Derya Akkaynak

Use of commercial off-the-shelf digital cameras for scientific data acquisition and scene-specific color calibration

Commercial off-the-shelf digital cameras are inexpensive and easy-to-use instruments that can be used for quantitative scientific data acquisition if images are captured in raw format and processed so that they maintain a linear relationship with scene radiance. Here we describe the image-processing steps required for consistent data acquisition with color cameras. In addition, we present a method for scene-specific color calibration that increases the accuracy of color capture when a scene contains colors that are not well represented in the gamut of a standard color-calibration target. We demonstrate applications of the proposed methodology in the fields of biomedical engineering, artwork photography, perception science, marine biology, and underwater imaging.

Smart Interface Materials Integrated with Microfluidics for On-Demand Local Capture and Release of Cells

Stimuli responsive, smart interface materials are integrated with microfluidic technologies creating new functions for a broad range of biological and clinical applications by controlling the material and cell interactions. Local capture and on-demand local release of cells are demonstrated with spatial and temporal control in a microfluidic system.

Biofluorescence in Catsharks (Scyliorhinidae): Fundamental Description and Relevance for Elasmobranch Visual Ecology

Biofluorescence has recently been found to be widespread in marine fishes, including sharks. Catsharks, such as the Swell Shark (Cephaloscyllium ventriosum) from the eastern Pacific and the Chain Catshark (Scyliorhinus retifer) from the western Atlantic, are known to exhibit bright green fluorescence. We examined the spectral sensitivity and visual characteristics of these reclusive sharks, while also considering the fluorescent properties of their skin. Spectral absorbance of the photoreceptor cells in these sharks revealed the presence of a single visual pigment in each species. Cephaloscyllium ventriosum exhibited a maximum absorbance of 484 ± 3 nm and an absorbance range at half maximum (λ1/2max) of 440–540 nm, whereas for S. retifer maximum absorbance was 488 ± 3 nm with the same absorbance range. Using the photoreceptor properties derived here, a “shark eye” camera was designed and developed that yielded contrast information on areas where fluorescence is anatomically distributed on the shark, as seen from other sharks’ eyes of these two species. Phylogenetic investigations indicate that biofluorescence has evolved at least three times in cartilaginous fishes. The repeated evolution of biofluorescence in elasmobranchs, coupled with a visual adaptation to detect it; and evidence that biofluorescence creates greater luminosity contrast with the surrounding background, highlights the potential importance of biofluorescence in elasmobranch behavior and biology.

A high throughput approach for analysis of cell nuclear deformability at single cell level

Various physiological and pathological processes, such as cell differentiation, migration, attachment, and metastasis are highly dependent on nuclear elasticity. Nuclear morphology directly reflects the elasticity of the nucleus. We propose that quantification of changes in nuclear morphology on surfaces with defined topography will enable us to assess nuclear elasticity and deformability. Here, we used soft lithography techniques to produce 3 dimensional (3-D) cell culture substrates decorated with micron sized pillar structures of variable aspect ratios and dimensions to induce changes in cellular and nuclear morphology. We developed a high content image analysis algorithm to quantify changes in nuclear morphology at the single-cell level in response to physical cues from the 3-D culture substrate. We present that nuclear stiffness can be used as a physical parameter to evaluate cancer cells based on their lineage and in comparison to non-cancerous cells originating from the same tissue type. This methodology can be exploited for systematic study of mechanical characteristics of large cell populations complementing conventional tools such as atomic force microscopy and nanoindentation.

What is the Space of Attenuation Coefficients in Underwater Computer Vision

Underwater image reconstruction methods require the knowledge of wideband attenuation coefficients per color channel. Current estimation methods for these coefficients require specialized hardware or multiple images, and none of them leverage the multitude of existing ocean optical measurements as priors. Here, we aim to constrain the set of physically-feasible wideband attenuation coefficients in the ocean by utilizing water attenuation measured worldwide by oceanographers. We calculate the space of valid wideband effective attenuation coefficients in the 3D RGB domain and find that a bound manifold in 3-space sufficiently represents the variation from the clearest to murkiest waters. We validate our model using in situ experiments in two different optical water bodies, the Red Sea and the Mediterranean. Moreover, we show that contradictory to the common image formation model, the coefficients depend on the imaging range and object reflectance, and quantify the errors resulting from ignoring these dependencies.

Changeable camouflage: how well can flounder resemble the colour and spatial scale of substrates in their natural habitats?

Flounder change colour and pattern for camouflage. We used a spectrometer to measure reflectance spectra and a digital camera to capture body patterns of two flounder species camouflaged on four natural backgrounds of different spatial scale (sand, small gravel, large gravel and rocks). We quantified the degree of spectral match between flounder and background relative to the situation of perfect camouflage in which flounder and background were assumed to have identical spectral distribution. Computations were carried out for three biologically relevant observers: monochromatic squid, dichromatic crab and trichromatic guitarfish. Our computations present a new approach to analysing datasets with multiple spectra that have large variance. Furthermore, to investigate the spatial match between flounder and background, images of flounder patterns were analysed using a custom program originally developed to study cuttlefish camouflage. Our results show that all flounder and background spectra fall within the same colour gamut and that, in terms of different observer visual systems, flounder matched most substrates in luminance and colour contrast. Flounder matched the spatial scales of all substrates except for rocks. We discuss findings in terms of flounder biology; furthermore, we discuss our methodology in light of hyperspectral technologies that combine high-resolution spectral and spatial imaging.

Using spectrometry and photography to study color underwater

Most underwater images are post-processed to look pleasing to human viewers. This often results in unrealistically saturated colors. Images taken for the purpose of studying color-sensitive topics such as marine animal coloration, must represent colors as accurately as possible and should not be arbitrarily enhanced. This first requires a transformation of colors from the camera color space to a device independent space. In this paper we present a method for transforming raw camera-RGB colors to a device independent space, optimizing this transformation for a particular underwater habitat. We have conducted an extensive study of the variation of color appearance underwater at a dive site in the Aegean Sea by taking 21 sets of spectrometry and irradiance readings with corresponding photographs of four different color standards. Spectral and photographic data were collected in the presence of natural daylight at various depths and under different weather conditions. In addition to the color charts, we have built a “habitat chart” to optimize this camera-specific transformation for a given dive site.

Use of spectroscopy for assessment of color discrimination in animal vision

Animals use color vision for a number of tasks including food localization, object recognition, communication, and mate selection. For these and other specific behaviors involving the use of color cues, models that quantify color discriminability have been developed. These models take as input the photoreceptor spectral sensitivities of the animal and radiance spectra of the surfaces of interest. These spectra are usually acquired using spectroscopic instruments that collect point-by-point data and can easily yield signals contaminated with neighboring colors if not operated carefully. In this paper, I present an equation that relates the optical fiber diameter and numerical aperture to the measurement angle and distance needed to record uncontaminated spectra. I demonstrate its utility by testing the discriminability of two solid colors for the visual systems of a dichromatic ferret and a trichromatic frog in (1) a conspicuous scenario where the colors have little spectral overlap and (2) a perfect camouflage scenario where the spectra are identical. This equation is derived from geometrical optics and is applicable to spectroscopic measurements in all fields.

Dramatic Fighting by Male Cuttlefish for a Female Mate

Male cuttlefish compete for females with a repertoire of visually dramatic behaviors. Laboratory experiments have explored this system in Sepia officinalis, but corroborative field data have eluded collection attempts by many researchers. While scuba diving in Turkey, we fortuitously filmed an intense sequence of consort/intruder behaviors in which the consort lost and then regained his female mate from the intruder. These agonistic bouts escalated in stages, leading to fast dramatic expression of the elaborate intense zebra display and culminating in biting and inking as the intruder male attempted a forced copulation of the female. When analyzed in the context of game theory, the patterns of fighting behavior were more consistent with mutual assessment than self-assessment of fighting ability. Additional observations of these behaviors in nature are needed to conclusively determine which models best represent conflict resolution, but our field observations agree with laboratory findings and provide a valuable perspective.