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
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
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
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
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
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
REMBI - Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology#
Ugis Sarkans, Wah Chiu, Lucy Collinson, Michele C. Darrow, Jan Ellenberg, David Grunwald, et al.
Published 2021-05-21
Licensed UNKNOWN
Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. The authors propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy.
Tags: Metadata, Bioimage Data, Image Data Management, Research Data Management
Content type: Publication
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8606015/
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
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
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
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
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/