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List of online training material with a focus on research data management for bioimaging and image analysis

Resource Keywords  
ELIXIR TeSS registry for microscopy bioimage analysis; Python,; Cell Profiler; Ontology Show details
ELIXIR UK RDM bites Metadata; REMBI; OMERO Show details
EuBI virtual pub: Biological & pre-clinical imaging data microscopy; pre-clinical imaging; XNAT; OME; NGFF; OMERO; Bio-Formats; IDR; file formats; metadata Show details
GBI Training Courses Repository; image data; OMERO; IDR; BIA; EMPIAR Show details
MyScope (Micr. Australia) RDM Training Data management plan; Research Data Management; data sharing; microscopy Show details
OMERO Wiki of BIOP EPFL OMERO; Research Data Management; data sharing; microscopy Show details
OMERO Galaxy Suite and Galaxy Imaging Platform Galaxy; Imaging; OMERO; REMBI; metadata Show details

ELIXIR TeSS registry for microscopy

Keywords
bioimage analysis; python; Cell Profiler; ontology

TeSS (Training eSupport System) is a resource provided by Elixir. It offers a registry to search for training material on specific topics.

Explanations:
Elixir = an intergovernmental organization focusing on the goal to provide infrastructures for bioinformatics

A registry showing a list of further resources. Here, the search is pre-set with the term microscopy.

ELIXIR UK RDM bites

Keywords
metadata; REMBI; OMERO

A short-video series by Elixir UK, mostly focused on metadata and the proposed REMBI standards for metadata curation.

Explanations:

Elixir = an intergovernmental organization focusing on the goal to provide infrastructures for bioinformatics

REMBI = recommended metadata for bioimaging, a proposed set of metadata items that researchers in bioimaging should adhere to. Find out more.

A series on short videos about the REMBI metadata, including a proposal for their adoption in the image data management system OMERO.

Duration: 3 – 5 min per video

Euro-BioImaging Virtual pub on biological and pre-clinical imaging data

Keywords
biological imaging; pre-clinical imaging; XNAT; OME; NGFF; OMERO; Bio-Formats; IDR; file formats; metadata

Euro-BioImaging offers the online “virtual pub”. This episode of the virtual pub focussed on data in biological and pre-clinical imaging.

Explanations:
Euro-BioImaging is a research infrastructure providing access to bioimaging equipment across Europe. It is part of the European Strategy Forum on Research Infrastructures (ESFRI) and became a European Research Infrastructure Consortium (ERIC) in 2019.

Recording of the online talk by Dario Longo, Sara Zullino, Jean-Marie Burel, and Joshua Moore.
Duration: 1.5 h incl. discussion

Global BioImaging Training Courses

Keywords
repositories; image data; OMERO; IDR; BIA; EMPIAR;

Training Courses and recorded workshops on Image Repositories and Data Management by Global BioImaging. Contains workshops on:

  • OMERO
  • Image Data Resource
  • BioImage Archive

Explanations:

Global BioImaging is a network of infrastructures focussing mainly on international exchange. It was funded by the EU Horizon 2020 programm.

OMERO = an image data management system by the OME consortium, open-source software

Workshops and walkthroughs including videos, slide presentations and supplementary workshop materials.

Duration: A few hours

MyScope by Microscopy Australia
Research Data Management Training

Keywords
data managment plan; research data management; data sharing; microscopy

High-level introduction to research data management in microscopy. Mostly refering to the Australian research landscape.

Explanations:
MyScope is an online training resource on microsopy including research data management. MyScope is provided by Microscopy Australia

Web-based tutorial with walk-through.

Duration: 15-30 min.

OMERO Wiki of the Bioimaging and Optics Platform (BIOP) at EPFL (Lausanne)

Keywords
OMERO; research data management; data sharing; microscopy

Hands-on training and information resource (Wiki-style) on the OMERO instance at the Bioimaging and Optics Platform (BIOP) at the Ecole Polytechnique Fédérale de Lausanne (EPFL)

Explanations:
OMERO = OME Remote Objects, an open-source research data management system from the Open Microscopy Consortium

A comprehensive Wiki tailored to the OMERO instance at the Bioimaging and Optics Platform at EPFL.

Galaxy Training with OMERO Suite and REMBI metadata

Keywords
OMERO; Galaxy; metadata; REMBI

Walk-through training resource on different bioimage informatics topics with detailed descriptions and hands-on exercises on bioimaging data annotation and metadata curation.
The material includes training on REMBI and on the OMERO-Suite

Explanations:
OMERO = OME Remote Objects, an open-source research data management system from the Open Microscopy Consortium

Galaxy = A cloud-based bioinformatics tool, free to use, with online training courses for self-paced learning.

REMBI = Recommended Metadata for Biological Images, a checklist for microscopy metadata annotation

An online bioinformatics task execution platform that comes with training courses.