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Software Developed to Quantify Single Cells Over Time

Tracking tool screen shot

Screen shot from The Tracking Tool showing cell lineage tree (ETH-Zurich)

20 July 2016. A team of computational biologists and engineers in Europe developed software that analyzes the growth and changes in individual cells over time. Researchers led by Fabian Theiss of the Helmholtz research center in Munich, Germany and Timm Schroeder at ETH technical university in Zurich, Switzerland described their software last week in the journal Nature Biotechnology (paid subscription required).

Theiss, Schroeder, and colleagues are seeking better tools for tracking and measuring properties of individual cells, particularly over extended periods of time. For example, stem cells are being used more frequently for designing new treatments and regenerating tissue, but most existing software is designed for data snapshots of cellular development at various points of time, not for continuous measurements.

A particular challenge in solving this problem is the enormous amounts of data generated. “On the one hand, it is necessary to take enough images in order not to lose track of the cells,” says Theiss in a Helmholtz center statement, “while on the other hand, this results in enormous data quantities, in some cases with millions of images.” Theiss is director of the center’s Institute of Computational Biology and chairs mathematical modeling of biological systems at Technical University of Munich.

Theiss and Schroeder, now a professor of biosystems science and engineering at ETH-Zurich and previously a researcher at Helmholtz center in Munich, took a modular approach for their software. “We put together two separate packages,” notes Schroeder, “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.”

Schroeder’s cell systems dynamics research group at ETH-Zurich — located in Basel, Switzerland — studies complex cell systems, particularly mammalian stem and progenitor cells. He and his colleagues are developing tools for long-term imaging, tracking and quantification of individual cells and their cellular and molecular behavior in cultures. Those investigations, says the lab, requires work in cell and molecular biology, as well as imaging, engineering, software development, statistics, and mathematical modeling.

The two software packages, The Tracking Tool (tTt) and qTfy, as well as the source code, can be downloaded from the ETH-Zurich web site. The software is made available under a GNU general public license.

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