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OMEGA: a software tool for the management, analysis, and dissemination of intracellular trafficking data that incorporates motion type classification and quality control

Alessandro Rigano, Vanni Galli, Jasmine M. Clark, Lara E. Pereira, Loris Grossi, View ORCID ProfileJeremy Luban, Raffaello Giulietti, Tiziano Leidi, Eric Hunter, Mario Valle, Ivo F. Sbalzarini, View ORCID ProfileCaterina Strambio-De-Castillia
doi: https://doi.org/10.1101/251850
Alessandro Rigano
University of Massachusetts Medical School, Worcester, MA, USA;
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Vanni Galli
Scuola Universitaria Superiore della Svizzera Italiana (SUPSI), Lugano, Ticino, Switzerland;
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Jasmine M. Clark
Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta Georgia;
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Lara E. Pereira
Division of Sexual Transmitted Diseases Prevention, Centers for Disease Control and Prevention;
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Loris Grossi
Scuola Universitaria Superiore della Svizzera Italiana (SUPSI), Lugano, Ticino, Switzerland;
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Jeremy Luban
University of Massachusetts Medical School, Worcester, MA, USA;
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Raffaello Giulietti
Scuola Universitaria Superiore della Svizzera Italiana (SUPSI), Lugano, Ticino, Switzerland;
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Tiziano Leidi
Scuola Universitaria Superiore della Svizzera Italiana (SUPSI), Lugano, Ticino, Switzerland;
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Eric Hunter
Emory Vaccine Center at Yerkes National Primate Research Center, Emory University;
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Mario Valle
Centro Svizzero di Calcolo Scientifico - Swiss National Supercomputing Centre;
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Ivo F. Sbalzarini
Max Planck Institute of Molecular Cell Biology and Genetics in Dresden
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Caterina Strambio-De-Castillia
University of Massachusetts Medical School, Worcester, MA, USA;
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  • ORCID record for Caterina Strambio-De-Castillia
  • For correspondence: caterina.strambio@umassmed.edu
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Abstract

MOTIVATION: Particle tracking coupled with time-lapse microscopy is critical for understanding the dynamics of intracellular processes of clinical importance. Under the impulse of advances in microscopic spatiotemporal resolution and automated computational methods, this field is increasingly amenable to multi-dimensional high-throughput data collection schemas (Snijder et al, 2012). Typically, complex particle tracking datasets generated by individual laboratories are produced with incompatible methodologies and cannot be compared to each other. There is therefore an unmet need for data management systems that facilitate data standardization, meta-analysis and structured data dissemination. The integration of analysis, visualization and quality control capabilities into such systems would eliminate the need for manually transferring the data to diverse downstream analysis tools while at the same time lying the foundations for shared trajectory data, particle tracking, and motion analysis standards. RESULTS: Here, we present Open Microscopy Environment inteGrated Analysis (OMEGA), a cross-platform data management, analysis and visualization system, for particle tracking data with particular emphasis on results from viral and vesicular trafficking experiments. OMEGA provides easy to use graphical interfaces to implement integrated particle tracking and motion analysis workflows while keeping track of error propagation and data provenance. Specifically, OMEGA: 1) imports image data and metadata from data management tools such as Open Microscopy Environment Remote Objects (OMERO; Allan et al., 2012); 2) tracks intracellular particles moving across time series of image planes; 3) facilitates parameter optimization and trajectory results inspection and validation; 4) performs downstream trajectory analysis and motion type classification; 5) estimates the uncertainty associated with motion analysis; and, 6) stores and facilitates dissemination of analysis results and analysis definition metadata on the basis of our newly proposed Minimum Information About Particle Tracking Experiments (MIAPTE; (Rigano & Strambio-De-Castillia, 2016; 2017) guidelines in combination with the OME-XML data model (Goldberg et al, 2005).

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Posted February 23, 2018.
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OMEGA: a software tool for the management, analysis, and dissemination of intracellular trafficking data that incorporates motion type classification and quality control
Alessandro Rigano, Vanni Galli, Jasmine M. Clark, Lara E. Pereira, Loris Grossi, Jeremy Luban, Raffaello Giulietti, Tiziano Leidi, Eric Hunter, Mario Valle, Ivo F. Sbalzarini, Caterina Strambio-De-Castillia
bioRxiv 251850; doi: https://doi.org/10.1101/251850
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OMEGA: a software tool for the management, analysis, and dissemination of intracellular trafficking data that incorporates motion type classification and quality control
Alessandro Rigano, Vanni Galli, Jasmine M. Clark, Lara E. Pereira, Loris Grossi, Jeremy Luban, Raffaello Giulietti, Tiziano Leidi, Eric Hunter, Mario Valle, Ivo F. Sbalzarini, Caterina Strambio-De-Castillia
bioRxiv 251850; doi: https://doi.org/10.1101/251850

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