Heidelberg scientists develop powerful automatic method for image analysis
In order to track the movements of biological particles in a cell, scientists at Heidelberg University and the German Cancer Research Center have developed a powerful analysis method for live cell microscopy images.
This so-called probabilistic particle tracking method is automatic, computer-based and can be used for time-resolved two- and three-dimensional microscopy image data. The Heidelberg method achieved the best overall result in an international competition that compared different methods for image analysis. The competition results were recently published in the journal “Nature Methods”.
The task of how to automatically track the movement of biological particles such as viruses, cell vesicles or cell receptors is of key importance in biomedical applications for the quantitative analysis of intracellular dynamic processes. Manually analysing time-resolved microscopy images with hundreds or thousands of moving objects is not feasible.
In recent years, therefore, there has been increasing emphasis on the development of automatic image analysis methods for particle tracking. These methods are computer-based and determine the positions of particles over time. To objectively compare the performance of these methods, an international competition was organised in 2012 for the first time.
A total of 14 research teams participated in the “Particle Tracking Challenge”, including Dr. William J. Godinez and Associate Professor Dr. Karl Rohr from Heidelberg University and the German Cancer Research Center (DKFZ). In the competition, the different image analysis methods were applied to a broad spectrum of two- and three-dimensional image data and their performance was quantified using different measures. The three best methods were determined for each category of data. With a total of 150 “Top 3 Rankings”, the Heidelberg scientists achieved the best overall result.
The particle tracking method developed by Dr. Godinez and Dr. Rohr is based on a mathematically sound method from probability theory that takes into account uncertainties in the image data, e.g. due to noise, and exploits knowledge of the application domain. “Compared to deterministic methods, our probabilistic approach achieves high accuracy, especially for complicated image data with a large number of objects, high object density and a high level of noise,” says Dr. Rohr. The method enables determining the movement paths of objects and quantifies relevant parameters such as speed, path length, motion type or object size. In addition, important dynamic events such as virus-cell fusions are detected automatically.
Karl Rohr heads the “Biomedical Computer Vision“ (BMCV) research group that develops computer science methods to automatically analyse cell microscopy images as well as radiological images. This group is located at the BioQuant Center of Heidelberg University. It is part of the department “Bioinformatics and Functional Genomics“ at Heidelberg University's Institute of Pharmacy and Molecular Biotechnology as well as the division “Theoretical Bioinformatics“ of the DKFZ, both of which are headed by Prof. Dr. Roland Eils. William J. Godinez is pursuing postdoctoral work in the BMCV group on the development of computer-based particle tracking methods.
Publication in Nature Methods:
N. Chenouard, I. Smal, F. de Chaumont, M. Maška, I.F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A.R. Cohen, W.J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K.E.G. Magnusson, J. Jaldén, H.M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J.Y. Tinevez, S.L. Shorte, J. Willemse, K. Celler, G.P. van Wezel, H.W. Dan, Y.S. Tsai, C. Ortiz de Solórzano, J.C. Olivo-Marin, E. Meijering: Objective comparison of particle tracking methods. Nature Methods (March 2014), Volume 11, Issue 3, 281-289, doi: 10.1038/nmeth.2808
Particle_Tracking_1.jpg und Particle_Tracking_2.jpg
Tracking result for virus particles. Microscopy image of time-resolved data overlaid with automatically determined movement paths of HIV-1 particles, shown in different colours. The small boxes indicate the positions found at the current time point. Image two shows an enlarged section of the area marked by the white rectangle in image one.
Source: W.J. Godinez, K. Rohr
Associate Professor Dr. Karl Rohr
“Biomedical Computer Vision” research group
Phone: +49 6221 51-298
Communications and Marketing
Press Office, phone: +49 6221 54-2311
Marietta Fuhrmann-Koch | idw - Informationsdienst Wissenschaft
A Fluttering Accordion
04.08.2015 | Friedrich-Schiller-Universität Jena
Molecular Spies to Fight Cancer - Procedure for improving tumor diagnosis successfully tested
03.08.2015 | Helmholtz-Zentrum Dresden-Rossendorf
Continuing current carbon dioxide (CO2) emission trends throughout this century and beyond would leave a legacy of heat and acidity in the deep ocean. These...
Glacier decline in the first decade of the 21st century has reached a historical record, since the onset of direct observations. Glacier melt is a global phenomenon and will continue even without further climate change. This is shown in the latest study by the World Glacier Monitoring Service under the lead of the University of Zurich, Switzerland.
The World Glacier Monitoring Service, domiciled at the University of Zurich, has compiled worldwide data on glacier changes for more than 120 years. Together...
Using ultracold atoms trapped in light crystals, scientists from the MPQ, LMU, and the Weizmann Institute observe a novel state of matter that never thermalizes.
What happens if one mixes cold and hot water? After some initial dynamics, one is left with lukewarm water—the system has thermalized to a new thermal...
Physicists from Regensburg and Marburg, Germany have succeeded in taking a slow-motion movie of speeding electrons in a solid driven by a strong light wave. In the process, they have unraveled a novel quantum phenomenon, which will be reported in the forthcoming edition of Nature.
The advent of ever faster electronics featuring clock rates up to the multiple-gigahertz range has revolutionized our day-to-day life. Researchers and...
Researchers have developed an ultrafast light-emitting device that can flip on and off 90 billion times a second and could form the basis of optical computing.
04.08.2015 | Event News
23.07.2015 | Event News
10.07.2015 | Event News
05.08.2015 | Physics and Astronomy
05.08.2015 | Ecology, The Environment and Conservation
05.08.2015 | Earth Sciences