Onur Burak Özdemir

Prospective PhD @ EPFL • onur.ozdemir@epfl.ch
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Hi, I’m Onur 👋🏻

I’m a physicist-engineer working across biology, electronics, and computation, with a focus on Syn-Bio. I have a diverse project background: from optical glucose sensors to forensics research to synthetic biology, and a heck of a lot of programming. I build sensors, analyze microscopy data, develop open-source tools, and engineer mammalian cells. Whether it’s image analysis, big data pipelines, or lab prototyping, I like working where disciplines overlap. This site collects my research, software projects, and ongoing experiments across those intersections.

My Master's Thesis

Applications of Synthetic Spatiotemporal Signals In Mammalian Cells @ Westmeyer Lab & Simmel Lab in Munich Technical University

MinDE protein oscillations expressed in HEK cells, with unique barcode frequencies. Green sfGFP-MinD, red MinE-mCherry.
This thesis explores whether self-organizing protein patterns inside mammalian cells can be used to move transmembrane proteins and generate synthetic signals at the cell surface. I reconstituted MinDE oscillations in HEK293T cells and developed image analysis tools to quantify their dynamics. My aim was to couple these intracellular waves to an engineered transmembrane protein in order to create a spatially modulated magnetic output signal outside the cell. The broader goal is to enable programmable cell–environment communication using synthetic intracellular dynamics.

Software Projects

3D Microscopy Segmentation and Analysis

CellPlotter Screenshot

CellPlotter

This is a Napari plugin I developed for interactive and automated cell segmentation, analysis, and publication-ready plotting.


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EncapsulinAnalyzer Screenshot" alt="EncapsulinAnalyzer Screenshot">

EncapsulinAnalyzer

Another Napari plugin I made for analyzing encapsulin protein EM images, enabling advanced quantitative analysis, and producing radial plots for further analysis.


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Solar-Cell-Assistant Screenshot

Solar-Cell-Assistant

A Matlab based tool I developed for analyzing space qualified solar cell performance and health. Has a UI and uses IOcontrol package to control various lab instruments. Generates dark I-V plots, and calculates deviation from standard profile.


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Published Papers

Paper 5 Image

Comparing the light response of D-glucose in polyacrylamide hydrogel and water in NIR spectral region

I investigated the near-infrared light response of D-glucose in polyacrylamide hydrogel versus water, for diagnostic applications.


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Paper 1 Image

Synthesis and characterization of PVA-based binary-gel electrolytes including massive ions

We developed a PVA-based gel electrolyte incorporating redox-active species to enhance EDLC energy density and capacitance.


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Paper 3 Image

Effect of conductive layer on the performance of gel electrolyte-based supercapacitors

We investigated the influence of conductive layers on the performance of gel electrolyte-based supercapacitors.


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Paper 2 Image

A 3D scanning based image processing technique for measuring the sequence of intersecting lines

A novel 3D scanning-based method for accurately measuring sequences of intersecting lines.


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Paper 4 Image

UVC-LED-based face mask design and efficacy against common germs

A UVC-LED-integrated face mask design and demonstrated its efficacy against common germs.


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My video journeys

Some Cool Lab Photos

First working OLED!

Gel successful

Teamwork!