An Intra-Tissue Radiometry Microprobe for Measuring Radiance In Situ in Living Tissue.

Organisms appear opaque largely because their outer tissue layers are strongly scattering to incident light; strongly absorbing pigments, such as blood, typically have narrow absorbances, such that the mean free path of light outside the absorbance peaks can be quite long. As people cannot see through tissue, they generally imagine that tissues like the brain, fat, and bone contain little or no light. However, photoresponsive opsin proteins are expressed within many of these tissues, and their functions are poorly understood. Radiance internal to tissue is also important for understanding photosynthesis. For example, giant clams are strongly absorbing yet maintain a dense population of algae deep in the tissue. Light propagation through systems like sediments and biofilms can be complex, and these communities can be major contributors to ecosystem productivity. Therefore, a method for constructing optical micro-probes for measuring scalar irradiance (photon flux intersecting a point) and downwelling irradiance (photon flux crossing a plane perpendicularly) to better understand these phenomena inside living tissue has been developed. This technique is also tractable in field laboratories. These micro-probes are made from heat-pulled optical fibers that are then secured in pulled glass pipettes. To change the angular acceptance of the probe, a 10-100 µm sized sphere of UV-curable epoxy mixed with titanium dioxide is then secured to the end of a pulled, trimmed fiber. The probe is inserted into living tissue, and its position is controlled using a micromanipulator. These probes are capable of measuring in situ tissue radiance at spatial resolutions of 10-100 µm or on the scale of single cells. These probes were used to characterize the light reaching the adipose and brain cells 4 mm below the skin of a living mouse and to characterize the light reaching similar depths within living algae-rich giant clam tissue.

Losing focus: how lens position and viewing angle affect the function of multifocal lenses in fishes.

Light rays of different wavelengths are focused at different distances when they pass through a lens (longitudinal chromatic aberration [LCA]). For animals with color vision this can pose a serious problem, because in order to perceive a sharp image the rays must be focused at the shallow plane of the photoreceptor's outer segments in the retina. A variety of fish and tetrapods have been found to possess multifocal lenses, which correct for LCA by assigning concentric zones to correctly focus specific wavelengths. Each zone receives light from a specific beam entrance position (BEP) (the lateral distance between incoming light and the center of the lens). Any occlusion of incoming light at specific BEPs changes the composition of the wavelengths that are correctly focused on the retina. Here, we calculated the effect of lens position relative to the plane of the iris and light entering the eye at oblique angles on how much of the lens was involved in focusing the image on the retina (measured as the availability of BEPs). We used rotational photography of fish eyes and mathematical modeling to quantify the degree of lens occlusion. We found that, at most lens positions and viewing angles, there was a decrease of BEP availability and in some cases complete absence of some BEPs. Given the implications of these effects on image quality, we postulate that three morphological features (aphakic spaces, curvature of the iris, and intraretinal variability in spectral sensitivity) may, in part, be adaptations to mitigate the loss of spectral image quality in the periphery of the eyes of fishes.

Examining the Effects of Chromatic Aberration, Object Distance, and Eye Shape on Image-Formation in the Mirror-Based Eyes of the Bay Scallop Argopecten irradians.

The eyes of scallops form images using a concave spherical mirror and contain two separate retinas, one layered on top of the other. Behavioral and electrophysiological studies indicate that the images formed by these eyes have angular resolutions of about 2°. Based on previous ray-tracing models, it has been thought that the more distal of the two retinas lies near the focal point of the mirror and that the proximal retina, positioned closer to the mirror at the back of the eye, receives light that is out-of-focus. Here, we propose three mechanisms through which both retinas may receive focused light: (1) chromatic aberration produced by the lens may cause the focal points for longer and shorter wavelengths to fall near the distal and proximal retinas, respectively; (2) focused light from near and far objects may fall on the distal and proximal retinas, respectively; and (3) the eyes of scallops may be dynamic structures that change shape to determine which retina receives focused light. To test our hypotheses, we used optical coherence tomography (OCT), a method of near-infrared optical depth-ranging, to acquire virtual cross-sections of live, intact eyes from the bay scallop Argopecten irradians Next, we used a custom-built ray-tracing model to estimate the qualities of the images that fall on an eye's distal and proximal retinas as functions of the wavelengths of light entering the eye (400-700 nm), object distances (0.01-1 m), and the overall shape of the eye. When we assume 550 nm wavelength light and object distances greater than 0.01 m, our model predicts that the angular resolutions of the distal and proximal retinas are 2° and 7°, respectively. Our model also predicts that neither chromatic aberration nor differences in object distance lead to focused light falling on the distal and proximal retinas simultaneously. However, if scallops can manipulate the shapes of their eyes, perhaps through muscle contractions, we speculate that they may be able to influence the qualities of the images that fall on their proximal retinas and-to a lesser extent-those that fall on their distal retinas as well.

Comment on "Open-ocean fish reveal an omnidirectional solution to camouflage in polarized environments".

Brady et al (Reports, 20 November 2015, p. 965) claimed that the silvery sides of certain fish are cryptic when viewed by animals with polarization sensitivity, which they termed "polarocrypsis." After examining their evidence, we find this claim to be unsupported due to (i) pseudoreplication, (ii) confounding polarization contrast with intensity contrast, and (iii) measurements taken at very shallow depths.

Intuitive representation of photopolarimetric data using the polarization ellipse.

Photopolarimetry is the spatial characterization of light polarization. Unlike intensity or wavelength, we are largely insensitive to polarization and therefore find it hard to explore the multidimensional data that photopolarimetry produces (two spatial dimensions plus four polarization dimensions). Many different ways for presenting and exploring this modality of light have been suggested. Most of these ignore circular polarization, include multiple image panes that make correlating structure with polarization difficult, and obscure the main trends with overly detailed information and often misleading colour maps. Here, we suggest a novel way for presenting the main results from photopolarimetric analyses. By superimposing a grid of polarization ellipses onto the RGB image, the full polarization state of each cell is intuitively conveyed to the reader. This method presents linear and circular polarization as well as ellipticity in a graphical manner, does not require multiple panes, facilitates the correlation between structure and polarization, and requires the addition of only three novel colours. We demonstrate its usefulness in a biological context where we believe it would be most relevant.

Circularly Polarized Light as a Communication Signal in Mantis Shrimps.

Animals that communicate using conspicuous body patterns face a trade-off between desired detection by intended receivers and undesired detection from eavesdropping predators, prey, rivals, or parasites. In some cases, this trade-off favors the evolution of signals that are both hidden from predators and visible to conspecifics. Animals may produce covert signals using a property of light that is invisible to those that they wish to evade, allowing them to hide in plain sight (e.g., dragonfish can see their own, otherwise rare, red bioluminescence). The use of the polarization of light is a good example of a potentially covert communication channel, as very few vertebrates are known to use polarization for object-based vision. However, even these patterns are vulnerable to eavesdroppers, as sensitivity to the linearly polarized component of light is widespread among invertebrates due to their intrinsically polarization sensitive photoreceptors. Stomatopod crustaceans appear to have gone one step further in this arms race and have evolved a sensitivity to the circular polarization of light, along with body patterns producing it. However, to date we have no direct evidence that any of these marine crustaceans use this modality to communicate with conspecifics. We therefore investigated circular polarization vision of the mantis shrimp Gonodactylaceus falcatus and demonstrate that (1) the species produces strongly circularly polarized body patterns, (2) they discriminate the circular polarization of light, and (3) that they use circular polarization information to avoid occupied burrows when seeking a refuge.

Photosymbiotic giant clams are transformers of solar flux.

'Giant' tridacnid clams have evolved a three-dimensional, spatially efficient, photodamage-preventing system for photosymbiosis. We discovered that the mantle tissue of giant clams, which harbours symbiotic nutrition-providing microalgae, contains a layer of iridescent cells called iridocytes that serve to distribute photosynthetically productive wavelengths by lateral and forward-scattering of light into the tissue while back-reflecting non-productive wavelengths with a Bragg mirror. The wavelength- and angle-dependent scattering from the iridocytes is geometrically coupled to the vertically pillared microalgae, resulting in an even re-distribution of the incoming light along the sides of the pillars, thus enabling photosynthesis deep in the tissue. There is a physical analogy between the evolved function of the clam system and an electric transformer, which changes energy flux per area in a system while conserving total energy. At incident light levels found on shallow coral reefs, this arrangement may allow algae within the clam system to both efficiently use all incident solar energy and avoid the photodamage and efficiency losses due to non-photochemical quenching that occur in the reef-building coral photosymbiosis. Both intra-tissue radiometry and multiscale optical modelling support our interpretation of the system's photophysics. This highly evolved 'three-dimensional' biophotonic system suggests a strategy for more efficient, damage-resistant photovoltaic materials and more spatially efficient solar production of algal biofuels, foods and chemicals.

Simplifying numerical ray tracing for characterization of optical systems.

Ray tracing, a computational method for tracing the trajectories of rays of light through matter, is often used to characterize mechanical or biological visual systems with aberrations that are larger than the effect of diffraction inherent in the system. For example, ray tracing may be used to calculate geometric point spread functions (PSFs), which describe the image of a point source after it passes through an optical system. Calculating a geometric PSF is useful because it gives an estimate of the detail and quality of the image formed by a given optical system. However, when using ray tracing to calculate a PSF, the accuracy of the estimated PSF directly depends on the number of discrete rays used in the calculation; higher accuracies may require more computational power. Furthermore, adding optical components to a modeled system will increase its complexity and require critical modifications so that the model will describe the system correctly, sometimes necessitating a completely new model. Here, we address these challenges by developing a method that represents rays of light as a continuous function that depends on the light's initial direction. By utilizing Chebyshev approximations (via the chebfun toolbox in MATLAB) for the implementation of this method, we greatly simplified the calculations for the location and direction of the rays. This method provides high precision and fast calculation speeds that allow the characterization of any symmetrical optical system (with a centered point source) in an analytical-like manner. Next, we demonstrate our methods by showing how they can easily calculate PSFs for complicated optical systems that contain multiple refractive and/or reflective interfaces.