OMEGA: an open-source tool to foster reproducibility and data sharing in particle tracking experiments
Suber cells and mimosa leaves (Robert Hooke, Micrographia, 1665).
The purpose of computing is insight, not numbers (Richard Hamming, 1962)
From its inception cell- biology has been founded on the development of technologies that would enable the real-time, spatially resolved and quantitative description of events occurring within the living system at scales ranging from single molecules to entire multi-cellular organisms.
Today, the sophistication of quantitative digital microscopy allows scientists to “watch life as it happens”. Nonetheless, much work remains to be done in order to take full advantage of these technologies in a manner that allows the transformation of large quantities of image data into meaningful scientific insight and knowledge.
Open Microscopy Environment inteGrated Analysis (OMEGA) is an open-source software development project led by Caterina Strambio De Castillia at the Program in Molecular Medicine (PMM) of the University of Massachusetts Medical School (UMMS). The OMEGA project is carried out in collaboration with a multidisciplinary team of scientists and software developers including Ivo Sbalzarini at the Max Plank Institute of Molecular Cell Biology and Genetics in Dresden, Alessandro Rigano, Jeremy Luban and Kevin Fogarty at UMass Medical School in Worcester, MA, Vanni Galli, Raffaello Giulietti, Tiziano Leidi and Roberto Mastropietro at the University of Applied Sciences of Southern Switzerland (SUPSI), Eric Hunter at the Emory University Vaccine Center and Bernd Rinn at ETH-Zurich.
OMEGA has received strategic support from the SystemsX.ch Biology IT initiative under the leadership of Peter Kunszt, from the SUPSI’s Institute for Information Systems and Networking under the leadership of Roberto Mastropietro, and from the Emory University Vaccine Center under the leadership of Eric Hunter. OMEGA is now funded by the Program in Molecular Medicine, and by the Luban Laboratory at the University of Massachusetts Medical School.
While the current focus of the OMEGA project is the development of tools for the quantitative, real-time, sub-cellular tracking of HIV-1 viral particles in living human cells, our more general aim is to develop universal tools that can be used across multiple scientific questions, model system, and experimental contexts.
The ultimate goal of the OMEGA project is to contribute to a paradigm shift that would put the quantitative potential of bioimaging at the service of a systematic understanding of living systems, under both physiological and pathological conditions.
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