Image Restoration Methods for Retinal Images: Denoising and Interpolation

Retinal imaging provides an opportunity to detect pathological and natural age-related physiological changes in the interior of the eye. Diagnosis of retinal abnormality requires an image that is sharp, clear and free of noise and artifacts. However, to prevent tissue damage, retinal imaging instruments use low illumination radiation, hence, the signal-to-noise ratio (SNR) is reduced which means the total noise power is increased. Furthermore, noise is inherent in some imaging techniques. For example, in Optical Coherence Tomography (OCT) speckle noise is produced due to the coherence between the unwanted backscattered light. Improving OCT image quality by reducing speckle noise increases the accuracy of analyses and hence the diagnostic sensitivity. However, the challenge is to preserve image features while reducing speckle noise. There is a clear trade-off between image feature preservation and speckle noise reduction in OCT. Averaging multiple OCT images taken from a unique position provides a high SNR image, but it drastically increases the scanning time. In this thesis, we develop a multi-frame image denoising method for Spectral Domain OCT (SD-OCT) images extracted from a very close locations of a SD-OCT volume. The proposed denoising method was tested using two dictionaries: nonlinear (NL) and KSVD-based adaptive dictionary. The NL dictionary was constructed by adding phases, polynomial, exponential and boxcar functions to the conventional Discrete Cosine Transform (DCT) dictionary. The proposed denoising method denoises nearby frames of SD-OCT volume using a sparse representation method and combines them by selecting median intensity pixels from the denoised nearby frames. The result showed that both dictionaries reduced the speckle noise from the OCT images; however, the adaptive dictionary showed slightly better results at the cost of a higher computational complexity. The NL dictionary was also used for fundus and OCT image reconstruction. The performance of the NL dictionary was always better than that of other analytical-based dictionaries, such as DCT and Haar. The adaptive dictionary involves a lengthy dictionary learning process, and therefore cannot be used in real situations. We dealt this problem by utilizing a low-rank approximation. In this approach SD-OCT frames were divided into a group of noisy matrices that consist of non-local similar patches. A noise-free patch matrix was obtained from a noisy patch matrix utilizing a low-rank approximation. The noise-free patches from nearby frames were averaged to enhance the denoising. The denoised image obtained from the proposed approach was better than those obtained by several state-of-the-art methods. The proposed approach was extended to jointly denoise and interpolate SD-OCT image. The results show that joint denoising and interpolation method outperforms several existing state-of-the-art denoising methods plus bicubic interpolation.4 month

Statistical Analysis of Hartmann-Shack Images of a Pre-school Population

The impact of uncoordinated growth of the optical components of the eye may stimulate different levels of monochromatic aberrations in the growing eyes of the children. This thesis aimed to examine the impact of age, visual acuity and refractive error on higher order aberrations as well as to determine the relationship between them. Hartman Shack images taken with the Welch Allyn® SureSight Autorefractor were calibrated in order to determine the Zernike coefficients up to the 8th order for a pupil diameter of 5mm. The MATLAB code proposed by Thibos et al that follows the standard for reporting the optical aberrations of the eye was the basis of code written for this study. Modification was required to suit the specific needs of the Welch Allyn® SureSight Autorefractor. After calibration the lower order aberrations could then be compared with the results from cyclopledged retinoscopy. RMS values of aberrations and Strehl ratios were computed to examine the optical performance of the eye. A total of 834 Hartmann-Shack images of 436 children (mean age 3.94± 0.94 years, range 3 to 6 years) were examined in this study (right eyes 436; left eyes 398).The sample had a mean (± STD) spherical equivalent of 1.19 ± 0.59D, a mean with-the-rule astigmatism (J0) of 0.055 ± 0.22D, and a mean oblique astigmatism (J45) of 0.01±0.14D. Visual acuity varied from 6/6 to 6/18. Moderate mirror symmetry was found between the eyes. Like refractive error, higher order aberrations declined with age in this sample. There was an impact of higher order aberrations on refractive error. Significantly higher ocular aberrations were found in the higher hyperopic group (SE>+2.0D) compared to emmetropic (-0.5<SE<+0.5D) and low hyperopic groups (+0.5<SE<+2.0D). The Strehl ratio was significantly lower in the high hyperopic group. Higher Strehl ratios were observed for better acuity groups but the average Strehl ratios among the different visual acuity groups were not statistically significant. In conclusion, there was an impact of age on the ocular aberrations. A wider range of age from birth to adolescence is required for further investigation. This could be indirectly influenced by the age related changes in refractive error as the correlation between refractive error and the higher order aberrations were significant. This finding also concludes that Strehl Ratio alone is not capable of perfectly describing the visual acuity of the eye; other metrics such as the neural transfer function and neural noise are necessary to describe the resultant visual performance of the eye

Comparison of super-resolution algorithms applied to retinal images

A critical challenge in biomedical imaging is to optimally balance the trade-off among image resolution, signal-to-noise ratio, and acquisition time. Acquiring a high-resolution image is possible; however, it is either expensive or time consuming or both. Resolution is also limited by the physical properties of the imaging device, such as the nature and size of the input source radiation and the optics of the device. Super-resolution (SR), which is an off-line approach for improving the resolution of an image, is free of these trade-offs. Several methodologies, such as interpolation, frequency domain, regularization, and learning-based approaches, have been developed over the past several years for SR of natural images. We review some of these methods and demonstrate the positive impact expected from SR of retinal images and investigate the performance of various SR techniques. We use a fundus image as an example for simulations

Improved trapping and handling of an arboreal, montane mammal: Red Panda Ailurus fulgens

It is sometimes essential to have an animal in the hand to study some of their ecological and biological characteristics. However, capturing a solitary, cryptic, elusive arboreal species such as the red panda in the wild is challenging. We developed and successfully tested a protocol for tracking, trapping, immobilization, and handling of red pandas in the wild in eastern Nepal. We established a red panda sighting rate of 0.89 panda/day with a capture success rate of 0.6. We trapped and collared one animal in 3.7 days. On average, we took nearly 136 (range 50–317) min to capture an animal after spotting it. Further processing was completed in 38.5 (21–70) min. Before capture, we found it difficult to recognize the sex of the red panda and to differentiate sub-adults above six months from adults. However, body weight, body length, tail length, shoulder height, and chest girth can be used for diagnosis, as these attributes are smaller in sub-adults. Our method is a welfare-friendly way of trapping and handling wild red pandas. We report new morphometric data that could serve as a guide for field identification

Light &amp; Optics Conceptual Evaluation Findings from First Year Optometry Students

ABSTRACT The Light and Optics Conceptual Evaluation (LOCE) was developed to examine conceptual understanding of basic geometric and physical optics for the Active Learning in Optics and Photonics program administered by UNESCO. This 50 item test (46 multiple choice, 4 ray-tracing short answer) was administered to entering students in the Optometry professional degree (OD) program. We wanted to determine how much of the physics/optics concepts from undergraduate physics courses (a pre-requisite for entry to the OD program) were retained. In addition, the test was administered after the first year students had taken a required course in geometric and visual optics as part of their first semester courses. The LOCE was completed by two consecutive classes to the program in 2010 (n=89) and 2011 (n=84). The tests were administered the first week of the term and the test was given without any prior notice. In addition, the test was administered to the class of 2010 students after they had completed the course in geometric and visual optics. The means of the test were 22.1 (SD=4.5; range: 12-35) and 21.3(SD=5.1; range: 11-35) for the two entering classes. There was no statistical significance between the two classes (t-test, p&gt;0.05). Similarly there was no difference between the scores in terms of gender. The post-course test (administered during the first week of the second term) showed a statistically significant improvement (mean score went from 22.1 to 31.1, a 35% improvement). It should be noted that both groups of students performed worse in questions related to physical optics as well as lens imaging, while scoring best in questions related to refraction and reflection. These data should be taken into consideration when designing optics curricula for optometry (and other allied health programs such as opticianry or ophthalmology)

Rapid and Low-Cost Detection and Quantification of SARS-CoV-2 Antibody Titers of ICU Patients with Respiratory Deterioration Using a Handheld Thermo-Photonic Device

While research suggests that COVID-19 vaccines are effective in producing anti-SARS-CoV-2 antibodies that reduce the risk of COVID-19 and its potentially severe complications, how long these antibodies persist after the infection/vaccination is unknown. Longitudinal studies and rapid and scalable platforms are needed for large-scale sero-diagnosis and vaccine evaluation. In this study, we examine the efficacy of our recently-developed handheld thermo-photonic device for rapid and low-cost assessment of the adaptive immune response of COVID+ and COVID&minus; patients admitted to the intensive care unit (ICU) at a local hospital due to respiratory deterioration. Antibody testing included detection and quantification of IgG and IgM via thermo-photonic sensing of a commercially available COVID-19 IgG/IgM rapid test as well as standard measurements with quantitative enzyme-linked immunosorbent assays (qELISA). The results demonstrate that the thermo-photonic reader in conjunction with COVID-19 IgG/IgM test cassettes can detect and quantify IgG levels in COVID-19 antibody assays within the clinically relevant range and with a high correlation to those obtained from qELISA. We also found that the IgG antibody is more reliable for detecting individuals with an adaptive immune response to SARS-CoV-2 compared to the IgM antibody. The developed reader offers a low-cost, portable, and scalable solution for accessing the antibody titer of individuals against SARS-CoV-2 and can be used in local hospital settings

Distribution and habitat use of red panda in the Chitwan-Annapurna Landscape of Nepal

In Nepal, the red panda (Ailurus fulgens) has been sparsely studied, although its range covers a wide area. The present study was carried out in the previously untapped Chitwan-Annapurna Landscape (CHAL) situated in central Nepal with an aim to explore current distributional status and identify key habitat use. Extensive field surveys conducted in 10 red panda range districts were used to estimate species distribution by presence-absence occupancy modeling and to predict distribution by presence-only modeling. The presence of red pandas was recorded in five districts: Rasuwa, Nuwakot, Myagdi, Baglung and Dhading. The predictive distribution model indicated that 1,904.44 km of potential red panda habitat is available in CHAL with the protected area covering nearly 41% of the total habitat. The habitat suitability analysis based on the probability of occurrence showed only 16.58% (A = 315.81 km ) of the total potential habitat is highly suitable. Red Panda occupancy was estimated to be around 0.0667, indicating nearly 7% (218 km ) of the total habitat is occupied with an average detection probability of 0.4482±0.377. Based on the habitat use analysis, altogether eight variables including elevation, slope, aspect, proximity to water sources, bamboo abundance, height, cover, and seasonal precipitation were observed to have significant roles in the distribution of red pandas. In addition, 25 tree species were documented from red panda sign plots out of 165 species recorded in the survey area. Most common was Betula utilis followed by Rhododendron spp. and Abies spectabilis. The extirpation of red pandas in previously reported areas indicates a need for immediate action for the long-term conservation of this species in CHAL

Landscape variables affecting the Himalayan red panda Ailurus fulgens occupancy in wet season along the mountains in Nepal.

The Himalayan red panda is an endangered mammal endemic to Eastern Himalayan and South Western China. Data deficiency often hinders understanding of their spatial distribution and habitat use, which is critical for species conservation planning. We used sign surveys covering the entire potential red panda habitat over 22,453 km2 along the mid-hills and high mountains encompassing six conservation complexes in Nepal. To estimate red panda distribution using an occupancy framework, we walked 1,451 km along 446 sampled grid cells out of 4,631 grid cells in the wet season of 2016. We used single-species, single-season models to make inferences regarding covariates influencing detection and occupancy. We estimated the probability of detection and occupancy based on model-averaging techniques and drew predictive maps showing site-specific occupancy estimates. We observed red panda in 213 grid cells and found covariates such as elevation, distance to water sources, and bamboo cover influencing the occupancy. Red panda detection probability [Formula: see text] estimated at 0.70 (0.02). We estimated red panda site occupancy (sampled grid cells) and landscape occupancy (across the potential habitat) [Formula: see text] at 0.48 (0.01) and 0.40 (0.02) respectively. The predictive map shows a site-specific variation in the spatial distribution of this arboreal species along the priority red panda conservation complexes. Data on their spatial distribution may serve as a baseline for future studies and are expected to aid in species conservation planning in priority conservation complexes