Cell under observation: "The software lets us study the development on video"

Interview with Prof. Fabian Theis, Director of the Institute of Computational Biology (ICB) at the Helmholtz Center Munich and Chair of Mathematical Modeling of Biological Systems at the Technical University of Munich (TU München)


What happens when stem cells differentiate? What molecular characteristics do they have? Questions that can now be easier answered with the help of a new open-source software. We spoke with Prof. Fabian Theis at the Helmholtz Center Munich, who participated in the software development.
Bild: Blond man with light blue shirt - Fabian Theis; Copyright: Helmholtz Zentrum München

Prof. Fabian Theis ; © Helmholtz Zentrum München

Prof. Theis, where is your software package being applied?

Prof. Fabian Theis: We developed the software in collaboration with the Schroeder lab during our daily operating processes to obtain answers to specific biological questions. To do this, we needed to analyze complex microscopy raw data. The microscope is one of the oldest tools applied in cell biology but is often only used as a qualitative technique. Meanwhile, cell biology is turning more and more into a quantitative science. That's why our software tool does not focus on conventional light microscopy but rather on fluorescence microscopy that allows you to label specific molecules with dyes and make them visible. This enables you to see the distribution of specific proteins for instance. You record a fluorescence microscopy image by activating a dye-tagged protein with a laser. The protein subsequently emits light and can be located. Our tool integrates and quantifies the amount of emitted light above the cell and lets you draw conclusions on the quantity of the tagged protein.

The software is also able to process microscopy movies. Today's fluorescence microscopes are able to record so-called time-lapse microscopy data. You monitor a biological process over a certain period of time. This is important because we keep discovering small differences in cell types and would like to know what causes this heterogeneity. Embryonic stem cells are particularly interesting for these types of studies because we want to know what exactly initiates a specific development. That's why "time-lapse" recordings are important to see the chronological sequence and the changes. This can be well illustrated with our own bodies. A fertilized human egg turns into a body with many different types of cells that all still share the same DNA. Studying only moments of this development is not enough to understand everything. Now we are able to study this development in a video thanks to the software.

Image: User interface of a software; Copyright: Helmholtz Zentrum München

Screenshot of the new software package; © Helmholtz Zentrum München

What is the integrated tracking tool able to accomplish?

Theis: You can examine individual cells with the tracking tool by changing image sequences with the mouse cursor. You can virtually "move" over the cell and accurately track it. That means there is no automated cell tracking; this is a semi-automatic quantification tool for single cell analysis. The tracking tool, tTt in short, was developed by Prof. Timm Schroeder who is now at the Department of Biosystems Science and Engineering at the ETH Zurich.

Can the software be loaded onto any computer?

Theis: The software is compatible with popular operating systems, provided there is enough disc space. Recording single images and editing them into a video creates big data but conventional hard drives are normally sufficient.

Foto: Simone Ernst; Copyright: B. Frommann

© B. Frommann

The interview was conducted by Simone Ernst and translated from German by Elena O'Meara.