Multidimensional Approach to Comparative Avian Visual Systems

Since the birth of visual ecology, comparative studies on how birds see their world have been limited to a small number of species and tended to focus on a single visual trait. This approach has constrained our ability to understand the diversity and evolution of the avian visual system. The goal of this dissertation was to characterize multiple visual dimensions on bird groups that are highly speciouse (e.g., Passeriformes), and test some hypotheses and predictions, using modern comparative tools, on the relationship between different visual traits and their association with visual information sampling behaviors. First, I developed a novel method for characterizing quantitatively the retinal topography (e.g., variation in cell density across the retina) of different bird species in a standardized manner. Second, using this method, I established that retinal configuration has converged particularly in terrestrial vertebrates into three types of retinal specializations: fovea, area, and visual streak, with the highest, intermediate, and lowest peak and peripheral ganglion cell densities, respectively. The implication is that foveate species may have more enhanced visual centers in the brain than non-foveate vertebrates. Third, forest passerines that form multi-species flocks and belong to an insectivore niche differ in their visual system configuration, which appeared associated to behavioral specializations to enhance foraging opportunities: species that searched for food at steep angles had relatively wide binocular fields with a high degree of eye movement right above their short bills, whereas species that searched for food at shallower angles had narrower binocular fields with a high degree of eye movement below their bills. Eye movement allows these species to move their fovea around to visually search for food in the complex forest environment. Fourth, I studied the visual system configuration of nine species of closely related emberizid sparrows, which appear to maximize binocular vision, even seeing their bill tips, to enhance food detection and handling. Additionally, species with more visual coverage had higher visual acuity, which may compensate for their larger blind spots above their foveae, enhancing predator detection. Overall, the visual configuration of these passive prey foragers is substantially different from previously studied avian groups (e.g., sit-and-wait and tactile foragers). Finally, I studied the visual system configuration and visual exploratory behavior of 29 North American bird species across 14 Families. I found that species with a wider blind spot in the visual field (pecten) tended to move their heads at a higher rate probably to compensate for the lack of visual information. Additionally, species with a more pronounced difference in cell density between the fovea and the retinal periphery tended to have a higher degree of eye movement likely to enhance their ability to move their fovea around to gather high quality information. Overall, the avian visual system seems to have specializations to enhance both foraging and anti-predator behaviors that differ greatly between species probably to adjust to specific environmental conditions

Change blindness: eradication of gestalt strategies

Arrays of eight, texture-defined rectangles were used as stimuli in a one-shot change blindness (CB) task where there was a 50% chance that one rectangle would change orientation between two successive presentations separated by an interval. CB was eliminated by cueing the target rectangle in the first stimulus, reduced by cueing in the interval and unaffected by cueing in the second presentation. This supports the idea that a representation was formed that persisted through the interval before being 'overwritten' by the second presentation (Landman et al, 2003 Vision Research 43149–164]. Another possibility is that participants used some kind of grouping or Gestalt strategy. To test this we changed the spatial position of the rectangles in the second presentation by shifting them along imaginary spokes (by ±1 degree) emanating from the central fixation point. There was no significant difference seen in performance between this and the standard task [F(1,4)=2.565, p=0.185]. This may suggest two things: (i) Gestalt grouping is not used as a strategy in these tasks, and (ii) it gives further weight to the argument that objects may be stored and retrieved from a pre-attentional store during this task

Computational cytometer based on magnetically modulated coherent imaging and deep learning.

Detecting rare cells within blood has numerous applications in disease diagnostics. Existing rare cell detection techniques are typically hindered by their high cost and low throughput. Here, we present a computational cytometer based on magnetically modulated lensless speckle imaging, which introduces oscillatory motion to the magnetic-bead-conjugated rare cells of interest through a periodic magnetic force and uses lensless time-resolved holographic speckle imaging to rapidly detect the target cells in three dimensions (3D). In addition to using cell-specific antibodies to magnetically label target cells, detection specificity is further enhanced through a deep-learning-based classifier that is based on a densely connected pseudo-3D convolutional neural network (P3D CNN), which automatically detects rare cells of interest based on their spatio-temporal features under a controlled magnetic force. To demonstrate the performance of this technique, we built a high-throughput, compact and cost-effective prototype for detecting MCF7 cancer cells spiked in whole blood samples. Through serial dilution experiments, we quantified the limit of detection (LoD) as 10 cells per millilitre of whole blood, which could be further improved through multiplexing parallel imaging channels within the same instrument. This compact, cost-effective and high-throughput computational cytometer can potentially be used for rare cell detection and quantification in bodily fluids for a variety of biomedical applications

Zebrafish Eye Development: Rac and the Creepy Crawlers of the Eye

During vertebrate eye development the optic vesicles protrude from either side of the brain and form the optic cups. As an optic cup starts to surround the lens a groove on the ventral side of the eye forms, known as the choroid fissure (CF). Normally, the CF will close around the optic nerve and hyaloid vasculature. If this process does not occur properly it results in a keyhole opening in the eye known as coloboma. This results in blindness and affects nearly 1 in 4-5,000 births. Zebrafish were utilized as a model for eye development to study CF closure (CFC) as they utilize similar gene expression and cellular signaling. Previously, a transient β-catenin/actin fusion seam within the fusing CF was observed indicating the formation of cell-to-cell contacts. Rac, a small G-protein, regulates actin cytoskeleton reorganization and formation of lamellipodia required for cell-to-cell adhesion. These lamellipodia increase interactions between cells increasing contacts that could form adherens junctions. I hypothesized Rac would be expressed prior to CFC and dissipate upon CFC completion, similar to adhesion proteins. To determine Rac’s localization, embryos were cryosectioned at 47 and 49-hours post-fertilization (hpf) and Rac immunofluorescence was observed. These data demonstrated Rac is present within the CF edges at 47 hpf and dissipates the CF fusion seam as CFC progresses in wildtypes embryos around 49 hpf. Quantification of these data further demonstrated a progressive fusion event that initiates in the central section of the CF and moves bidirectionally towards the proximal and distal edges, emulating a zipper-like fashion. in vivo analysis of Rx3:GFP embryos (neuroretina labeled) identified a subpopulation of cells that are present within the CF at 24 hpf. This population of cells appear highly protrusive and “reach” in multiple directions. Further analysis of Rac embryos identified these “reaching cells” as Rac positive. in vivo analysis of this cell population revealed that seven identified categories of reaching cells can be divided into three stages of CFC. Rac is also required for reaching cells. When observing the Rac-DN embryo no reaching cells were ever observed, regardless of heat-shocking time. The Rac-DN embryos showed an abnormal optic cup angle and unusual cuboidal cells shapes (early heat-shock). In later heat-shocked times the abnormal angle and unusual cell shapes were resolved, however, there were unusual division patterns that were observed. Further investigation is ongoing to identify the role of Rac in this cell population and the role of “reaching cells” during zebrafish eye development

Adaptive Optical Devices in Vision Science

In this thesis we investigate the use of adaptive optical devices in three different areas of vision science. These areas are defocus perception, retinal imaging and severe vision loss. Birefringent material has been utilised to produce optical components that can control the angle of refraction of incident light. Using a ferroelectric liquid crystal (FLC) the orientation of linear polarised light can be controlled. This provides us with the ability to switch between the two refractive indices of birefringent materials at very high speeds. A focus switchable lens (FSL) has been made from barium borate (BBO), and a ferroelectric liquid crystal to switch between equal and opposite defocus levels to determine the optimum focus correction by making use of the human eye's sensitivity to flicker. Flicker simulation result indicate that there is a high dependence of flicker sensitivity to the flicker frequency. High spatial frequencies also increased the ability to perceive small defocus shifts. Promising results have been obtained showing a person is able to find a point of equal defocus using flicker more accurately than they would be able to find perfect focus. The same focus switching lens system has the ability to produce fast focus switching cameras. Its potential has been analysed for the use in retinal cameras to ease the process of obtaining good quality images of the optic nerve and providing such cameras with the ability to switch focus within the depth of the optic nerve head at high speeds. Simulation results showed that two FSLs positioned within the zoom system of the imaging arm are able to create focal point shifts of very small amounts. Finally, collaborative research has been conducted in the use of a birefringent prism in conjunction with an FLC to create image jitter that can enhance visual performance in people with severe visual impairment. Image jitter created on-screen and via an optical system was tested. Patients were able to increase their reading speed and improve their ability to discriminate between happy and sad faces