A quantitative and global view of transport and tracking in plant cells using computational approaches
I work on automated, computational frameworks to analysis microscopy images by quantifying certain processes in plants. Here, I focus especially on cytoskeletal components, such as the actin filaments. In my first project, we developed an automated framework which extracts and analyzes actin filaments from images and represents them as networks. These networks can then be used for quantitative analysis of actin in time series, between different conditions or for the testing against random networks.
In my second project I work on another framework to describe the complex shape of pavement cells in plant leaves. Pavement cells are shaped like puzzle pieces and are hard to describe in a quantitative manner because of their complexity. In contrast to other published tools, we try to quantify the shapes using networks and ultimately combining this framework with the cytoskeleton extraction framework.
My work is mostly done at the computer where I use Python to implement the frameworks, but I also work with R and the imaging software Fiji. The major topics of my research include image analysis, graph theory and statistics.
Project Duration: 2016-2020
- The University of Potsdam: Dr Zoran Nikoloski
- The University of Melbourne: Professor Staffan Persson
GR Student Profile:
I started my studies in 2009 at the University of Potsdam doing a Bachelor in Biosciences, specializing in Biochemistry. During my last year I came into contact with Bioinformatics and decided to continue my studies with a master’s in bioinformatics at the same University. I really enjoyed the course in Bioimaging and worked on a bioimaging-related project at the Max-Planck Institute of Molecular Plant Physiology during my second year, which I later continued during my PhD. I wrote my master thesis on a different topic (sequence analysis, microRNAs) in Stockholm at the Karolinska Institute. After finishing, I took the opportunity to continue the work on my previous project as a PhD student with the chance to do part of my PhD in Melbourne. When I started my joint PhD in Melbourne in 2016 it was also the start of the Melbourne-Potsdam Joint PhD Program (MelPoPP). I spent my first year in Melbourne, before continuing my studies in Germany for a year. At the begin of 2019 I came back to Melbourne to do another half year in Melbourne, before finishing and wrapping up in Germany.
In my free time I like to read and play the guitar. I am also a long-time member of an accordion orchestra in Germany with regular concerts throughout the year.
- Breuer D, Nowak J, Ivakov A, Somssich M, Persson S, Nikoloski (2017). System-wide organization of actin cytoskeleton determines organelle transport in hypocotyl plant cells, PNAS 114(28): E5741-5749.
- Yu Y, Wu S, Nowak J, Wang G, Han L, Feng Z, Mendrinna A, Ma Y, Wang H, Zhang X, Tian J, Dong L, Nikoloski Z, Persson S, Kong Z (2019). Live-cell imaging of the cytoskeleton in elongating cotton fibers, Nature Plants 5: 498-504.