Readme and Citation updated

Author: akramhar

CITATION

@@ -0,0 +1,127 @@
+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: v0.37
+doi:
+date-released: 2017-10-27
+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 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: "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/
+  - 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: "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