectral detector, our PIE-sFLIM system can effectively excite multiple fluorophores and collect their emission over a broad spectrum for analysis. Combining our system with the advanced live-cell labeling techniques and the lifetime/spectral phasor analysis, our PIE-sFLIM approach can well unmix the fluorescence of six fluorophores acquired in a single measurement, thus improving the imaging speed in live-specimen investigation.

BMEntored: Enhancing the First-Year Experience in a BME Doctoral Program.

We describe our experiences with the first offering of a new program, BMEntored, for supporting first-year doctoral students in Biomedical Engineering (BME) during their first semester. The goal of BMEntored was to enhance the first-semester experience of first-year doctoral students in BME with an emphasis on guiding students in selecting a research supervisor and promoting cross-cohort, cross-lab social connections.

Generative adversarial network enables rapid and robust fluorescence lifetime image analysis in live cells.

Fluorescence lifetime imaging microscopy (FLIM) is a powerful tool to quantify molecular compositions and study molecular states in complex cellular environment as the lifetime readings are not biased by fluorophore concentration or excitation power. However, the current methods to generate FLIM images are either computationally intensive or unreliable when the number of photons acquired at each pixel is low. Here we introduce a new deep learning-based method termed flimGANE (fluorescence lifetime imaging based on Generative Adversarial Network Estimation) that can rapidly generate accurate and high-quality FLIM images even in the photon-starved conditions. We demonstrated our model is up to 2,800 times faster than the gold standard time-domain maximum likelihood estimation (TD_MLE) and that flimGANE provides a more accurate analysis of low-photon-count histograms in barcode identification, cellular structure visualization, Förster resonance energy transfer characterization, and metabolic state analysis in live cells. With its advantages in speed and reliability, flimGANE is particularly useful in fundamental biological research and clinical applications, where high-speed analysis is critical.

Path-length-multiplexed scattering-angle-diverse optical coherence tomography for retinal imaging.

A low-resolution path-length-multiplexed scattering angle diverse optical coherence tomography (PM-SAD-OCT) is constructed to investigate the scattering properties of the retinal nerve fiber layer (RNFL). Low-resolution PM-SAD-OCT retinal images acquired from a healthy human subject show the variation of RNFL scattering properties at retinal locations around the optic nerve head. The results are consistent with known retinal ganglion cell neural anatomy and principles of light scattering. Application of PM-SAD-OCT may provide potentially valuable diagnostic information for clinical retinal imaging.

Thickness, phase retardation, birefringence, and reflectance of the retinal nerve fiber layer in normal and glaucomatous non-human primates.

PURPOSE: We identified candidate optical coherence tomography (OCT) markers for early glaucoma diagnosis. Time variation of retinal nerve fiber layer (RNFL) thickness, phase retardation, birefringence, and reflectance using polarization sensitive optical coherence tomography (PS-OCT) were measured in three non-human primates with induced glaucoma in one eye. We characterized time variation of RNFL thickness, phase retardation, birefringence, and reflectance with elevated intraocular pressure (IOP). METHODS: One eye of each of three non-human primates was laser treated to increase IOP. Each primate was followed for a 30-week period. PS-OCT measurements were recorded at weekly intervals. Reflectance index (RI) is introduced to characterize RNFL reflectance. Associations between elevated IOP and RNFL thickness, phase retardation, birefringence, and reflectance were characterized in seven regions (entire retina, inner and outer rings, and nasal, temporal, superior and inferior quadrants) by linear and non-linear mixed-effects models. RESULTS: Elevated IOP was achieved in three non-human primate eyes with an average increase of 13 mm Hg over the study period. Elevated IOP was associated with decreased RNFL thickness in the nasal region (P = 0.0002), decreased RNFL phase retardation in the superior (P = 0.046) and inferior (P = 0.021) regions, decreased RNFL birefringence in the nasal (P = 0.002) and inferior (P = 0.029) regions, and loss of RNFL reflectance in the outer rings (P = 0.018). When averaged over the entire retinal area, only RNFL reflectance showed a significant decrease (P = 0.028). CONCLUSIONS: Of the measured parameters, decreased RNFL reflectance was the most robust correlate with glaucomatous damage. Candidate cellular mechanisms are considered for decreased RNFL reflectance, including mitochondrial dysfunction and retinal ganglion cell apoptosis.

Complex polarization ratio to determine polarization properties of anisotropic tissue using polarization-sensitive optical coherence tomography.

Complex polarization ratio (CPR) in materials with birefringence and biattenuance is shown as a logarithmic spiral in the complex plane. A multi-state Levenberg-Marquardt nonlinear fitting algorithm using the CPR trajectory collected by polarization sensitive optical coherence tomography (PS-OCT) was developed to determine polarization properties of an anisotropic scattering medium. The Levenberg-Marquardt nonlinear fitting algorithm using the CPR trajectory is verified using simulated PS-OCT data with speckle noise. Birefringence and biattenuance of a birefringent film, ex-vivo rodent tail tendon and in-vivo primate retinal nerve fiber layer were determined using measured CPR trajectories and the Levenberg-Marquardt nonlinear fitting algorithm.

The relationship between retinal ganglion cell axon constituents and retinal nerve fiber layer birefringence in the primate.

PURPOSE: To determine the degree of correlation between spatial characteristics of the retinal nerve fiber layer (RNFL) birefringence (Delta n(RNFL)) surrounding the optic nerve head (ONH) with the corresponding anatomy of retinal ganglion cell (RGC) axons and their respective organelles. METHODS: RNFL phase retardation per unit depth (PR/UD, proportional to Delta n(RNFL)) was measured in two cynomolgus monkeys by enhanced polarization-sensitive optical coherence tomography (EPS-OCT). The monkeys were perfused with glutaraldehyde and the eyes were enucleated and prepared for transmission electron microscopy (TEM) histologic analysis. Morphologic measurements from TEM images were used to estimate neurotubule density (rho(RNFL)), axoplasmic area (A(x)) mode, axon area (A(a)) mode, slope (u) of the number of neurotubules versus axoplasmic area (neurotubule packing density), fractional area of axoplasm in the nerve fiber bundle (f), mitochondrial fractional area in the nerve fiber bundle (x(m)), mitochondria-containing axon profile fraction (m(p)), and length of axonal membrane profiles per unit of nerve fiber bundle area (L(am)/A(b)). Registered PR/UD and morphologic parameters from corresponding angular sections were then correlated by using Pearson's correlation and multilevel models. RESULTS: In one eye there was a statistically significant correlation between PR/UD and rho(RNFL) (r = 0.67, P = 0.005) and between PR/UD and neurotubule packing density (r = 0.70, P = 0.002). Correlation coefficients of r = 0.81 (P = 0.01) and r = 0.50 (P = 0.05) were observed between the PR/UD and A(x) modes for each respective subject. CONCLUSIONS: Neurotubules are the primary source of birefringence in the RNFL of the primate retina.

Quality assessment for spectral domain optical coherence tomography (OCT) images.

Retinal nerve fiber layer (RNFL) thickness, a measure of glaucoma progression, can be measured in images acquired by spectral domain optical coherence tomography (OCT). The accuracy of RNFL thickness estimation, however, is affected by the quality of the OCT images. In this paper, a new parameter, signal deviation (SD), which is based on the standard deviation of the intensities in OCT images, is introduced for objective assessment of OCT image quality. Two other objective assessment parameters, signal to noise ratio (SNR) and signal strength (SS), are also calculated for each OCT image. The results of the objective assessment are compared with subjective assessment. In the subjective assessment, one OCT expert graded the image quality according to a three-level scale (good, fair, and poor). The OCT B-scan images of the retina from six subjects are evaluated by both objective and subjective assessment. From the comparison, we demonstrate that the objective assessment successfully differentiates between the acceptable quality images (good and fair images) and poor quality OCT images as graded by OCT experts. We evaluate the performance of the objective assessment under different quality assessment parameters and demonstrate that SD is the best at distinguishing between fair and good quality images. The accuracy of RNFL thickness estimation is improved significantly after poor quality OCT images are rejected by automated objective assessment using the SD, SNR, and SS.

Fibre orientation contrast for depth-resolved identification of structural interfaces in birefringent tissue.

Incorporation of polarimetric sensitivity into optical coherence tomography can provide additional image contrast when structures of interest are optically anisotropic (e.g., fibrous tissue). We present a generalized technique based on polarization-sensitive optical coherence tomography to detect changes in depth-resolved fibre orientation and thus increase image contrast in multiple-layered birefringent tissues. A high contrast B-scan image of collagen fibre orientation is shown for a porcine intervertebral disc cartilage specimen that exhibited low backscattering intensity contrast. Interfaces in the annulus fibrosus identified using depth-resolved fibre orientation allowed quantification of lamellae thickness. Moreover, the technique detects changes in fibre orientation without intense processing needed to effectively quantify tissue retardation and diattenuation.

Differential geometry of normalized Stokes vector trajectories in anisotropic media.

Trajectory of the normalized Stokes vector on the Poincaré sphere corresponding to light propagation in anisotropic tissues with birefringence and biattenuance is derived. Analytic expressions are determined from the Serret-Frenet formulas and derivatives of arc length for five quantities including the tangent, normal, and binormal vectors with curvature and torsion. Depth variation of curvature and torsion of normalized Stokes vector trajectories corresponding to light propagating in rodent tail tendon are given. Use of analytic expressions for depth variation of curvature and torsion of the normalized Stokes vector trajectories on the Poincaré sphere is discussed for analysis of polarization-sensitive optical coherence tomography data recorded from anisotropic biological tissues with birefringence and biattenuance.

Birefringence of the primate retinal nerve fiber layer.

The purpose of this study was to measure the peripapillary retinal nerve fiber layer (RNFL) thickness, phase retardation (PR), and depth-resolved birefringence (Deltan) of the normal primate eye using Enhanced Polarization-Sensitivity Optical Coherence Tomography (EPS-OCT). Both eyes of two rhesus monkeys were imaged with EPS-OCT. A multiple incident polarization state nonlinear fitting algorithm was used to determine RNFL phase retardation. RNFL thickness (RNFLT) was determined from the corresponding EPS-OCT intensity image and phase retardation per unit depth (PR/UD, proportional to Deltan) was calculated by dividing PR by RNFLT. Peripapillary area maps consisting of pixels uniformly distributed along a radius from 0.8 to 1.8 mm from the center of the optic nervehead were constructed for RNFLT, PR, and PR/UD. Average PR/UD in the superior and inferior quadrants was 18 degrees /100 mivrom (Deltan=4.2 x 10(-4)) and average PR/UD in the nasal and temporal quadrants was 6.3 degrees /100 microm (Deltan=1.5 x 10(-4)). Relative magnitude of PR radial gradient is similar to that of RNFLT radial gradient and no radial gradient was observed for PR/UD. Polarization-dependent amplitude attenuation per unit depth (PDAA/UD) was 0.02 rad/100 microm in thick RNFL regions. RNFL birefringence was higher in the arcuate bundles compared to nasal and temporal fibers (P=0.001). Birefringence was nearly equal in nasal and temporal quadrants. No statistically significant (P=0.01) radial gradient of birefringence was observed in any quadrant. RNFL birefringence is believed to originate from anisotropic structures within the cytoskeleton of the parallel axons. Birefringence differences presented in this study cannot be explained by the known axon diameter distribution around the optic nervehead and suggest other sources of the birefringence signal including neurotubules and neurofilaments.

High-sensitivity determination of birefringence in turbid media with enhanced polarization-sensitive optical coherence tomography.

Polarization-sensitive optical coherence tomography provides high-resolution cross-sectional characterization of birefringence in turbid media. Weakly birefringent biological tissues such as the retinal nerve fiber layer (RNFL) require advanced speckle noise reduction for high-sensitivity measurement of form birefringence. We present a novel method for high-sensitivity birefringence quantification by using enhanced polarization-sensitive optical coherence tomography (EPS-OCT) and introduce the polarimetric signal-to-noise ratio, a mathematical tool for analyzing speckle noise in polarimetry. Multiple incident polarization states and non-linear fitting of normalized Stokes vectors allow determination of retardation with +/-1 degrees uncertainty with invariance to unknown unitary polarization transformations. Results from a weakly birefringent turbid film and in vivo primate RNFL are presented. In addition, we discuss the potential of EPS-OCT for noninvasive quantification of intracellular filamentous nanostructures, such as neurotubules in the RNFL that are lost during the progression of glaucoma.

Imaging tissue response to electrical and photothermal stimulation with nanometer sensitivity.

BACKGROUND AND OBJECTIVES: Tissue response to thermal, electrical, or chemical stimuli are important in the health and survival of tissue. We report experimental results to assess tissue response to various stimuli using a low coherence differential phase interferometer. STUDY DESIGN/MATERIALS AND METHODS: The optical system utilized to measure tissue response is a novel fiber-based phase sensitive optical low coherence reflectometer (PS-OLCR). Inasmuch as the PS-OLCR works with back-reflected light, noninvasive sensing of tissue response to stimuli is possible. In addition to high lateral (approximately 10 microm) and longitudinal (approximately 10 microm) resolution, PS-OLCR can measure sub-wavelength changes in optical path-length (Angstrom/nanometer range) by extracting the phase difference between interference fringes in two channels corresponding to orthogonal polarization modes. RESULTS: When light spatially splits into two polarization states, precise analysis of surface topography or tissue surface response such as swelling or collapse are possible. Time resolved measurements of nanometer-scale path length changes in response to electrical and thermal stimuli are demonstrated using longitudinally delayed polarization channels. CONCLUSIONS: Since PS-OLCR is a useful tool to detect ultra-small path length changes, the system has potential to aid scientists in investigating important phenomena in biomaterials and developing useful diagnostic and therapeutic imaging modalities. Applications include tissue surface profilometry, measurement of tissue, and cell response to various stimuli, high-resolution intensity and phase imaging.