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Big Data for small cells – a new tracking and quantification tool for single cells


Working with colleagues from the ETH Zürich, scientists at the Helmholtz Zentrum München and the Technical University of Munich have developed software that allows observing cells for weeks while also measuring molecular properties. The software is freely available and has now been introduced in 'Nature Biotechnology'.

Certain questions in modern cell biology can only be answered by specifically observing the fate of individual cells. For example, researchers are interested in how stem cells develop into other cell types. Since in some cases such processes take several days to complete, the analysis with standard methods, which often measure only a single time point of the process, is not adequate.

Screenshot of the new Software

Source: Helmholtz Zentrum München

But the recording and analysis of so-called time-lapse microscopy movies* is not trivial: "On the one hand, it is necessary to take enough images in order not to lose track of the cells, while on the other hand, this results in enormous data quantities, in some cases with millions of images," reports Prof. Dr. Dr. Fabian Theis as he explains the previous dilemma.

"The idea was consequently to make this emerging big data utilizable for science." Theis is Director of the Institute of Computational Biology (ICB) at the Helmholtz Zentrum München and holds the Chair of Mathematical Modeling of Biological Systems at the Technical University of Munich. He led the study together with Prof. Dr. Timm Schroeder from the Department of Biosystems Science and Engineering (D-BSSE) at the ETH Zürich, which is headquartered in Basel.

Software available online

Schroeder himself conducted research at the Helmholtz Zentrum München until 2013 and has been investigating the dynamics of stem cells for some time. And so he knew perfectly well what the new software should be able to do: "We put together two separate packages: a manual tracking tool and a semi-automatic quantification tool for individual cell analyses in time-lapse microscopy movies.** The two together allow measurements of properties such as the length of the cell cycle, the expression dynamics of certain proteins, and correlations of these properties between sister cells."

As far as the scientists are concerned, the new possibilities that these programs offer should be available to as many researchers around the world as possible. Therefore the software is freely available, and can be downloaded from the following link:

Technical obstacles were removed as far as possible. "Our focus was on making the application also available to researchers who do not have background IT know-how," Schroeder explains. And the application appears to work well: Two high-ranking publications can be traced back to the spyware for cells.

Further information

* A time-lapse microscopy movie consists of many individual images that allow an approximately continuous observation of cells.

** The two software packages are tTt (The Tracking Tool), which tracks individual cells, and the program qTfy, which facilitates the quantification of cellular and molecular properties.

Original Publication:
Hilsenbeck, O. & Schwarzfischer, M. & Skylaki S. et al. (2016). A software for single-cell quantification of cellular and molecular dynamics in long-term time-lapse microscopy, Nature Biotechnology, DOI: 10.1038/nbt.3626

Publications based on the new Software:

Filipczyk, A. (2015). Network plasticity of pluripotency transcription factors in embryonic stem cells. Nature Cell Biology, DOI: 10.1038/ncb3237

Hoppe, P. (2016). Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios. Nature, DOI: 10.1038/nature18320

The Helmholtz Zentrum München, the German Research Center for Environmental Health, pursues the goal of developing personalized medical approaches for the prevention and therapy of major common diseases such as diabetes and lung diseases. To achieve this, it investigates the interaction of genetics, environmental factors and lifestyle. The Helmholtz Zentrum München is headquartered in Neuherberg in the north of Munich and has about 2,300 staff members. It is a member of the Helmholtz Association, a community of 18 scientific-technical and medical-biological research centers with a total of about 37,000 staff members.

The Institute of Computational Biology (ICB) develops and applies methods for the model-based description of biological systems, using a data-driven approach by integrating information on multiple scales ranging from single-cell time series to large-scale omics. Given the fast technological advances in molecular biology, the aim is to provide and collaboratively apply innovative tools with experimental groups in order to jointly advance the understanding and treatment of common human diseases.

Technical University of Munich (TUM) is one of Europe’s leading research universities, with more than 500 professors, around 10,000 academic and non-academic staff, and 39,000 students. Its focus areas are the engineering sciences, natural sciences, life sciences and medicine, reinforced by schools of management and education. TUM acts as an entrepreneurial university that promotes talents and creates value for society. In that it profits from having strong partners in science and industry. It is represented worldwide with a campus in Singapore as well as offices in Beijing, Brussels, Cairo, Mumbai, San Francisco, and São Paulo. Nobel Prize winners and inventors such as Rudolf Diesel, Carl von Linde, and Rudolf Mößbauer have done research at TUM. In 2006 and 2012 it won recognition as a German "Excellence University." In international rankings, TUM regularly places among the best universities in Germany.

Freedom and individual responsibility, entrepreneurial spirit and open-mindedness: ETH Zurich stands on a bedrock of true Swiss values. Our university for science and technology dates back to the year 1855, when the founders of modern-day Switzerland created it as a centre of innovation and knowledge. At ETH Zurich, students discover an ideal environment for independent thinking, researchers a climate which inspires top performance. Situated in the heart of Europe, yet forging connections all over the world, ETH Zurich is pioneering effective solutions to the global challenges of today and tomorrow.

Some 500 professors teach around 20,000 students – including 4,000 doctoral students – from over 120 countries. Their collective research embraces many disciplines: natural sciences and engineering sciences, architecture, mathematics, system-oriented natural sciences, as well as management and social sciences. The results and innovations produced by ETH researchers are channelled into some of Switzerland’s most high-tech sectors: from computer science through to micro- and nanotechnology and cutting-edge medicine. Every year ETH registers around 90 patents and 200 inventions on average. Since 1996, the university has produced a total of 330 commercial spin-offs. ETH also has an excellent reputation in scientific circles: 21 Nobel laureates have studied, taught or researched here, and in international league tables ETH Zurich regularly ranks as one of the world’s top universities.

Contact for the media:
Department of Communication, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg - Tel. +49 89 3187 2238 - Fax: +49 89 3187 3324 - E-mail:

Media relations, ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland – Tel. +41 61387 3201 - E-mail:

Scientific Contact:
Prof. Dr. Dr. Fabian Theis, Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Ingolstädter Landstr. 1, 85764 Neuherberg - Tel. +49 89 3187 4030, E-mail:

Prof. Dr. Timm Schroeder, ETH Zürich, Department of Biosystems Science and Engineering, Mattenstr 26, 4058 Basel, Switzerland - E-mail:

Sonja Opitz | Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt

Further reports about: Big Data Computational Biology ETH ETH Zurich Helmholtz single cells stem cells

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