Bioimage data (20)#
Bio-Image Data Strudel for Workshop on Research Data Management in TU Dresden Core Facilities#
Cornelia Wetzker
Published 2023-11-08
Licensed CC-BY-4.0
This presentation gives a short outline of the complexity of data and metadata in the bioimaging universe. It introduces NFDI4BIOIMAGE as a newly formed consortium as part of the German ‘Nationale Forschungsdateninfrastruktur’ (NFDI) and its goals and tools for data management including its current members on TU Dresden campus.
Tags: Research Data Management, Tu Dresden, Bioimage Data, Nfdi4Bioimage
Content type: Slide
BioFormats Command line (CLI) tools#
Published 2024-10-24
Licensed CC-BY-4.0
Bio-Formats is a standalone Java library for reading and writing life sciences image file formats. There are several scripts for using Bio-Formats on the command line, which are listed here.
Tags: Bioimage Data
Content type: Documentation
https://bio-formats.readthedocs.io/en/v8.0.0/users/comlinetools/index.html
Checklists for publishing images and image analysis#
Christopher Schmied
Published 2023-09-14
Licensed CC0-1.0
In this paper we introduce two sets of checklists. One is concerned with the publication of images. The other one gives instructions for the publication of image analysis.
Tags: Bioimage Data, Microscopy Image Analysis
Content type: Forum Post
https://forum.image.sc/t/checklists-for-publishing-images-and-image-analysis/86304
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
I3D bio – Information Infrastructure for BioImage Data - Bioimage Metadata#
Christian Schmidt
Licensed UNKNOWN
A Microscopy Research Data Management Resource.
Tags: Metadata, I3Dbio, Research Data Management, Bioimage Data
Content type: Collection
https://gerbi-gmb.de/i3dbio/i3dbio-rdm/i3dbio-bioimage-metadata/
KNIME Image Processing#
None
Licensed GPLV3
The KNIME Image Processing Extension allows you to read in more than 140 different kinds of images and to apply well known methods on images, like preprocessing. segmentation, feature extraction, tracking and classification in KNIME.
Tags: Imagej, OMERO, Bioimage Data, Workflow
Content type: Tutorial, Online Tutorial, Documentation
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
NGFF Converter#
Licensed GPL-2.0
An easy to use and open source converter for bioimaging data. NGFF-Converter is a GUI application for conversion of bioimage formats into OME-NGFF (Next-Generation File Format) or OME-TIFF.
Tags: Bioimage Data, Open Source Software
Content type: Application
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
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
Reporting and reproducibility in microscopy#
Published 2021-12-03
Licensed UNKNOWN
This Focus issue features a series of papers offering guidelines and tools for improving the tracking and reporting of microscopy metadata with an emphasis on reproducibility and data re-use.
Tags: Reproducibility, Metadata, 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
bioformats2raw Converter#
Melissa Linkert, Chris Allan, Josh Moore, Sébastien Besson, David Gault, et al.
Licensed GPL-2.0
Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification.
Tags: Open Source Software, Bioimage Data
Content type: Application, Github Repository
ome-ngff-validator#
Will Moore, Josh Moore, Yaroslav Halchenko, Sébastien Besson
Published 2022-09-29
Licensed BSD-2-CLAUSE
Web page for validating OME-NGFF files.
Tags: Bioimage Data
Content type: Github Repository, Application
raw2ometiff Converter#
Melissa Linkert, Chris Allan, Sébastien Besson, Josh Moore
Licensed GPL-2.0
Java application to convert a directory of tiles to an OME-TIFF pyramid. This is the second half of iSyntax/.mrxs => OME-TIFF conversion.
Tags: Open Source Software, Bioimage Data
Content type: Application, Github Repository