micrometaapp-omero

This is a limited-functionality, beta - implementation of the integration of Micro-Meta App in the OMERO.web client

https://github.com/wu-bimac/micrometaapp-omero

Science Score: 77.0%

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CITATION.cff file
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Found 10 DOI reference(s) in README
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Links to: arxiv.org, biorxiv.org, nature.com, zenodo.org
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3 of 5 committers (60.0%) from academic institutions
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Low similarity (12.3%) to scientific vocabulary

Keywords

annotation-tool metadata metadata-editor metadata-extraction metadata-management microscopy-data microscopy-metadata omero omero-web reporting-tool reproducibility

Keywords from Contributors

research-data-management json-schema metadata-standard reporting

Last synced: 6 months ago · JSON representation ·

Repository

This is a limited-functionality, beta - implementation of the integration of Micro-Meta App in the OMERO.web client

Basic Info

Host: GitHub
Owner: WU-BIMAC
License: gpl-3.0
Language: JavaScript
Default Branch: master
Homepage:
Size: 27.9 MB

Statistics

Stars: 4
Watchers: 2
Forks: 2
Open Issues: 14
Releases: 6

Topics

annotation-tool metadata metadata-editor metadata-extraction metadata-management microscopy-data microscopy-metadata omero omero-web reporting-tool reproducibility

Created over 6 years ago · Last pushed over 1 year ago

Metadata Files

Readme Contributing License Code of conduct Citation

README.md

This software is a Micro-Meta App dependency, which was developed as part of a global community initiative including the 4D Nucleome Imaging Working Group, BINA Quality Control and Data Management Working Group and QUAREP-LiMi.

News! The works of this global community effort resulted in multiple publications featured on a recent Nature Methods FOCUS ISSUE dedicated to Reporting and reproducibility in microscopy.

Learn More! For a thorought description of Micro-Meta App consult our recent Nature Methods and BioRxiv.org publications!

Background If you want to learn more about the importannce of metadata and quality control to ensure full reproducibility, quality and scientific value in light microscopy, please take a look at our recent publications describing the development of community-driven light microscopy metadata specifications (Nature Methods and BioRxiv.org) and our overview manuscript entitled "A perspective on Microscopy Metadata: data provenance and quality control", which is available on ArXiv.org.

4DN Micro-Meta App OMERO plugin -- alpha prototype

Quick start guide

Use these videos to get started with using Micro-Meta App after intallation into OMERO and downloading the example data files: 1. Video 1 2. Video 2

Summary

Micro-Meta App is an interactive tool that was developed by Alex Rigano in the Strambio De Castillia's lab at the University of Massachusetts Chan Medical School to facilitate the documentation of light microscopy experiments on the basis of the scalable 4DN-BINA-OME Microscopy Metadata specifications that extend the OME Data Model.

Micro-Meta App is used to visually and intuitively document the microscopy conditions used to acquire specific datasets based on community-driven 4DN-BINA-OME Microscopy Metadata specifications.

This repository contains a prototype of a plugin to be integrated into the OMERO.web browser.

Other available implementations of Micro-Meta App include:

A web-app version implemented in React
A stand-alone version implemented in Electron

Micro-Meta App: Create Microscope GUI Micro-Meta App is designed to aid in the collection of both Microscope Hardware Specifications and Image Acquisition Settings metadata. In this example, a previously saved Microscope file was selected from an available repository and opened for further editing. In order to add the metadata associated with a newly purchased objective to a Microscope file the “Magnification” drop-down menu is opened [1] and an additional “Objective” [2] is dragged onto the workspace.

Background

Adequate recordkeeping is essential for most experiments as it is necessary in order to evaluate results, share data and allow experiments to be repeated. Keeping notes on microscopy experiments should be relatively unchallenging, as the microscope is a machine equipped with a limited number of known parts and settings. Nevertheless, to this date no widely adopted set of metadata guidelines to be recorded or published with imaging data exists. Metadata automatically recorded by microscopes from different companies vary widely and pose a substantial challenge for microscope users to create a good faith record of their work. Similarly, the complexity and aim of experiments using microscopes varies leading to different reporting requirements from the simple description of a sample to the need to document the complexities of sub-diffraction resolution imaging in living cells and beyond. To address this challenge, the 4DN consortium has put forth a 4DN extension of the OME Core metadata model, which includes a tiered system of reporting guidelines that scales quality control and reporting requirements with experimental complexity and a comprehensive list of metadata key-value pairs that should be recorded for each tier, and a detailed explanation of why these values matter. Micro-Meta App was developed in order to lessen the recordkeeping burden, support the collection of microscopy provenance medatata and facilitate the wide adoption of these standards by the the imaging community at large.

Description

Micro-Meta App is a novel application that provides an interactive and intuitive approach for rigorous record-keeping in fluorescence microscopy and is based on the 4DN-OME Microscopy metadata standard and on the proposed tiered-system of guidelines. The user’s data processing workflow consists of multiple steps. First, in the Create Microscope modality (Figure 1), the App allows the users to build a graphical representation of the microscope hardware by dragging-and-dropping individual components onto the workspace and entering the relevant attribute values based on the selected tier level. Second, Micro-Meta App generates tier-specific descriptions of the microscope hardware and exports them in a Microscope file that can be used as a template and shared with the community, with a significant reduction in the recordkeeping burden. Then, in the Use Microscope modality, Micro-Meta App opens an existing Microscope file, imports Image Acquisition settings from the header of image data files to be annotated and interactively guides the user through the collection of all missing instrument-specific and tier-appropriate image acquisition settings and calibration metrics required to ensure reuse and reproducibility of image data. Finally, the App generates JSON files that contain comprehensive descriptions of the conditions utilized to produce individual microscopy datasets, and that can be stored on the user’s file system, or on third party repositories. To lower the barrier of adoption of Micro-Meta App by a wide community of users the application is available as a stand-alone program, as a plugin of the OMERO web client and as a service of the 4DN data portal.

Installation

Requirements

The Micro-Meta App Omero.web plugin requires a working Omero.server and Omero.web environment to be installated.

Install

Download the latest pip friendly (.tar.gz) release from here.
Run pip install </path/to/package/folder/nameofthefile.tar.gz> Or if you prefer a manual installation unpack the file in your pluging folder (that should be added to your python path).
Add the plugin to your omero with omero config append omero.web.apps '"omero_microMetaApp"'
Optionally add a top menu link with omero config append omero.web.ui.top_links '["Micro-Meta-App", "microMetaAppOmero_index", {"title": "Micro-Meta-App", "target": "_blank"}]'

Owner

Name: Worcester Image Data Management
Login: WU-BIMAC
Kind: organization
Email: worcesterimagedatamanagement@gmail.com
Location: University of Massachusetts Medical School, Worcester, MA

Repositories: 14
Profile: https://github.com/WU-BIMAC

The UMass Chan Medical School Research Data Management 4 Microscopy Image Data Group

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: Micro-Meta App - OMERO plugin
message: >-
  If you use this software please cite both the software using the metadata indicated below, and the papers as indicated in the scope of each reference
type: software
authors:
  - given-names: Alessandro
    family-names: Rigano
    email: alessandro.rigano@umassmed.edu
    affiliation: >-
      Program in Molecular Medicine, UMass Chan
      Medical School, Worcester MA 01605, USA
  - given-names: Balashov
    family-names: Alexander
    affiliation: >-
      Department of Biomedical Informatics, Harvard
      Medical School, Boston, MA 02115, USA
  - affiliation: >-
      Department of Biomedical Informatics, Harvard
      Medical School, Boston, MA 02115, USA
    given-names: Shannon
    family-names: Ehmsen
  - given-names: Serkan Utku
    family-names: Ozturk
    orcid: 'https://orcid.org/0000-0001-8835-787X'
    affiliation: >-
      Karya SMD + Department of Biomedical
      Informatics, Harvard Medical School, Boston, MA
      02115, USA
  - given-names: Alver
    family-names: Burak
    orcid: >-
      https://orcid.org/https://orcid.org/0000-0002-5019-7652
    affiliation: >-
      Department of Biomedical Informatics, Harvard
      Medical School, Boston, MA 02115, USA
  - affiliation: >-
      Program in Molecular Medicine, UMass Chan
      Medical School, Worcester MA 01605, USA
    orcid: >-
      https://orcid.org/https://orcid.org/0000-0002-1069-1816
    family-names: Strambio-De-Castillia
    given-names: Caterina
    email: caterina.strambio@umassmed.edu
repository-code: 'https://github.com/WU-BIMAC/MicroMetaApp-Omero'
url: 'https://wu-bimac.github.io/MicroMetaApp.github.io/'
doi: 10.5281/zenodo.4750762
abstract: >-
  Micro-Meta App is an intuitive Graphical User Interface (GUI)-based open-source software that helps scientists to interactively build graphical representations of microscope hardware by dragging-and-dropping individual components onto the workspace and entering the relevant attribute values based on the 4D Nucleome (4DN) - BioImaging North America (BINA) Microscopy Metadata guidelines that scale experimental complexity. From this, Micro-Meta App automatically generates structured Microscope files that can be saved locally, consumed by existing data portals, shared with other scientists, and used repeatedly whenever the same microscope is used to produce image data. Thus, when the image acquisition settings utilized to produce a given image dataset need to be recorded, the user selects the desired image data alongside the relevant Microscope file. Then, Micro-Meta App imports the relevant metadata from the header of image data files to be annotated and interactively guides the user through the collection of all missing attributes. Finally, the App generates a Settings-file, which coupled with the Microscope-file contains comprehensive descriptions of the conditions utilized to produce individual microscopy datasets.
keywords:
  - metadata
  - microscopy
  - standards
  - data model
  - OME
  - open science
  - reproducibility
  - quality control
  - data provenance
license: GPL-3.0-or-later
version: 1.2.2-b1-1 stable beta
date-released: '2021-05-11'
references:
  - authors:
      - family-names: Rigano
        given-names: Alessandro
        affiliation: Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester MA 01605, USA
        email: alex.rigano@umassmed.edu
      - family-names: Ehmsen
        given-names: Shannon
        affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
      - family-names: Ozturk
        given-names: Serkan Utku
        affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
        orcid: https://orcid.org/0000-0001-8835-787
      - family-names: Ryan
        given-names: Joel
        affiliation: Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, H3G 0B1, Canada
      - family-names: Balashov
        given-names: Alexander
        affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
      - family-names: Hammer
        given-names: Mathias
        affiliation: RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester MA 01605, USA
      - family-names: Kirli
        given-names: Koray
        affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
      - family-names: Boehm
        given-names: Ulrike
        affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
        orcid: https://orcid.org/0000-0001-7471-2244
      - family-names: Brown
        given-names: Claire M. 
        affiliation: Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, H3G 0B1, Canada
        orcid: https://orcid.org/0000-0003-1622-663X
      - family-names: Bellve
        given-names: Karl
        affiliation: Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester MA 01605, USA
      - family-names: Chambers
        given-names: James
        affiliation: Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA 01003, USA
        orcid: https://orcid.org/0000-0003-3883-8215
      - family-names: Cosolo
        given-names: Andrea
        affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
      - family-names: Coleman
        given-names: Robert
        affiliation: Gruss-Lipper Biophotonics Center, Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461
      - family-names: Faklaris
        given-names: Orestis
        affiliation: Biocampus, CNRS UMS 3426, Montpellier 34293, France
        orcid: https://orcid.org/0000-0001-5965-5405
      - family-names: Fogarty
        given-names: Kevin
        affiliation: Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester MA 01605, USA
      - family-names: Guilbert
        given-names: Thomas
        affiliation:  Plateforme IMAG'IC, Institut Cochin, Inserm U1016-CNRS UMR8104-Université de Paris, 75014 Paris
      - family-names: Hamacher
        given-names: Anna B.
        affiliation: Center for Advanced Imaging, Heinrich-Heine University Duesseldorf, 40225 Düsseldorf, Germany
      - family-names: Itano
        given-names: Michelle
        affiliation: UNC Neuroscience Microscopy Core Facility, Chapel Hill, NC 27599-7250
      - family-names: Keeley
        given-names: Daniel P.
        affiliation: UNC Neuroscience Microscopy Core Facility, Chapel Hill, NC 27599-7250
      - family-names: Kunis
        given-names: Susanne
        affiliation: Department of Biology/Chemistry and Centre for Cellular Nanoanalytics, University Osnabrueck, 49076 Osnabrück, Germany
      - family-names: Lacoste
        given-names: Judith
        affiliation: MIA Cellavie Inc., Montreal, Quebec, H1K 4G6, Canada
      - family-names: Laude
        given-names: Alex
        affiliation: Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
        orcid: https://orcid.org/0000-0002-3853-1187
      - family-names: Ma
        given-names: Willa Y.
        affiliation: UNC Neuroscience Microscopy Core Facility, Chapel Hill, NC 27599-7250
      - family-names: Marcello
        given-names: Marco
        affiliation: Center for Cell Imaging, University of Liverpool, Liverpool, L69 3BE, UK
      - family-names: Montero-Llopis
        given-names: Paula
        affiliation: Microscopy Resources of the North Quad, University of Harvard Medical School, Boston, MA 02115
        orcid: https://orcid.org/0000-0002-5983-2296
      - family-names: Nelson
        given-names: Glyn
        affiliation: Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
        orcid: http://orcid.org/0000-0002-1895-4772
      - family-names: Nitschke
        given-names: Roland
        affiliation: Life Imaging Center and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
        orcid: https://orcid.org/0000-0002-9397-8475
      - family-names: Pimentel
        given-names: Jaime A.
        affiliation: Instituto de Biotecnologıa, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, 62210, México
        orcid: https://orcid.org/0000-0001-8569-0466
      - family-names: Weidtkamp-Peters
        given-names: Stefanie
        affiliation: Center for Advanced Imaging, Heinrich-Heine University Duesseldorf, 40225 Düsseldorf, Germany
      - family-names: Park
        given-names: Peter
        affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
      - family-names: Alver
        given-names: Burak
        affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
        orcid: https://orcid.org/https://orcid.org/0000-0002-5019-7652
      - family-names: Grunwald
        given-names: David
        affiliation: RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester MA 01605, USA
      - family-names: Strambio-De-Castillia
        given-names: Caterina
        affiliation: Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester MA 01605, USA
        email: caterina.strambio@umassmed.edu
        orcid: https://orcid.org/0000-0002-1069-1816
    doi: 10.1038/s41592-021-01315-z
    journal: "Nature Methods"
    volume: 18
    pages: 1489
    scope: "Cite this paper every time you use this software."
    title: "Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications"
    type: article
    year: 2021
  - authors:
      - family-names: Rigano
        given-names: Alessandro
        affiliation: Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester MA 01605, USA
        email: alex.rigano@umassmed.edu
      - family-names: Ehmsen
        given-names: Shannon
        affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
      - family-names: Ozturk
        given-names: Serkan Utku
        affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
        orcid: https://orcid.org/0000-0001-8835-787
      - family-names: Ryan
        given-names: Joel
        affiliation: Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, H3G 0B1, Canada
      - family-names: Balashov
        given-names: Alexander
        affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
      - family-names: Hammer
        given-names: Mathias
        affiliation: RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester MA 01605, USA
      - family-names: Kirli
        given-names: Koray
        affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
      - family-names: Boehm
        given-names: Ulrike
        affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
        orcid: https://orcid.org/0000-0001-7471-2244
      - family-names: Brown
        given-names: Claire M. 
        affiliation: Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, H3G 0B1, Canada
        orcid: https://orcid.org/0000-0003-1622-663X
      - family-names: Chambers
        given-names: James
        affiliation: Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA 01003, USA
        orcid: https://orcid.org/0000-0003-3883-8215
      - family-names: Coleman
        given-names: Robert
        affiliation: Gruss-Lipper Biophotonics Center, Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461
      - family-names: Cosolo
        given-names: Andrea
        affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
      - family-names: Faklaris
        given-names: Orestis
        affiliation: Biocampus, CNRS UMS 3426, Montpellier 34293, France
        orcid: https://orcid.org/0000-0001-5965-5405
      - family-names: Fogarty
        given-names: Kevin
        affiliation: Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester MA 01605, USA
      - family-names: Guilbert
        given-names: Thomas
        affiliation:  Plateforme IMAG'IC, Institut Cochin, Inserm U1016-CNRS UMR8104-Université de Paris, 75014 Paris
      - family-names: Hamacher
        given-names: Anna B.
        affiliation: Center for Advanced Imaging, Heinrich-Heine University Duesseldorf, 40225 Düsseldorf, Germany
      - family-names: Itano
        given-names: Michelle
        affiliation: UNC Neuroscience Microscopy Core Facility, Chapel Hill, NC 27599-7250
      - family-names: Keeley
        given-names: Daniel P.
        affiliation: UNC Neuroscience Microscopy Core Facility, Chapel Hill, NC 27599-7250
      - family-names: Kunis
        given-names: Susanne
        affiliation: Department of Biology/Chemistry and Centre for Cellular Nanoanalytics, University Osnabrueck, 49076 Osnabrück, Germany
      - family-names: Lacoste
        given-names: Judith
        affiliation: MIA Cellavie Inc., Montreal, Quebec, H1K 4G6, Canada
      - family-names: Laude
        given-names: Alex
        affiliation: Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
        orcid: https://orcid.org/0000-0002-3853-1187
      - family-names: Ma
        given-names: Willa
        affiliation: UNC Neuroscience Microscopy Core Facility, Chapel Hill, NC 27599-7250
      - family-names: Marcello
        given-names: Marco
        affiliation: Center for Cell Imaging, University of Liverpool, Liverpool, L69 3BE, UK
      - family-names: Montero-Llopis
        given-names: Paula
        affiliation: Microscopy Resources of the North Quad, University of Harvard Medical School, Boston, MA 02115
        orcid: https://orcid.org/0000-0002-5983-2296
      - family-names: Nelson
        given-names: Glyn
        affiliation: Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
        orcid: http://orcid.org/0000-0002-1895-4772
      - family-names: Nitschke
        given-names: Roland
        affiliation: Life Imaging Center and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
        orcid: https://orcid.org/0000-0002-9397-8475
      - family-names: Pimentel
        given-names: Jaime A.
        affiliation: Instituto de Biotecnologıa, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, 62210, México
        orcid: https://orcid.org/0000-0001-8569-0466
      - family-names: Weidtkamp-Peters
        given-names: Stefanie
        affiliation: Center for Advanced Imaging, Heinrich-Heine University Duesseldorf, 40225 Düsseldorf, Germany
      - family-names: Park
        given-names: Peter
        affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
      - family-names: Alver
        given-names: Burak
        affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
        orcid: https://orcid.org/https://orcid.org/0000-0002-5019-7652
      - family-names: Grunwald
        given-names: David
        affiliation: RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester MA 01605, USA
      - family-names: Strambio-De-Castillia
        given-names: Caterina
        affiliation: Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester MA 01605, USA
        email: caterina.strambio@umassmed.edu
        orcid: https://orcid.org/0000-0002-1069-1816
    doi: 10.1101/2021.05.31.44638
    journal: "BioRxiv.org"
    scope: "Cite this paper every time you use this software."
    title: "Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications"
    type: article
    year: 2021
  - authors:
      - family-names: Mathias
        given-names: Hammer
        affiliation: RNA Therapeutic Institute, University of Massachusetts Chan Medical School
      - family-names: Maximiliaan
        given-names: Huisman
        affiliation: RNA Therapeutic Institute, University of Massachusetts Chan Medical School
        orcid: https://orcid.org/0000-0003-3363-8791
      - family-names: Rigano
        given-names: Alessandro
        affiliation: Program in Molecular Medicine, University of Massachusetts Chan Medical School
      - family-names: Boehm
        given-names: Ulrike
        affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
        orcid: https://orcid.org/0000-0001-7471-2244
      - family-names: Chambers
        given-names: James
        affiliation: Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA 01003, USA
        orcid: https://orcid.org/0000-0003-3883-8215
      - family-names: Gaudreault
        given-names: Nathalie
        affiliation: Allen Institute for Cell Science, Seattle, WA 98109, USA
      - family-names: North
        given-names: Alison J.
        affiliation: The Rockefeller University, New York, NY 10065, USA
        orcid: https://orcid.org/0000-0002-0577-7949
      - family-names: Pimentel
        given-names: Arturo
        affiliation: Instituto de Biotecnologıa, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, 62210, México
        orcid: https://orcid.org/0000-0001-8569-0466
      - family-names: Sudar
        given-names: Damir
        affiliation: Quantitative Imaging Systems LLC, Portland, OR 97209, USA
        orcid: https://orcid.org/0000-0002-2510-7272
      - family-names: Bajcsy
        given-names: Peter
        affiliation: National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
        orcid: https://orcid.org/0000-0002-6968-2615
      - family-names: Brown
        given-names: Claire M. 
        affiliation: Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, H3G 0B1, Canada
        orcid: https://orcid.org/0000-0003-1622-663X
      - family-names: Corbett
        given-names: Alexander D. 
        affiliation: Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QL, UK
        orcid: https://orcid.org/0000-0003-1645-5475
      - family-names: Faklaris
        given-names: Orestis
        affiliation: Biocampus, CNRS UMS 3426, Montpellier 34293, France
        orcid: https://orcid.org/0000-0001-5965-5405
      - family-names: Lacoste
        given-names: Judith
        affiliation: MIA Cellavie Inc., Montreal, Quebec, H1K 4G6, Canada
      - family-names: Laude
        given-names: Alex
        affiliation: Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
        orcid: https://orcid.org/0000-0002-3853-1187
      - family-names: Nelson
        given-names: Glyn
        affiliation: Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
        orcid: http://orcid.org/0000-0002-1895-4772
      - family-names: Nitschke
        given-names: Roland
        affiliation: Life Imaging Center and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
        orcid: https://orcid.org/0000-0002-9397-8475
      - family-names: Gopinathan
        given-names: Renu
        affiliation: RNA Therapeutics Institute, UMass Medical School, Worcester MA 01605, USA 
      - family-names: Farzam
        given-names: Farzin
        affiliation: RNA Therapeutics Institute, UMass Medical School, Worcester MA 01605, USA
      - family-names: Carlas
        given-names: Smith
        affiliation: Dutch Optics Center, Technische Universiteit Delft, Delft, 2600 AA, The Netherlands
      - family-names: David
        given-names: Grunwald
        affiliation: University of Massachusetts Medical School
      - 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
    doi: 10.1101/2021.04.25.441198
    journal: "BioRxiv.org"
    scope: "Cite this paper when you want to discuss the background context for this software."
    title: "Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model"
    type: article
    year: 2021
  - authors:
      - family-names: Maximiliaan
        given-names: Huisman
        affiliation: University of Massachusetts Medical School
      - family-names: Mathias
        given-names: Hammer
        affiliation: University of Massachusetts Medical School
        orcid: https://orcid.org/0000-0003-3363-8791
      - family-names: Rigano
        given-names: Alessandro
        affiliation: University of Massachusetts Medical School
      - family-names: Boehm
        given-names: Ulrike
        affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
        orcid: https://orcid.org/0000-0001-7471-2244
      - family-names: Chambers
        given-names: James
        affiliation: Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA 01003, USA
        orcid: https://orcid.org/0000-0003-3883-8215
      - family-names: Gaudreault
        given-names: Nathalie
        affiliation: Allen Institute for Cell Science, Seattle, WA 98109, USA
      - family-names: North
        given-names: Alison J.
        affiliation: The Rockefeller University, New York, NY 10065, USA
        orcid: https://orcid.org/0000-0002-0577-7949
      - family-names: Pimentel
        given-names: Arturo
        affiliation: Instituto de Biotecnologıa, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, 62210, México
        orcid: https://orcid.org/0000-0001-8569-0466
      - family-names: Sudar
        given-names: Damir
        affiliation: Quantitative Imaging Systems LLC, Portland, OR 97209, USA
        orcid: https://orcid.org/0000-0002-2510-7272
      - family-names: Bajcsy
        given-names: Peter
        affiliation: National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
        orcid: https://orcid.org/0000-0002-6968-2615
      - family-names: Brown
        given-names: Claire M. 
        affiliation: Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, H3G 0B1, Canada
        orcid: https://orcid.org/0000-0003-1622-663X
      - family-names: Corbett
        given-names: Alexander D. 
        affiliation: Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QL, UK
        orcid: https://orcid.org/0000-0003-1645-5475
      - family-names: Faklaris
        given-names: Orestis
        affiliation: Biocampus, CNRS UMS 3426, Montpellier 34293, France
        orcid: https://orcid.org/0000-0001-5965-5405
      - family-names: Lacoste
        given-names: Judith
        affiliation: MIA Cellavie Inc., Montreal, Quebec, H1K 4G6, Canada
      - family-names: Laude
        given-names: Alex
        affiliation: Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
        orcid: https://orcid.org/0000-0002-3853-1187
      - family-names: Nelson
        given-names: Glyn
        affiliation: Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
        orcid: http://orcid.org/0000-0002-1895-4772
      - family-names: Nitschke
        given-names: Roland
        affiliation: Life Imaging Center and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
        orcid: https://orcid.org/0000-0002-9397-8475
      - family-names: David
        given-names: Grunwald
        affiliation: University of Massachusetts Medical School
      - 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
    url: https://arxiv.org/abs/1910.11370
    journal: "arXiv.org"
    scope: "Cite this paper when you want to discuss the background context for this software."
    title: "A perspective on Microscopy Metadata: data provenance and quality control"
    type: article
    year: 2021
  - authors:
      - family-names: Mathias
        given-names: Hammer
        affiliation: RNA Therapeutic Institute, University of Massachusetts Chan Medical School
      - family-names: Maximiliaan
        given-names: Huisman
        affiliation: RNA Therapeutic Institute, University of Massachusetts Chan Medical School
        orcid: https://orcid.org/0000-0003-3363-8791
      - family-names: Rigano
        given-names: Alessandro
        affiliation: Program in Molecular Medicine, University of Massachusetts Chan Medical School
      - family-names: Boehm
        given-names: Ulrike
        affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
        orcid: https://orcid.org/0000-0001-7471-2244
      - family-names: Chambers
        given-names: James
        affiliation: Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA 01003, USA
        orcid: https://orcid.org/0000-0003-3883-8215
      - family-names: Gaudreault
        given-names: Nathalie
        affiliation: Allen Institute for Cell Science, Seattle, WA 98109, USA
      - family-names: North
        given-names: Alison J.
        affiliation: The Rockefeller University, New York, NY 10065, USA
        orcid: https://orcid.org/0000-0002-0577-7949
      - family-names: Pimentel
        given-names: Arturo
        affiliation: Instituto de Biotecnologıa, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, 62210, México
        orcid: https://orcid.org/0000-0001-8569-0466
      - family-names: Sudar
        given-names: Damir
        affiliation: Quantitative Imaging Systems LLC, Portland, OR 97209, USA
        orcid: https://orcid.org/0000-0002-2510-7272
      - family-names: Bajcsy
        given-names: Peter
        affiliation: National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
        orcid: https://orcid.org/0000-0002-6968-2615
      - family-names: Brown
        given-names: Claire M. 
        affiliation: Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, H3G 0B1, Canada
        orcid: https://orcid.org/0000-0003-1622-663X
      - family-names: Corbett
        given-names: Alexander D. 
        affiliation: Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QL, UK
        orcid: https://orcid.org/0000-0003-1645-5475
      - family-names: Faklaris
        given-names: Orestis
        affiliation: Biocampus, CNRS UMS 3426, Montpellier 34293, France
        orcid: https://orcid.org/0000-0001-5965-5405
      - family-names: Lacoste
        given-names: Judith
        affiliation: MIA Cellavie Inc., Montreal, Quebec, H1K 4G6, Canada
      - family-names: Laude
        given-names: Alex
        affiliation: Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
        orcid: https://orcid.org/0000-0002-3853-1187
      - family-names: Nelson
        given-names: Glyn
        affiliation: Bioimaging Unit, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
        orcid: http://orcid.org/0000-0002-1895-4772
      - family-names: Nitschke
        given-names: Roland
        affiliation: Life Imaging Center and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
        orcid: https://orcid.org/0000-0002-9397-8475
      - family-names: Gopinathan
        given-names: Renu
        affiliation: RNA Therapeutics Institute, UMass Medical School, Worcester MA 01605, USA 
      - family-names: Farzam
        given-names: Farzin
        affiliation: RNA Therapeutics Institute, UMass Medical School, Worcester MA 01605, USA
      - family-names: Carlas
        given-names: Smith
        affiliation: Dutch Optics Center, Technische Universiteit Delft, Delft, 2600 AA, The Netherlands
      - family-names: David
        given-names: Grunwald
        affiliation: University of Massachusetts Medical School
      - 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
    doi: 10.1038/s41592-021-01327-9
    journal: "Nature Methods"
    volume: 18
    pages: 1428
    scope: "Cite this paper when you want to discuss the background context for this software."
    title: "Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model"
    type: article
    year: 2021

GitHub Events

Total

Last Year

Committers

Last synced: 8 months ago

All Time

Total Commits: 114
Total Committers: 5
Avg Commits per committer: 22.8
Development Distribution Score (DDS): 0.474

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
akramhar	a**3@b**h	60
Caterina Strambio De Castillia	c**o@u**u	19
akramhar	a**3@r**h	16
Akramhar	a**o@u**u	13
William Moore	w**e@d**k	6

Committer Domains (Top 20 + Academic)

umassmed.edu: 2 dundee.ac.uk: 1 rigano.ch: 1 bluewin.ch: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time

Total issues: 17
Total pull requests: 27
Average time to close issues: 4 months
Average time to close pull requests: 3 months
Total issue authors: 5
Total pull request authors: 5
Average comments per issue: 2.18
Average comments per pull request: 0.63
Merged pull requests: 5
Bot issues: 0
Bot pull requests: 21

Past Year

Issues: 0
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 0.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

strambc (13)
will-moore (1)
mathomH (1)
abhamacher (1)

Pull Request Authors

dependabot[bot] (21)
will-moore (3)
Tom-TBT (2)
Akramhar (1)
strambc (1)

Top Labels

Issue Labels

bug (10) High (6) help wanted (2) question (2) New Feature (2) enhancement (2) Medium (1)

Pull Request Labels

dependencies (21)

Dependencies

package-lock.json npm

1144 dependencies

package.json npm

@babel/cli ^7.17.0 development
@babel/core ^7.17.2 development
@babel/eslint-parser 7.17.0 development
@babel/plugin-proposal-class-properties ^7.16.7 development
@babel/plugin-proposal-object-rest-spread ^7.16.7 development
@babel/plugin-syntax-dynamic-import ^7.8.3 development
@babel/plugin-syntax-flow ^7.16.7 development
@babel/preset-env ^7.16.11 development
@babel/preset-react ^7.16.7 development
@babel/register ^7.17.0 development
@swc/core ^1.2.140 development
@swc/wasm ^1.2.140 development
ajv ^8.10.0 development
babel-loader ^8.2.3 development
babel-preset-react-app ^10.0.1 development
bufferutil ^4.0.6 development
canvas ^2.9.0 development
case-sensitive-paths-webpack-plugin ^2.3.0 development
css-loader ^6.6.0 development
dotenv ^16.0.0 development
dotenv-expand ^8.0.1 development
encoding ^0.1.13 development
eslint ^8.9.0 development
eslint-plugin-flowtype ^8.0.3 development
eslint-plugin-import ^2.25.4 development
eslint-plugin-jsx-a11y ^6.5.1 development
eslint-plugin-react ^7.28.0 development
eslint-webpack-plugin ^3.1.1 development
fancy-log ^2.0.0 development
gulp ^4.0.2 development
jest ^27.5.1 development
jest-pnp-resolver ^1.2.2 development
jest-resolve ^27.5.1 development
jest-watch-typeahead ^1.0.0 development
mini-css-extract-plugin ^2.5.3 development
node-notifier ^10.0.1 development
plugin-error ^1.0.1 development
pnp-webpack-plugin ^1.7.0 development
postcss-flexbugs-fixes ^5.0.2 development
postcss-loader ^6.2.1 development
postcss-preset-env ^7.3.3 development
postcss-safe-parser ^6.0.0 development
style-loader ^3.3.1 development
ts-node ^10.5.0 development
typescript ^4.5.5 development
utf-8-validate ^5.0.8 development
webpack ^5.68.0 development
webpack-cli ^4.9.2 development
micro-meta-app-react github:WU-BIMAC/MicroMetaApp-React#master
react ^17.0.2
react-bootstrap 1.4.0
react-dom ^17.0.2

setup.py pypi

omero_web >=5.6.0

pyproject.toml pypi