Derya Akkaynak

Derya Akkaynak
Massachusetts Institute of Technology | MIT · Department of Mechanical Engineering

Oceanographer, Aerospace engineer, Mechanical engineer BS, MSc, PhD

About

42
Publications
28,667
Reads
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875
Citations
Introduction
I am an oceanographer, generally interested in underwater imaging and most interested in camouflage of animals like octopus and cuttlefish. I work with optical data from one or multi-channel spectral imagers or RGB cameras, and use image processing, computer vision and machine learning; also interested in medical and bio-medical image problems. I am the founder of the citizen science project www.divers4oceanography.org.
Additional affiliations
September 2008 - June 2014
Massachusetts Institute of Technology
Position
  • PhD Student
June 2005 - July 2005
Massachusetts Institute of Technology
Position
  • Research Assistant
Description
  • Reactor technology course for utility executives
January 2005 - May 2005
Massachusetts Institute of Technology
Position
  • Research Assistant
Description
  • 2.005 Thermal Fluids I
Education
September 2008 - June 2014
Massachusetts Institute of Technology
Field of study
  • Mechanical and Oceanographic Engineering
September 2003 - June 2005
Massachusetts Institute of Technology
Field of study
  • Aeronautics and Astronautics
August 2000 - August 2001
University of California, San Diego
Field of study
  • Mechanical and Aerospace Engineering

Publications

Publications (42)
Article
Full-text available
Coral reefs are well-studied ecosystems, yet there are still many untold stories regarding the animals they are home to, especially those active at night. We spent nearly 300 nights observing what happens on a coral reef at night and report our observations on the behavior of a nocturnal crab. Even though the crab was described ~250 years ago, alm...
Article
Full-text available
In the summer of 2015, we began an intensive, long-term nighttime survey campaign in the Gulf of Eilat and Aqaba, Red Sea, to build a calendar of the reproduction of corals and other coral-reef dwellers. By the end of 2019, we had spent 280 nights in the water, snorkeling, free diving, and frantically swimming, to witness and document every nocturn...
Article
Full-text available
In reef-building corals, larval settlement and its rapid calcification provides a unique opportunity to study the bio-calcium carbonate formation mechanism involving skeleton morphological changes. Here we investigate the mineral formation of primary polyps, just after settlement, in two taxa of the pocilloporoid corals: Stylophora pistillata (Espe...
Chapter
Full-text available
The attenuation of light with increasing depth, along with reduced exposure to wave stress, plays an important role in vertically structuring coral reef communities. Benthic photosynthetic organisms exhibit different depth distributions and abundance patterns which cause changes in community composition of associated reef fauna. This vertical zonat...
Article
Full-text available
Robust recovery of lost colors in underwater images remains a challenging problem. We recently showed that this was partly due to the prevalent use of an atmospheric image formation model for underwater images and proposed a physically accurate model. The revised model showed: 1) the attenuation coefficient of the signal is not uniform across the s...
Article
Full-text available
The use of artificially coloured stimuli, especially to test hypotheses about sexual selection and anti-predator defence, has been common in behavioural ecology since the pioneering work of Tinbergen. To investigate the effects of colour on animal behaviour, many researchers use paints, markers and dyes to modify existing colours or to add colour t...
Preprint
Full-text available
The attenuation of light with increasing depth, along with reduced exposure to wave stress, plays an important role in vertically structuring coral reef communities. Benthic photosynthetic organisms exhibit different depth distributions and abundance patterns which cause changes in community composition of associated reef fauna. This vertical zonat...
Article
Full-text available
The current underwater image formation model descends from atmospheric dehazing equations where attenu-ation is a weak function of wavelength. We recently showed that this model introduces significant errors and dependencies in the estimation of the direct transmission signal because underwater, light attenuates in a wavelength-dependent manner. He...
Article
Full-text available
Mating behaviour and predation avoidance in Heliconius involve visual colour signals; however, there is considerable inter-individual phenotypic variation in the appearance of colours. In particular, the red pigment varies from bright crimson to faded red. It has been thought that this variation is primarily due to pigment fading with age, although...
Data
Raw data Individual collection number, colour category, days after emergence, sex, and “a” value from photographs.
Data
Example photograph of raw data Shows dorsal forewing of Heliconius melpomene rosina from collection (#6216) used in this study.
Article
Full-text available
Recruitment is a fundamental process that influences coral population dynamics as well as reef community structure. To date, coral recruitment success rates are poorly quantified because survey methods are labor-intensive and require manual interpretation. Thus, they are prone to human errors and have low repeatability—a gap we aim to bridge in thi...
Conference Paper
Full-text available
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 physic...
Article
Full-text available
Avian egg shape is generally explained as an adaptation to life history, yet we currently lack a global synthesis of how egg-shape differences arise and evolve. Here, we apply morphometric, mechanistic, and macroevolutionary analyses to the egg shapes of 1400 bird species. We characterize egg-shape diversity in terms of two biologically relevant va...
Article
Full-text available
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...
Article
Full-text available
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 an...
Article
Full-text available
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 as...
Article
Full-text available
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...
Article
Full-text available
The slender filefish is a master of adaptive camouflage and can change its appearance within 1–3 s. Videos and photographs of this animal's cryptic body patterning and behavior were collected in situ under natural light on a Caribbean coral reef. We present an ethogram of body patterning components that includes large- and small-scale spots, stripe...
Article
Full-text available
Cuttlefish are able to camouflage to a wide variety of natural backgrounds that contain varying colors, intensities and patterns. Numerous studies have investigated the visual cues that influence cuttlefish body pattern expression, yet none have addressed experimentally how well overall intensity is matched between animal and substrate. Here, cu...
Article
Full-text available
Evolutionary pressures have led to some astonishing camouflage strategies in the animal kingdom. Cephalopods like cuttlefish and octopus mastered a rather unique skill: they can rapidly adapt the way their skin looks in color, texture and pattern, blending in with their backgrounds. Showing a general resemblance to a visual background is one of the...
Article
Full-text available
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...
Article
Full-text available
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 wi...
Article
Full-text available
Cephalopods are renowned for their ability to adaptively camouflage on diverse backgrounds. Sepia officinalis camouflage body patterns have been characterized spectrally in the laboratory but not in the field due to the challenges of dynamic natural light fields and the difficulty of using spectrophotometric instruments underwater. To assess cuttle...
Article
Full-text available
Every COTS digital camera captures images in its own RGB (red, green and blue) color space. Transforming these images to a device-independent color space is done through a transformation matrix. For land photography, the transformation from the camera color space to human color space is usually done through the use of photographic calibration targe...
Article
Full-text available
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...
Conference Paper
Full-text available
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 transform...
Article
Full-text available
To assure safe shutdown of a nuclear power plant, there must always be reliable means of decay heat removal provided, in last resort, by an Emergency Core Cooling System (ECCS). Currently the majority of nuclear power plants in the US utilize diesel generator sets as on-site emergency power generating units. In addition to the loss of off-site powe...

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Projects

Project (1)
Archived project
Developing a noval imaging method for coral recruits.