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

https://zenodo.org/records/10083555

https://doi.org/10.5281/zenodo.10083555


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

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


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

https://www.knime.com/community/image-processing


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


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

https://www.glencoesoftware.com/products/ngff-converter/


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



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/


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

https://www.nature.com/collections/djiciihhjh


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/


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

glencoesoftware/bioformats2raw


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

https://ome.github.io/ome-ngff-validator/

ome/ome-ngff-validator


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

glencoesoftware/raw2ometiff