Robert Haase is computer scientist by training and follows his curiosity deeper and deeper into the life sciences. He received a PhD from the Faculty of Medicine Carl Gustav Carus of the TU Dresden for his work on swarm intelligence based algorithms for medical image segmentation in the cancer research context. He is lecturer for bio-image analysis, bio-statistics and programming at the Biotechnology Center of the TU Dresden. His postdoctoral research in Gene Myers lab at the Center for Systems Biology and the Max Planck Institute for Molecular Cell Biology and Genetics concentrates on bridging the disciplines computer science and biology to forward understanding of how tissues and organisms form. He studies Tribolium castaneum embryo development and for that programs smart microscopes, real-time image analysis and machine learning tools easing the way how scientists interact with multi-dimensional image data to gain new insights.
Microscopy background: Image Analysis
Posted by Robert Haase, on 23 May 2022When analysing microscopy image data of biological systems, a major bottleneck is to identify image-based features that describe the phenotype we observe. For example when characterising phenotypes of nuclei in 2D images, often questions come up such as “Shall we use circularity, solidity, extend, elongation, aspect radio, roundness or Feret’s diameter to describe the shape
Posted by Robert Haase, on 4 September 2021TL;DR: I’m a computer scientist who often collaborates with biologists on bio-image analysis scripts. We are using more and more git, a version control program, for working on code collaboratively. When using git, we speak about repositories, commits and pushing to the origin. We also make forks, send pull-requests and merge code. This blog post
Posted by Robert Haase, on 14 July 2020Do you also spend a substantial amount of your time waiting for automated image analysis to finish? I did, again and again for more than a decade. And, then, the morning after running a script overnight, you realize that a parameter was wrongly set. It was about time to change that. History Processing on graphics