Light sheet fluorescence microscopy for in situ cell interaction analysis in mouse lymph nodes.

Reactive lymph nodes (LNs) are sites where pMHC-loaded dendritic cells (DCs) interact with rare cognate T cells, leading to their clonal expansion. While DC interactions with T cell subsets critically shape the ensuing immune response, surprisingly little is known on their spatial orchestration at physiologically T cell low precursor frequencies. Light sheet fluorescence microscopy and one of its implementations, selective plane illumination microscopy (SPIM), is a powerful method to obtain precise spatial information of entire organs of 0.5-10mm diameter, the size range of murine LNs. Yet, its usefulness for immunological research has thus far not been comprehensively explored. Here, we have tested and defined protocols that preserve fluorescent protein function during lymphoid tissue clearing required for SPIM. Reconstructions of SPIM-generated 3D data sets revealed that calibrated numbers of adoptively transferred T cells and DCs are successfully detected at a single cell level within optically cleared murine LNs. Finally, we define parameters to quantify specific interactions between antigen-specific T cells and pMHC-bearing DCs in murine LNs. In sum, our studies describe the successful application of light sheet fluorescence microscopy to immunologically relevant tissues.

Variation in Coral Photosynthesis, Respiration and Growth Characteristics in Contrasting Light Microhabitats: An Analogue to Plants in Forest Gaps and Understoreys?

1. The often complex architecture of coral reefs forms a diversity of light microhabitats. Analogous to patterns in forest plants, light variation may drive strategies for efficient light utilization and metabolism in corals. 2. We investigated the spatial distribution of light regimes in a spur-and-groove reef environment and examine the photophysiology of the coral Montipora monasteriata (Forskal 1775), a species with a wide habitat distribution. Specifically, we examined the variation in tissue and skeletal thickness, and photosynthetic and metabolic responses among contrasting light microhabitats. 3. Daily irradiances reaching corals in caves and under overhangs were 1-5 and 30-40% of those in open habitats at similar depth (3-5 m), respectively. Daily rates of net photosynthesis of corals in cave habitats approximated zero, suggesting more than two orders of magnitude variation in scope for growth across habitats. 4. Three mechanisms of photoadaptation or acclimation were observed in cave and overhang habitats: (1) a 20-50% thinner tissue layer and 40-60% thinner skeletal plates, maximizing light interception per unit mass; (2) a two- to threefold higher photosynthetic efficiency per unit biomass; and (3) low rates of dark respiration. 5. Specimens from open and cave habitats displayed a high capacity to acclimate to downshifts or upshifts in irradiance, respectively. However, specimens in caves displayed limited acclimation to further irradiance reduction, indicating that these live near their irradiance limit. 6. Analogous to patterns for some plant species in forest gaps, the morphological plasticity and physiological flexibility of M. monasteriata enable it to occupy light habitats that vary by more than two orders of magnitude.

Demonstration of the spatial separation of the entangled quantum sidebands of an optical field

Quantum optics experiments on bright beams are based on the spectral analysis of field fluctuations and typically probe correlations between radio-frequency sideband modes. However, the extra degree of freedom represented by this dual-mode picture is generally ignored. We demonstrate the experimental operation of a device which can be used to separate the quantum sidebands of an optical field. We use this device to explicitly demonstrate the quantum entanglement between the sidebands of a squeezed beam.

Ross River virus disease clusters and spatial relationship with mosquito biting exposure in Redland Shire, southern Queensland, Australia

The spatial heterogeneity in the risk of Ross River virus (family Togaviridae, genus Alphavirus, RRV) disease, the most common mosquito-borne disease in Australia, was examined in Redland Shire in southern Queensland, Australia. Disease cases, complaints from residents of intense mosquito biting exposure, and human population data were mapped using a geographic information system. Surface maps of RRV disease age-sex standardized morbidity ratios and mosquito biting complaint morbidity ratios were created. To determine whether there was significant spatial variation in disease and complaint patterns, a spatial scan analysis method was used to test whether the number of cases and complaints was distributed according to underlying population at risk. Several noncontiguous areas in proximity to productive saline water habitats of Aedes vigilax (Skuse), a recognized vector of RRV, had higher than expected numbers of RRV disease cases and complaints. Disease rates in human populations in areas which had high numbers of adult Ae. vigilax in carbon dioxide- and octenol-baited light traps were up to 2.9 times those in areas that rarely had high numbers of mosquitoes. It was estimated that targeted control of adult Ae. vigilax in these high-risk areas could potentially reduce the RRV disease incidence by an average of 13.6%. Spatial correlation was found between RRV disease risk and complaints from residents of mosquito biting. Based on historical patterns of RRV transmission throughout Redland Shire and estimated future human population growth in areas with higher than average RRV disease incidence, it was estimated that RRV incidence rates will increase by 8% between 2001 and 2021. The use of arbitrary administrative areas that ranged in size from 4.6 to 318.3 km2, has the potential to mask any small scale heterogeneity in disease patterns. With the availability of georeferenced data sets and high-resolution imagery, it is becoming more feasible to undertake spatial analyses at relatively small scales.

Local edge detectors: A substrate for fine spatial vision at low temporal frequencies in rabbit retina

Visual acuity is limited by the size and density of the smallest retinal ganglion cells, which correspond to the midget ganglion cells in primate retina and the beta- ganglion cells in cat retina, both of which have concentric receptive fields that respond at either light- On or light- Off. In contrast, the smallest ganglion cells in the rabbit retina are the local edge detectors ( LEDs), which respond to spot illumination at both light- On and light- Off. However, the LEDs do not predominate in the rabbit retina and the question arises, what role do they play in fine spatial vision? We studied the morphology and physiology of LEDs in the isolated rabbit retina and examined how their response properties are shaped by the excitatory and inhibitory inputs. Although the LEDs comprise only similar to 15% of the ganglion cells, neighboring LEDs are separated by 30 - 40 mu m on the visual streak, which is sufficient to account for the grating acuity of the rabbit. The spatial and temporal receptive- field properties of LEDs are generated by distinct inhibitory mechanisms. The strong inhibitory surround acts presynaptically to suppress both the excitation and the inhibition elicited by center stimulation. The temporal properties, characterized by sluggish onset, sustained firing, and low bandwidth, are mediated by the temporal properties of the bipolar cells and by postsynaptic interactions between the excitatory and inhibitory inputs. We propose that the LEDs signal fine spatial detail during visual fixation, when high temporal frequencies are minimal.

Mach edges: a key role for 3rd derivative filters in spatial vision

Edges are key points of information in visual scenes. One important class of models supposes that edges correspond to the steepest parts of the luminance profile, implying that they can be found as peaks and troughs in the response of a gradient (first-derivative) filter, or as zero-crossings (ZCs) in the second-derivative. A variety of multi-scale models are based on this idea. We tested this approach by devising a stimulus that has no local peaks of gradient and no ZCs, at any scale. Our stimulus profile is analogous to the classic Mach-band stimulus, but it is the local luminance gradient (not the absolute luminance) that increases as a linear ramp between two plateaux. The luminance profile is a smoothed triangle wave and is obtained by integrating the gradient profile. Subjects used a cursor to mark the position and polarity of perceived edges. For all the ramp-widths tested, observers marked edges at or close to the corner points in the gradient profile, even though these were not gradient maxima. These new Mach edges correspond to peaks and troughs in the third-derivative. They are analogous to Mach bands - light and dark bars are seen where there are no luminance peaks but there are peaks in the second derivative. Here, peaks in the third derivative were seen as light-to-dark edges, troughs as dark-to-light edges. Thus Mach edges are inconsistent with many standard edge detectors, but are nicely predicted by a new model that uses a (nonlinear) third-derivative operator to find edge points.

Low spatial frequencies are suppressively masked across spatial scale, orientation, field position, and eye of origin

Masking is said to occur when a mask stimulus interferes with the visibility of a target (test) stimulus. One widely held view of this process supposes interactions between mask and test mechanisms (cross-channel masking), and explicit models (e.g., J. M. Foley, 1994) have proposed that the interactions are inhibitory. Unlike a within-channel model, where masking involves the combination of mask and test stimulus within a single mechanism, this cross-channel inhibitory model predicts that the mask should attenuate the perceived contrast of a test stimulus. Another possibility is that masking is due to an increase in noise, in which case, perception of contrast should be unaffected once the signal exceeds detection threshold. We use circular patches and annuli of sine-wave grating in contrast detection and contrast matching experiments to test these hypotheses and investigate interactions across spatial frequency, orientation, field position, and eye of origin. In both types of experiments we found substantial effects of masking that can occur over a factor of 3 in spatial frequency, 45° in orientation, across different field positions and between different eyes. We found the effects to be greatest at the lowest test spatial frequency we used (0.46 c/deg), and when the mask and test differed in all four dimensions simultaneously. This is surprising in light of previous work where it was concluded that suppression from the surround was strictly monocular (C. Chubb, G. Sperling, & J. A. Solomon, 1989). The results confirm that above detection threshold, cross-channel masking involves contrast suppression and not (purely) mask-induced noise. We conclude that cross-channel masking can be a powerful phenomenon, particularly at low test spatial frequencies and when mask and test are presented to different eyes. © 2004 ARVO.

Spatial contrast sensitivity and external noise: applications to optical and neural modulation transfer functions

The thesis will show how to equalise the effect of quantal noise across spatial frequencies by keeping the retinal flux (If-2) constant. In addition, quantal noise is used to study the effect of grating area and spatial frequency on contrast sensitivity resulting in the extension of the new contrast detection model describing the human contrast detection system as a simple image processor. According to the model the human contrast detection system comprises low-pass filtering due to ocular optics, addition of light dependent noise at the event of quantal absorption, high-pass filtering due to the neural visual pathways, addition of internal neural noise, after which detection takes place by a local matched filter, whose sampling efficiency decreases as grating area is increased. Furthermore, this work will demonstrate how to extract both the optical and neural modulation transfer functions of the human eye. The neural transfer function is found to be proportional to spatial frequency up to the local cut-off frequency at eccentricities of 0 - 37 deg across the visual field. The optical transfer function of the human eye is proposed to be more affected by the Stiles-Crawford -effect than generally assumed in the literature. Similarly, this work questions the prevailing ideas about the factors limiting peripheral vision by showing that peripheral optical acts as a low-pass filter in normal viewing conditions, and therefore the effect of peripheral optics is worse than generally assumed.

The effect of intraocular scattered light on the contrast sensitivity function

Intraocular light scatter is high in certain subject groups eg the elderly, due to increased optical media turbidity, which scatters and attenuates light travelling towards the retina. This causes reduced retinal contrast especially in the presence of glare light. Such subjects have depressed Contrast Sensitivity Functions (CSF). Currently available clinical tests do not effectively reflect this visual disability. Intraocular light scatter may be quantified by measuring the CSF with and without glare light and calculating Light Scatter Factors (LSF). To record the CSF on clinically available equipment (Nicolet CS2000), several psychophysical measurement techniques were investigated, and the 60 sec Method of Increasing Contrast was selected as the most appropriate. It was hypothesised that intraocular light scatter due to particles of different dimensions could be identified by glare sources at wide (30°) and narrow (3.5°) angles. CSFs andLSFs were determined for: (i) Subjects in young, intermediate and old age groups. (ii) Subjects during recovery from large amounts of induced corneal oedema. (iii) A clinical sample of contact lens (CL) wearers with a group of matched controls. The CSF was attenuated at all measured spatial frequencies with the intermediate and old group compared to the young group. High LSF values were found only in the old group (over 60 years). It was concluded that CSF attenuation in the intermediate group was due to reduced pupil size, media absorption and/or neural factors. In the old group, the additional factor was high intraocular light scatter levels of lenticular origin. The rate of reduction of the LSF for the 3.5° glare angle was steeper than that for the 30° angle, following induced corneal oedema. This supported the hypothesis, as it was anticipated that epithelial oedema would recover more rapidly than stromal oedema. CSFs and LSFs were markedly abnormal in the CL wearers. The analytical details and the value of these investigative techniques in contact lens research are discussed.

Multispectral imaging of the ocular fundus using light emitting diode illumination

We present an imaging system based on light emitting diode (LED) illumination that produces multispectral optical images of the human ocular fundus. It uses a conventional fundus camera equipped with a high power LED light source and a highly sensitive electron-multiplying charge coupled device camera. It is able to take pictures at a series of wavelengths in rapid succession at short exposure times, thereby eliminating the image shift introduced by natural eye movements (saccades). In contrast with snapshot systems the images retain full spatial resolution. The system is not suitable for applications where the full spectral resolution is required as it uses discrete wavebands for illumination. This is not a problem in retinal imaging where the use of selected wavelengths is common. The modular nature of the light source allows new wavelengths to be introduced easily and at low cost. The use of wavelength-specific LEDs as a source is preferable to white light illumination and subsequent filtering of the remitted light as it minimizes the total light exposure of the subject. The system is controlled via a graphical user interface that enables flexible control of intensity, duration, and sequencing of sources in synchrony with the camera. Our initial experiments indicate that the system can acquire multispectral image sequences of the human retina at exposure times of 0.05 s in the range of 500-620 nm with mean signal to noise ratio of 17 dB (min 11, std 4.5), making it suitable for quantitative analysis with application to the diagnosis and screening of eye diseases such as diabetic retinopathy and age-related macular degeneration.

Mach bands and multiscale models of spatial vision:the role of first, second, and third derivative operators in encoding bars and edges

Ernst Mach observed that light or dark bands could be seen at abrupt changes of luminance gradient in the absence of peaks or troughs in luminance. Many models of feature detection share the idea that bars, lines, and Mach bands are found at peaks and troughs in the output of even-symmetric spatial filters. Our experiments assessed the appearance of Mach bands (position and width) and the probability of seeing them on a novel set of generalized Gaussian edges. Mach band probability was mainly determined by the shape of the luminance profile and increased with the sharpness of its corners, controlled by a single parameter (n). Doubling or halving the size of the images had no significant effect. Variations in contrast (20%-80%) and duration (50-300 ms) had relatively minor effects. These results rule out the idea that Mach bands depend simply on the amplitude of the second derivative, but a multiscale model, based on Gaussian-smoothed first- and second-derivative filtering, can account accurately for the probability and perceived spatial layout of the bands. A key idea is that Mach band visibility depends on the ratio of second- to first-derivative responses at peaks in the second-derivative scale-space map. This ratio is approximately scale-invariant and increases with the sharpness of the corners of the luminance ramp, as observed. The edges of Mach bands pose a surprisingly difficult challenge for models of edge detection, but a nonlinear third-derivative operation is shown to predict the locations of Mach band edges strikingly well. Mach bands thus shed new light on the role of multiscale filtering systems in feature coding. © 2012 ARVO.

The two forms of visuo-spatial perspective taking are differently embodied and subserve different spatial prepositions

We set out to distinguish level 1 (VPT-1) and level 2 (VPT-2) perspective taking with respect to the embodied nature of the underlying processes as well as to investigate their dependence or independence of response modality (motor vs. verbal). While VPT-1 reflects understanding of what lies within someone else’s line of sight, VPT-2 involves mentally adopting someone else’s spatial point of view. Perspective taking is a high-level conscious and deliberate mental transformation that is crucially placed at the convergence of perception, mental imagery, communication, and even theory of mind in the case of VPT-2. The differences between VPT-1 and VPT-2 mark a qualitative boundary between humans and apes, with the latter being capable of VPT-1 but not of VPT-2. However, our recent data showed that VPT-2 is best conceptualized as the deliberate simulation or emulation of a movement, thus underpinning its embodied origins. In the work presented here we compared VPT-2 to VPT-1 and found that VPT-1 is not at all, or very differently embodied. In a second experiment we replicated the qualitatively different patterns for VPT-1 and VPT-2 with verbal responses that employed spatial prepositions. We conclude that VPT-1 is the cognitive process that subserves verbal localizations using “in front” and “behind,” while VPT-2 subserves “left” and “right” from a perspective other than the egocentric. We further conclude that both processes are grounded and situated, but only VPT-2 is embodied in the form of a deliberate movement simulation that increases in mental effort with distance and incongruent proprioception. The differences in cognitive effort predict differences in the use of the associated prepositions. Our findings, therefore, shed light on the situated, grounded and embodied basis of spatial localizations and on the psychology of their use.

Optical modulators with 2D layered materials

Light modulation is an essential operation in photonics and optoelectronics. With existing and emerging technologies increasingly demanding compact, efficient, fast and broadband optical modulators, high-performance light modulation solutions are becoming indispensable. The recent realization that 2D layered materials could modulate light with superior performance has prompted intense research and significant advances, paving the way for realistic applications. In this Review, we cover the state of the art of optical modulators based on 2D materials, including graphene, transition metal dichalcogenides and black phosphorus. We discuss recent advances employing hybrid structures, such as 2D heterostructures, plasmonic structures, and silicon and fibre integrated structures. We also take a look at the future perspectives and discuss the potential of yet relatively unexplored mechanisms, such as magneto-optic and acousto-optic modulation.

Conical refraction with low-coherent light sources

We report on conical refraction (CR) experiments with low-coherent light sources such as light-emitting diodes (LEDs) that demonstrated different CR patterns. The change of a pinhole size from 25 to 100 μm reduced the spatial coherence of the LED radiation and resulted in the disappearance of the dark Poggendorf ring in the Lloyd's plane. This is attributed to the interference nature of the Lloyd's distribution and is found to be in excellent agreement with the paraxial dual-cone model of CR.

Multimode Atomic Pattern Formation via Enhanced Light-atom Interactions

The nonlinear interaction between light and atoms is an extensive field of study with a broad range of applications in quantum information science and condensed matter physics. Nonlinear optical phenomena occurring in cold atoms are particularly interesting because such slowly moving atoms can spatially organize into density gratings, which allows for studies involving optical interactions with structured materials. In this thesis, I describe a novel nonlinear optical effect that arises when cold atoms spatially bunch in an optical lattice. I show that employing this spatial atomic bunching provides access to a unique physical regime with reduced thresholds for nonlinear optical processes and enhanced material properties. Using this method, I observe the nonlinear optical phenomenon of transverse optical pattern formation at record-low powers. These transverse optical patterns are generated by a wave- mixing process that is mediated by the cold atomic vapor. The optical patterns are highly multimode and induce rich non-equilibrium atomic dynamics. In particular, I find that there exists a synergistic interplay between the generated optical pat- terns and the atoms, wherein the scattered fields help the atoms to self-organize into new, multimode structures that are not externally imposed on the atomic sample. These self-organized structures in turn enhance the power in the optical patterns. I provide the first detailed investigation of the motional dynamics of atoms that have self-organized in a multimode geometry. I also show that the transverse optical patterns induce Sisyphus cooling in all three spatial dimensions, which is the first observation of spontaneous three-dimensional cooling. My experiment represents a unique means by which to study nonlinear optics and non-equilibrium dynamics at ultra-low required powers.