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omega

Open Microscopy Environment inteGrated Analysis (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.

https://github.com/omegaproject/omega

Science Score: 18.0%

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    CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
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    DOI references
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    Academic publication links
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    Scientific vocabulary similarity
    Low similarity (12.4%) to scientific vocabulary

Keywords

data-model error error-handling error-monitoring metadata microscopy motion-analysis omega particle-tracking standardization trajectory
Last synced: 6 months ago · JSON representation ·

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Open Microscopy Environment inteGrated Analysis (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.

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  • Stars: 2
  • Watchers: 3
  • Forks: 1
  • Open Issues: 1
  • Releases: 0
Topics
data-model error error-handling error-monitoring metadata microscopy motion-analysis omega particle-tracking standardization trajectory
Created over 7 years ago · Last pushed over 4 years ago
Metadata Files
Readme License Citation

README.md

Open Microscopy Environment inteGrated Analysis (OMEGA)

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.

Owner

  • Name: Open Microscopy Environment inteGrated Analysis
  • Login: OmegaProject
  • Kind: organization
  • Email: caterina.strambio@umassmed.edu
  • Location: UMass Medical School, Worcester, MA

Citation (CITATION) 

cff-version: 1.0.3
message: If you use OMEGA, please cite both the software and the papers as indicated in the scope of each reference.
authors:
  - family-names: Rigano
    given-names: Alessandro
    affiliation: University of Massachusetts Medical School
    email: alessandro.rigano@umassmed.edu
  - family-names: Galli
    given-names: Vanni
    affiliation: Scuola Universitaria Superiore della Svizzera Italiana (SUPSI)
    email: vanni.galli@supsi.ch
  - family-names: Strambio-De-Castillia
    given-names: Caterina
    affiliation: University of Massachusetts Medical School
    email: caterina.strambio@umassmed.edu
    orcid: https://orcid.org/0000-0002-1069-1816
title: Open Microscopy Environment inteGrated Analysis (OMEGA)
version: v0.45.3-beta
doi: 10.5281/zenodo.2535523 
date-released: 2019-01-08
repository: https://github.com/OmegaProject/Omega
description: 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).
keywords:
  - java
  - cell-biology
  - particle-tracking
  - particle-localization
  - particle-detection
  - motion-analysis
  - error-propagation
  - data-provenance
  - data-management
  - classification
  - trajectory-segmentation
license: GNU General Public License v.3
references:
  - type: article
    scope: Cite this paper every time you use the software
    authors:
      - family-names: Rigano
        given-names: Alessandro
        affiliation: University of Massachusetts Medical School
        email: alessandro.rigano@umassmed.edu
      - family-names: Galli
        given-names: Vanni
        affiliation: Scuola Universitaria Superiore della Svizzera Italiana (SUPSI)
      - family-names: Clark
        given-names: Jasmine M
        affiliation: Nell Hodgson Woodruff School of Nursing, Emory University
      - family-names: Pereira
        given-names: Lara E
        affiliation: Division of Sexual Transmitted Diseases Prevention, Centers for Disease Control and Prevention
      - family-names: Grossi
        given-names: Loris
        affiliation:  Scuola Universitaria Superiore della Svizzera Italiana (SUPSI)
      - family-names: Luban
        given-names: Jeremy
        affiliation: University of Massachusetts Medical School
        orcid: https://orcid.org/0000-0001-5650-4054
      - family-names: Giulietti
        given-names: Raffaello
        affiliation: Scuola Universitaria Superiore della Svizzera Italiana (SUPSI)
      - family-names: Leidi
        given-names: Tiziano
        affiliation: Scuola Universitaria Superiore della Svizzera Italiana (SUPSI)
      - family-names: Hunter
        given-names: Eric
        affiliation: Emory Vaccine Center at Yerkes National Primate Research Center
      - family-names: Valle
        given-names: Mario
        affiliation: Swiss National Supercomputing Centre
      - family-names: Sbalzarini
        given-names: Ivo F.
        affiliation: Max Planck Institute of Molecular Cell Biology and Genetics in Dresden
      - family-names: Strambio-De-Castillia
        given-names: Caterina
        affiliation: University of Massachusetts Medical School
        email: caterina.strambio@umassmed.edu
        orcid: https://orcid.org/0000-0002-1069-1816
    title: "OMEGA: a software tool for the management, analysis, and dissemination of 	intracellular trafficking data that incorporates motion type classification and quality control"
    year: 2018
    journal: bioRxiv.org
    doi: 10.1101/251850
    url: https://doi.org/10.1101/251850
  - type: article
    scope: Cite this paper every time you discuss or utilize the data provenance aspects of the sofware
    authors:
      - family-names: Rigano
        given-names: Alessandro
        affiliation: University of Massachusetts Medical School
        email: alessandro.rigano@umassmed.edu
      - family-names: Strambio-De-Castillia
        given-names: Caterina
        affiliation: University of Massachusetts Medical School
        email: caterina.strambio@umassmed.edu
        orcid: https://orcid.org/0000-0002-1069-1816
    title: "Proposal for minimum information guidelines to report and reproduce results of particle tracking and motion analysis"
    year: 2017
    journal: bioRxiv.org
    doi: 10.1101/155036
    url: https://doi.org/10.1101/155036 
  - type: article
    scope: Cite this paper every time you discuss or utilize the error propagation aspects of the sofware
    authors: 
      - family-names: Rigano
        given-names: Alessandro
        affiliation: University of Massachusetts Medical School
        email: alessandro.rigano@umassmed.edu
      - family-names: Galli
        given-names: Vanni
        affiliation: Scuola Universitaria Superiore della Svizzera Italiana (SUPSI)
      - family-names: Gonciarz
        given-names: Krzysztof
        affiliation: Max Planck Institute of Molecular Cell Biology and Genetics in Dresden
      - family-names: Sbalzarini
        given-names: Ivo F.
        affiliation: Max Planck Institute of Molecular Cell Biology and Genetics in Dresden
      - family-names: Strambio-De-Castillia
        given-names: Caterina
        affiliation: University of Massachusetts Medical School
        email: caterina.strambio@umassmed.edu
        orcid: https://orcid.org/0000-0002-1069-1816
    title: "An algorithm-centric Monte Carlo method to empirically quantify motion type estimation uncertainty in single-particle tracking"
    year: 2018
    journal: bioRxiv.org
    doi: 10.1101/379255
    url: https://doi.org/10.1101/379255

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