Image data management (14)#

BIOMERO - A scalable and extensible image analysis framework#

Torec T. Luik, Rodrigo Rosas-Bertolini, Eric A.J. Reits, Ron A. Hoebe, Przemek M. Krawczyk

Published None

Licensed CC-BY-4.0

The authors introduce BIOMERO (bioimage analysis in OMERO), a bridge connecting OMERO, a renowned bioimaging data management platform, FAIR workflows, and high-performance computing (HPC) environments.

Tags: OMERO, Workflow, Bioimage Analysis, Image Data Management

Content type: Publication

https://doi.org/10.1016/j.patter.2024.101024


Bio-image Data Science#

Robert Haase

Licensed CC-BY-4.0

This repository contains training resources for Students at Uni Leipzig who want to dive into bio-image data science with Python.

Tags: Image Data Management, Deep Learning, Microscopy Image Analysis, Python

Content type: Notebook

ScaDS/BIDS-lecture-2024


Data management at France BioImaging#

Published 2023-07-05

Licensed CC-BY-SA-4.0

Tags: Research Data Management, Bioimage Analysis, Image Data Management, Open Science

Content type: Slides, Presentation

https://omero-fbi.fr/slides/elmi23_cfd/main.html#/title-slide


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

SciPy, Erick Martins Ratamero

Published 2024-08-19

Licensed YOUTTUBE STANDARD LICENSE

Tags: Image Data Management, OMERO, Bioimage Analysis

Content type: Video, Presentation

https://www.youtube.com/watch?v=GmhyDNm1RsM


FAIR High Content Screening in Bioimaging#

Rohola Hosseini, Matthijs Vlasveld, Joost Willemse, Bob van de Water, Sylvia E. Le Dévédec, Katherine J. Wolstencroft

Published 2023-07-17

Licensed CC-BY-4.0

The authors show the utility of Minimum Information for High Content Screening Microscopy Experiments (MIHCSME) for High Content Screening (HCS) data using multiple examples from the Leiden FAIR Cell Observatory, a Euro-Bioimaging flagship node for high content screening and the pilot node for implementing FAIR bioimaging data throughout the Netherlands Bioimaging network.

Tags: FAIR-Principles, Metadata, Research Data Management, Image Data Management, Bioimage Data

Content type: Publication

https://www.nature.com/articles/s41597-023-02367-w


Microscopy-BIDS - An Extension to the Brain Imaging Data Structure for Microscopy Data#

Marie-Hélène Bourget, Lee Kamentsky, Satrajit S. Ghosh, Giacomo Mazzamuto, Alberto Lazari, et al.

Published 2022-04-19

Licensed CC-BY-4.0

The Brain Imaging Data Structure (BIDS) is a specification for organizing, sharing, and archiving neuroimaging data and metadata in a reusable way.

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

Content type: Publication

https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2022.871228/full


NFDI4BIOIMAGE - An Initiative for a National Research Data Infrastructure for Microscopy Data#

Christian Schmidt, Elisa Ferrando-May

Published 2021-04-29

Licensed CCY-BY-SA-4.0

Align existing and establish novel services & solutions for data management tasks throughout the bioimage data lifecycle.

Tags: Nfdi4Bioimage, Image Data Management, Bioimage Data, Research Data Management

Content type: Conference Abstract, Slide

https://doi.org/10.11588/heidok.00029489


RDM_system_connector#

SaibotMagd

Licensed UNKNOWN

This tool is intended to link different research data management platforms with each other.

Tags: Research Data Management, Image Data Management

Content type: Github Repository

SaibotMagd/RDM_system_connector



REMBI Overview#

Licensed CC0-1.0

Recommended Metadata for Biological Images (REMBI) provides guidelines for metadata for biological images to enable the FAIR sharing of scientific data.

Tags: FAIR-Principles, Metadata, Image Data Management, Research Data Management, Bioimage Data

Content type: Collection

https://www.ebi.ac.uk/bioimage-archive/rembi-help-overview/


Research data management for bioimaging - the 2021 NFDI4BIOIMAGE community survey#

Christian Schmidt, Janina Hanne, Josh Moore, Christian Meesters, Elisa Ferrando-May, et al.

Published 2022-09-20

Licensed CC-BY-4.0

As an initiative within Germany’s National Research Data Infrastructure, the authors conducted this community survey in summer 2021 to assess the state of the art of bioimaging RDM and the community needs.

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

Content type: Publication

https://f1000research.com/articles/11-638/v2


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/


The BioImage Archive – Building a Home for Life-Sciences Microscopy Data#

Matthew Hartley, Gerard J. Kleywegt, Ardan Patwardhan, Ugis Sarkans, Jason R. Swedlow, Alvis Brazma

Published 2022-06-22

Licensed UNKNOWN

The BioImage Archive is a new archival data resource at the European Bioinformatics Institute (EMBL-EBI).

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

Content type: Publication

https://www.sciencedirect.com/science/article/pii/S0022283622000791?via%3Dihub

https://doi.org/10.1016/j.jmb.2022.167505


Towards community-driven metadata standards for light microscopy - tiered specifications extending the OME model#

Mathias Hammer, Maximiliaan Huisman, Alessandro Rigano, Ulrike Boehm, James J. Chambers, et al.

Published 2022-07-10

Licensed UNKNOWN

Rigorous record-keeping and quality control are required to ensure the quality, reproducibility and value of imaging data. The 4DN Initiative and BINA here propose light Microscopy Metadata specifications that extend the OME data model, scale with experimental intent and complexity, and make it possible for scientists to create comprehensive records of imaging experiments.

Tags: Reproducibility, Microscopy Image Analysis, Metadata, Image Data Management, Bioimage Data

Content type: Publication

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9271325/