SUMMARY --> OMEGA is 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).

MOTIVATION --> Particle tracking coupled with time-lapse microscopy is critical for understanding the dynamics of intracellular processes of clinical importance. Spurred on by advances in the spatiotemporal resolution of microscopy and automated computational methods, this field is increasingly amenable to multi-dimensional high-throughput data collection schemes (Snijder et al, 2012). Typically, complex particle tracking datasets generated by individual laboratories are produced with incompatible methodologies that preclude comparison 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 manual transfer of data to diverse downstream analysis tools. At the same time, it would lay the foundation for shared trajectory data, particle tracking, and motion analysis standards.

DESCRIPTION --> The OMEGA application carries out all steps of the complete tracking and motion analysis workflow described above. In addition, because of its flexibility and modularity, it can also be used to support other data flows depending on user needs. OMEGA operates by way of a rich graphical user interface (GUI), a modular structure and a relational database in the back end to store data arising from image analysis . The functional logic of the OMEGA Java application is organized around six analysis and data management modules, called Image Browser, Particle Tracking, Signal-to-Noise Ratio (SNR) Estimation, Trajectory Manager, Tracking Measures, and Data Browser, which in turn implement nine interchangeable plugins that work sequentially to implements the typical steps of particle tracking and motion analysis experiments. At time of writing, workflows supported by OMEGA are mainly interactive, requiring user supervision at each subsequent step. In subsequent releases we plan to develop batch processing of entire image datasets.