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

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).

Availability and implementation OMEGA is a cross-platform, open-source software developed in Java. Source code and cross-platform binaries are freely available on GitHub at https://github.com/OmegaProject/Omega, under the GNU General Public License v.3.

Contact caterina.strambio{at}umassmed.edu and alex.rigano{at}umassmed.edu