Video (24)

Christian Schmidt, Michele Bortolomeazzi, Tom Boissonnet, Carsten Fortmann-Grote, Julia Dohle, Peter Zentis, Niraj Kandpal, Susanne Kunis, Thomas Zobel, Stefanie Weidtkamp-Peters, Elisa Ferrando-May

Published 2023-11-13

Licensed CC-BY-4.0

The open-source software OME Remote Objects (OMERO) is a data management software that allows storing, organizing, and annotating bioimaging/microscopy data. OMERO has become one of the best-known systems for bioimage data management in the bioimaging community. The Information Infrastructure for BioImage Data (I3D:bio) project facilitates the uptake of OMERO into research data management (RDM) practices at universities and research institutions in Germany. Since the adoption of OMERO into researchers’ daily routines requires intensive training, a broad portfolio of training resources for OMERO is an asset. On top of using the OMERO guides curated by the Open Microscopy Environment Consortium (OME) team, imaging core facility staff at institutions where OMERO is used often prepare additional material tailored to be applicable for their own OMERO instances. Based on experience gathered in the Research Data Management for Microscopy group (RDM4mic) in Germany, and in the use cases in the I3D:bio project, we created a set of reusable, adjustable, openly available slide decks to serve as the basis for tailored training lectures, video tutorials, and self-guided instruction manuals directed at beginners in using OMERO. The material is published as an open educational resource complementing the existing resources for OMERO contributed by the community.

Tags: OMERO, Research Data Management, Nfdi4Bioimage, I3Dbio

Content type: Slide, Video

https://zenodo.org/records/8323588

https://www.youtube.com/playlist?list=PL2k-L-zWPoR7SHjG1HhDIwLZj0MB_stlU

https://doi.org/10.5281/zenodo.8323588

Ibiology. Bioimage Analysis Course. The Life Cycle of an Image Data Set#

Licensed CC BY-NC-ND 3.0 DEED

Tags: Bioimage Analysis

Content type: Collection, Video

https://www.ibiology.org/online-biology-courses/bioimage-analysis-course/

Imaris Tutorials#

Tags: Bioimage Analysis

Content type: Collection, Video

https://imaris.oxinst.com/tutorials

Melbourne Advanced Microscopy Facility#

Collection of tutorial videos for Fiji users

Tags: Bioimage Analysis

Content type: Collection, Video

https://www.youtube.com/@melbourneadvancedmicroscop2617

Methods in bioimage analysis#

Christian Tischer

Licensed CC-BY-4.0

Tags: Bioimage Analysis

Content type: Online Tutorial, Video, Slide

https://www.ebi.ac.uk/training/events/methods-bioimage-analysis/

https://doi.org/10.6019/TOL.BioImageAnalysis22-w.2022.00001.1

https://drive.google.com/file/d/1MhuqfKhZcYu3bchWMqogIybKjamU5Msg/view

Microscopy data analysis: machine learning and the BioImage Archive#

Andrii Iudin, Anna Foix-Romero, Anna Kreshuk, Awais Athar, Beth Cimini, Dominik Kutra, Estibalis Gomez de Mariscal, Frances Wong, Guillaume Jacquemet, Kedar Narayan, Martin Weigert, Nodar Gogoberidze, Osman Salih, Petr Walczysko, Ryan Conrad, Simone Weyend, Sriram Sundar Somasundharam, Suganya Sivagurunathan, Ugis Sarkans

Licensed CC-BY-4.0

The Microscopy data analysis: machine learning and the BioImage Archive course, which focused on introducing programmatic approaches used in the analysis of bioimage data via the BioImage Archive, ran in May 2023.

Tags: Microscopy Image Analysis, Python, Deep Learning

Content type: Video, Slides

https://www.ebi.ac.uk/training/materials/microscopy-data-analysis-machine-learning-and-the-bioimage-archive-materials/

NEUBIAS YouTube Channel#

A collection of bio-image analysis webinars where commonly authors of open-source bio-image analysis software explain how to use their tools.

Tags: Neubias

Content type: Collection, Video

https://www.youtube.com/neubias

Open Micoscropy Environment (OME) Youtube Channel#

Published None

Licensed CC-BY-4.0

OME develops open-source software and data format standards for the storage and manipulation of biological microscopy data

Tags: Open Source Software, Microscopy Image Analysis, Bioimage Data

Content type: Video, Collection

https://www.youtube.com/@OpenMicroscopyEnvironment

Open Microscopy Environment YouTube channel#

YouTube channel collecting videos and webinar recordings about the Open Microscopy Environment (OME), the Next Generation File Format OME-NGFF, the Image Data Resource (IDR), the Omero platform and Omero plugins.

Tags: OMERO

Content type: Collection, Video

https://www.youtube.com/OpenMicroscopyEnvironment

RDM4mic#

Licensed UNKNOWN

Tags: Research Data Management, OMERO

Content type: Collection, Video

https://www.youtube.com/@RDM4mic

RDMBites BioImage metadata#

Content type: Collection, Video

https://www.youtube.com/watch?v=aRHNHk07t3Q&list=PLyCNTVs-UBvuJF7WausQ5q7v7pI1vEpI1

Structuring of Data and Metadata in Bioimaging: Concepts and technical Solutions in the Context of Linked Data#

Susanne Kunis

Published 2022-08-24

Licensed CC-BY-4.0

guided walkthrough of poster at https://doi.org/10.5281/zenodo.6821815

which provides an overview of contexts, frameworks, and models from the world of bioimage data as well as metadata and the techniques for structuring this data as Linked Data.

You can also watch the video in the browser on the I3D:bio website.

Tags: Nfdi4Bioimage, Research Data Management

Content type: Video

https://zenodo.org/record/7018929

https://doi.org/10.5281/zenodo.7018929

Submitting data to the BioImage Archive#

Licensed CC0-1.0

To submit, you’ll need to register an account, organise and upload your data, prepare a file list, and then submit using our web submission form. These steps are explained here.

Tags: Research Data Management, Image Data Management, Bioimage Data

Content type: Tutorial, Video

https://www.ebi.ac.uk/bioimage-archive/submit/

arivis Vision4D Tutorials#

Tags: Bioimage Analysis

Content type: Collection, Video

https://www.youtube.com/playlist?list=PLRc9dt9lEZh_SVRC4G5moOvgHuvjPwmv0

Video (24)

Contents

Video (24)#

Bio Image Analysis Lecture 2020#

COBA: Center for Open Bioimage Analysis YouTube Channel#

Chris Halvin YouTube channel#

DigitalSreeni YouTube Channel#

Erick Martins Ratamero - Expanding the OME ecosystem for imaging data management | SciPy 2024#

Euro-BioImaging Communication YouTube Channel#

FAIR BioImage Data#

Fiji Is Just ImageJ Tutorials#

Global BioImaging YouTube channel#

How to get started with Jupyter and Colab#

I3D:bio’s OMERO training material: Re-usable, adjustable, multi-purpose slides for local user training#

Ibiology. Bioimage Analysis Course. The Life Cycle of an Image Data Set#

Imaris Tutorials#

Melbourne Advanced Microscopy Facility#

Methods in bioimage analysis#

Microscopy data analysis: machine learning and the BioImage Archive#

NEUBIAS YouTube Channel#

Open Micoscropy Environment (OME) Youtube Channel#

Open Microscopy Environment YouTube channel#

RDM4mic#

RDMBites BioImage metadata#

Structuring of Data and Metadata in Bioimaging: Concepts and technical Solutions in the Context of Linked Data#

Submitting data to the BioImage Archive#

arivis Vision4D Tutorials#