HiWi at Detsches Zentrum für Neurodegenerative Erkrankungen (DZNE)
From September 2021 to April 2022 I worked at DZNE in Magdeburg as a student assistant.
DZNE is a well-known research institute in Germany that focuses on studying neurodegenerative diseases (e.g., Alzheimer's disease).
My main tasks as a student assistant were helping with recruiting the participants for the study called Layer PRF and conducting behavioral experiments. The aim of this study was to investigate layer-specific population receptive field changes in younger and older adults. 20 young and 20 old subjects participated in this study. The study included two types of behavioral experiments, with and without computers
The experiments done with computer were written with MATLAB by one of the Ph.D. students and were aimed at finding the suitable threshold values for the index and middle finger while being stimulated by Qaerosys tactile stimulator. This simulator was used to activate the receptive fields. The threshold values obtained in this computer-based behavioral experiment were later used inside of MRI to acquire the functional MRI images for each subject. The non-computer-based experiments consisted of three different tests. I explain one of the tets briefly. The test was done using a grooved pegboard (Fig.1).
Fig.1: Grooved Pegboard
The participants were asked to take the sticks initially with two and then with three fingers and place them into the holes. The time which was required for the completion of each round was recorded for each participant.
After acquiring the threshold values and behavioral data functional MRI images were collected from all the participants. The behavioral experiments were performed one more time while patients were being scanned based on the threshold values obtained in the computer-based behavioral experiment. Similarly, the behavioral tests during MRI scanning focused on the index finger and middle finger. For image data acquisition, a whole-brain MP2RAGE sequence was employed for structural scanning (0.7 mm iso), together with a gradient-echo EPI sequence. As for pilot data analysis, the data was already acquired from one subject. This subject was measured four times by a 7T MRI for anatomical image and functional image, along with a 3T MRI scan for the structural image.
Data Scientist Intern at Boehringer Ingelheim
From September 2020 to April 2021 I completed a six-month voluntary internship with Boehringer Ingelheim (central nervous system disease department in Biberach, Baden Wüttemberg).
Boehringer Ingelheim is one of the world's leading research-driven pharmaceutical companies.
I started my job as a python developer/ data scientist. My main task was to develop a python package to help scientists speed up drug discovery and increase the precision of the results. The package was developed for the analysis and quantification of electrophysiological data obtained from brain slices or iPSC cells. The developed package contains the main class that is responsible for the quantification of the dataset. The parameters like the threshold of the neuronal spike train, rise-time, decay-time, etc could be quantified with this class. These quantified values then are organized in a pandas dataframe using a function called Events which locates outside of the main class. To facilitate the process of code implementation, I also developed a jupyter notebook environment in which they can interact with the codes, insert their desired parameter values, see the final data frame and also observe the neuronal spike train graphically and interact with the images. During this internship, I had the privilege to obtain advanced Python programming skills and work with one of the best pharmaceutical companies. Due to the privacy policy, I am not able to share the source codes however, i have provided a demo video of the final package which you can check down below.
demo video Boehringer Ingelheim (1)
EEG Data Analyst Intern at Leibniz Institute for Neurobiology
From November 2019 to February 2020, I did a voluntary internship at the Leibniz institute for neurobiology in Magdeburg.
Leibniz institute is an internationally renowned centre for learning and memory research.
The research focus of the laboratory that I was working at was on the development of attention, learning and memory in childhood and the underlying neuronal mechanisms. During my internship, I had the opportunity to learn more about EEG and eye-tracking experiments and obtain knowledge about EEG data analysis. I worked on the pre-processing the EEG data using independent component analysis approach which includes identifying artifacts in an EEG signal (e.g., eye, muscle, heart, etc artifacts) and removing them to obtain the signal which solely comes from the brain (all the analysis process done with EEGLAB in MATLAB and it can be observed in figure 2).
Fig.2: Pre-processing of the EEG signal with EEGLAB
Research assistant at Otto Von Guericke University Magdeburg
In December 2019 i was awarded with a research scholarship which was offered MEMoRIAL (an international graduate school for Medical Engineering and Engineering Materials at OVGU).
I was involved in research called Epipolar Constrained Optical Flow Triangulation for the Interior Problem in CBCT which was later on published as a paper (you can find the full description of the project in the publication tab of the main menu).
In this research, I was responsible for the processing of the truncated datasets with MATLAB which were acquired from cone beam CT scans and apply the most efficient pre-processing steps (e.g., filters, segmentation, filtering parameters, etc) to increase the efficiency and accuracy of the results.