Mr. Mert Karakaya Profile

Mert Karakaya

at NYU Tandon School of Engg

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Publications (3)

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Proceedings Article | 22 March 2021 Presentation + Paper

Just like Star Trek, but a little less fancy: behavioral teleporting of live zebrafish

Mert Karakaya, Simone Macrì, Maurizio Porfiri

Proceedings Volume 11586, 115860T (2021) https://doi.org/10.1117/12.2581431

KEYWORDS: Stars, Robots, Robotics, Imaging systems, Cameras, Animal model studies

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Zebrafish is a popular animal model for behavioral, neurological, and pharmacological studies. Particularly enticing is the possibility of studying the underpinnings of social behavior through hypotheses-driven experiments where we systematically intervene on key experimental variables. Robots offer an ideal avenue for performing such experimental manipulations, by affording the creation of highly-controlled, versatile, and customizable stimuli. Within this domain of investigation, we explore the possibility of using robots to “teleport” zebrafish from a tank to the other. More concretely, we propose the development of inanimate robots that allow remotely- located zebrafish to interact with each other in real time by mirroring movement of live fish. Each of the systems consists of a two-dimensional robotic platform, a magnetically- connected replica, a circular tank, and an overhead camera. A real-time tracking software is established to track fish and robots and afford behavioral teleporting. In a series of preliminary experiments, we examine the appraisal of the teleported zebrafish by the live animal and explore the potential use of the approach to study the basis of leadership and conduct unprecedented studies on drug administration. Behavioral analysis shows that behavioral teleporting is a viable strategy to afford remote interactions between zebrafish, laying the foundations for a new area of exploration in behavioral, neurological, and pharmacological studies.

Proceedings Article | 22 April 2020 Presentation + Paper

Invasive alien species respond to biologically-inspired robotic predators

Mert Karakaya, Maurizio Porfiri, Giovanni Polverino

Proceedings Volume 11374, 113740C (2020) https://doi.org/10.1117/12.2557871

KEYWORDS: Robotics, Dynamical systems, Ecosystems, Information theory

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Invasive alien species threaten natural ecosystems worldwide, prey on native species, and deplete their food sources. Mosquitofish is one of the most invasive freshwater fish worldwide and its negative impacts on the native fauna are alarming. Despite the urgency of contrasting the mosquitofish invasion, we have access to very few methods to combat them. Even when successful, these methods can be excessively labor-intensive or dangerous to native species. Robotic predators may constitute a promising tool in combating mosquitofish. Our group has recently proposed the use of a robotic predator that can perform targeted attacks against mosquitofish. The robotic predator consists of three operational parts: a two-dimensional robotic platform, a magnetically connected replica of a native mosquitofish predator, and an in-house developed live tracking software. The robotic replica was programmed to swim along a predetermined trajectory and randomly target mosquitofish in real time through a dedicated tracking software. Building on available experimental results, we put forward a comprehensive mathematical toolbox based on symbolic dynamics, recurrence quantification, and information theory to detail the behavioral interaction between the robotic predator and mosquitofish.

Proceedings Article | 22 April 2020 Presentation + Paper

Towards three-dimensional point cloud reconstruction of fish swimming

Mert Karakaya, Chen Feng, Maurizio Porfiri

Proceedings Volume 11374, 1137407 (2020) https://doi.org/10.1117/12.2558095

KEYWORDS: Water, Refraction, Cameras, Stereoscopic cameras, Calibration

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Zebrafish is extensively used in behavioral, pharmacological, and neurological studies due to a number of method- ological and practical advantages, including genetic and neurobiological homologies with humans and a fully se- quenced genome. Critical to a biologically-based understanding of zebrafish behavior is the ability to reconstruct their complex behavioral repertoire in three-dimensions. Toward this aim, several efforts have been made to score their ethogram in three-dimensions, but most of these studies are constrained by a single-view imaging. A promising line of approach to extract refined information about the mechanosensory and perceptual systems of zebrafish is point cloud reconstruction. Here, we provide an initial review of the state of knowledge in zebrafish tracking and we propose a potential methodology that can capture the dynamic three-dimensional geometry of fish swimming. We utilize a stereo vision camera, calibrated with a pinhole camera model with refraction cor- rection to allow for multi-medium imaging. The corrected pinhole camera model accounts for refraction through multiple mediums and allows for more accurate point cloud reconstruction from two cameras. From the point cloud data, we could recreate the three-dimensional geometric model of the fish and analyze its swimming be- havior in three dimensions. The extracted dynamic fish geometry should allow for an improved understanding of mechanosensation and perception, which are critical to elucidate how zebrafish process visual cues and perceive flow structures.

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