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
New Model of T Cell Activation
27.05.2016 | Albert-Ludwigs-Universität Freiburg im Breisgau
Fungi – a promising source of chemical diversity
27.05.2016 | Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie - Hans-Knöll-Institut (HKI)
A biological and energy-efficient process, developed and patented by the University of Innsbruck, converts nitrogen compounds in wastewater treatment facilities into harmless atmospheric nitrogen gas. This innovative technology is now being refined and marketed jointly with the United States’ DC Water and Sewer Authority (DC Water). The largest DEMON®-system in a wastewater treatment plant is currently being built in Washington, DC.
The DEMON®-system was developed and patented by the University of Innsbruck 11 years ago. Today this successful technology has been implemented in about 70...
Permanent magnets are very important for technologies of the future like electromobility and renewable energy, and rare earth elements (REE) are necessary for their manufacture. The Fraunhofer Institute for Mechanics of Materials IWM in Freiburg, Germany, has now succeeded in identifying promising approaches and materials for new permanent magnets through use of an in-house simulation process based on high-throughput screening (HTS). The team was able to improve magnetic properties this way and at the same time replaced REE with elements that are less expensive and readily available. The results were published in the online technical journal “Scientific Reports”.
The starting point for IWM researchers Wolfgang Körner, Georg Krugel, and Christian Elsässer was a neodymium-iron-nitrogen compound based on a type of...
In the Beyond EUV project, the Fraunhofer Institutes for Laser Technology ILT in Aachen and for Applied Optics and Precision Engineering IOF in Jena are developing key technologies for the manufacture of a new generation of microchips using EUV radiation at a wavelength of 6.7 nm. The resulting structures are barely thicker than single atoms, and they make it possible to produce extremely integrated circuits for such items as wearables or mind-controlled prosthetic limbs.
In 1965 Gordon Moore formulated the law that came to be named after him, which states that the complexity of integrated circuits doubles every one to two...
Characterization of high-quality material reveals important details relevant to next generation nanoelectronic devices
Quantum mechanics is the field of physics governing the behavior of things on atomic scales, where things work very differently from our everyday world.
When current comes in discrete packages: Viennese scientists unravel the quantum properties of the carbon material graphene
In 2010 the Nobel Prize in physics was awarded for the discovery of the exceptional material graphene, which consists of a single layer of carbon atoms...
24.05.2016 | Event News
20.05.2016 | Event News
19.05.2016 | Event News
27.05.2016 | Awards Funding
27.05.2016 | Life Sciences
27.05.2016 | Life Sciences