Image-based Systems Biology

Dynamics, Function & Morphology of Infection Processes

The research group Applied Systems Biology is concerned with the mathematical modeling and computer simulation of infection processes caused by human-pathogenic fungi. The spatio-temporal data basis for these models is acquired by automatizing the data analysis of microscopy images on infection processes for high-throughput scanning. Our aim is to unravel secrets of the dynamical, functional and morphological aspects of the host-pathogen interaction using approaches of image-based systems biology.

Image Analysis, Data Quantification & Mathematical Modeling

The research group Applied Systems Biology provides open-source software tools at GitHub: https://github.com/applied-systems-biology

Image-based Systems Biology seeks to take full advantage of the information contained in images and includes the following three steps:

• Automated analysis of image data for high-content and high-throughput screening,
• Quantitative description of biological processes by appropriate characteristic measures,
• Construction of image-derived spatio-temporal models and predictive computer simulations.

During recent years, we have implemented a variety of software tools supporting the various steps, e.g. including the following software tools:

• MISA++ - Modular Image Stack Analysis for C++ that combines the high efficiency of C++ with the user-friendliness of ImageJ,
• JIPipe - a Java Image Processing Pipeline (JIPipe) that is a graphical batch processing language for the ImageJ ecosystem,
• DevonvTest - a python-based simulation framework that allows the user to quantify and compare the performance of different deconvolution methods,
• Droplet-segmentation - a Python code for the customized segmentation of microfluidc droplets using OpenCV,
• Dynamic SPHARM - a Python code for spherical harmonics analysis of three-dimensional objects that are dynamically changing with time like migrating cells do.

Collaborations, Funding & Teaching

Image-based systems biology represents a generic link between experiment and theory in interdisciplinary studies and offers an enormous range of opportunities for cooperation, since microscopic and spectroscopic data are routinely collected in nowadays experiments. This explains why the research group Applied Systems Biology is an active collaboration partner in the BMBF-funded Center for Sepsis Control and Care at the Jena University Hospital as well as in two DFG-funded collaborative research centers in Jena: FungiNet 124 – “Pathogenic fungi and their human host – networks of interaction” (Project B4) and PolyTarget 1278 – “Polymer-based nanoparticle libraries for targeted anti-inflammatory strategies” (Project Z01). In the newly established Excellence Cluster – “Balance of the Microverse” at the Friedrich Schiller University Jena, Prof. Figge is coordinator of the research area on “Data Synopsis” as well as a member in the interdisciplinary management board of the “Microverse Imaging Center”. Furthermore, Prof. Figge is the speaker of the Leibniz-funded ScienceCampus InfectoOptics, which is a collaborative initiative where researchers from the life sciences and optics/photonics closely work together with the aim of investigating and combating infectious diseases by means of novel optical technologies. In the Research Campus InfectoGnostics, methods for application in the diagnosis of infections are being further developed; for example, in the ADA project, where a platform for screening for Staphylococcus aureus / MRSA in human and veterinary medicine is being developed.

Every year, the research group Applied Systems Biology is involved in the organization of an international symposium with two alternating topics: Image-based Systems Biology (IbSB) in the even years and Systems Biology of Microbial Infection (SBMI) in the uneven years. Each of these events attracts an international audience to the HKI of more than 70 participants.

Last but not least, the research concept is further supported by the lectures on Image-based Systems Biology and Systems Biology of Immunology to educate bachelor and master students in this modern research approach and to teach the basics of analytical and quantitative methods for modeling dynamic systems.

Taken together, the research group Applied Systems Biology is a link between the two profile lines LIGHT and LIFE of the Friedrich Schiller University Jena. This is also reflected by Prof. Figge’s membership in the faculties of the Jena School for Microbial Communication, the International Leibniz Research School for Microbial and Biomolecular Interactions, as well as the Jena Center for Soft Matter and the Michael Stifel Center Jena.