Page Menu

Software tools for Research Data Management and Sharing

OMEGA: Open Microscopy Environment Integrated Analysis

Depicted is a schematic representation of the OMEGA workflow
OMEGA provides end to-end supports for the reproducibility and repeatability of particle tracking and motion analysis experiments by providing an integrated platform that: 1) executes all basic steps of a particle tracking and motion analysis steps workflow. 2) Tracks uncertainty propagation across the analysis pipeline. 3) Automatically maintains persistent links between the chain of data, harvests data provenance and utilizes it to annotate analysis result. 4) Utilizes a domain-relevant community standards to describe data, metadata and processing steps. Figure adapted from: Rigano et al., 2019. bioRxiv. https://doi.org/10.1101/251850

 

Dissecting the interplay between HIV-1 and human cells during viral entry

After HIV-1 fuses with a target cell membrane, the virion core is delivered into the cytosol of the infected cell. A DNA copy (cDNA) of the HIV-1 RNA genome is produced by the HIV-1 reverse transcriptase (RT), and the cDNA is ligated to host cell chromosomal DNA by HIV-1 integrase.

Quantitative analysis of viral trajectories gives insight into viral-host interactions

The complex interplay between HIV-1 and cellular components can be solved using dynamic imaging followed by rigorous computational analysis of viral particle trajectories. A major hurdle has been the difficulty of keeping track of multiple moving viral particles with sufficient temporal and spatial resolution while probing multiple experimental contexts.

A three-pronged multidisciplinary approach

To meet this challenge, the Strambio De Castillia group is engaged in a multidisciplinary, collaborative effort to develop integrated workflows that will provide the analysis, data management, and visualization capabilities required to drive a complete understanding of viral-host interactions in the context of living human tissues. The project articulates on three fronts:

  1. Real-time recording of HIV-1 viral core movement in infected human cells.
  2. Viral particle tracking and motion analysis.
  3. Building a novel bio-image informatics framework, called OMEGA, to support the comprehensive examination of particle movement across multiple experimental models and conditions. 

OMEGA project output

  1. Rigano A, Galli V, Clark JM, Pereira LE, Grossi L, Luban J, et al. OMEGA: a software tool for the management, analysis, and dissemination of intracellular trafficking data that incorporates motion type classification and quality control. bioRxiv 2018. Available from: http://dx.doi.org/10.1101/251850.
  2. Rigano A, Galli V, Gonciarz K, Sbalzarini IF, Strambio-De-Castillia C. An algorithm-centric Monte Carlo method to empirically quantify motion-type estimation uncertainty in single-particle tracking. bioRxiv 2018. Available from: http://dx.doi.org/10.1101/379255.
  3. Rigano A, Strambio-De-Castillia C. Proposal for minimum information guidelines to report and reproduce results of particle tracking and motion analysis. bioRxiv 2017. Available from: http://dx.doi.org/10.1101/155036.