NFDI4BIOIMAGE from A to Z. Z as in Zenodo. Zenodo is a general-purpose data repository built on open source software that accepts all forms of research output from data files to presentation files. It was developed by the European Organization for Nuclear Research (CERN), but is open to researchers from outside the EU. Data is stored in the CERN Data Center, which provides long-term preservation. Source: https://datamanagement.hms.harvard.edu/share-publish/data-repositories/zenodo

#NFDI4BIOIMAGEfromAtoZ - Z as in Zenodo
For us as a consortium committed to helping others make their data #FAIR, Zenodo is a useful platform where we make presentations, training materials, posters, and papers publicly available for everyone.
Find our materials here:
👉 zenodo.org/communities/...

#NFDI4BIOIMAGEfromAtoZ - Y as in YAML
If your research involves lots of files and metadata, YAML can help you structure everything clearly and transparently. This text-based format can be used to describe image metadata and analysis parameters in a human-readable and machine-processable way.

NFDI4BIOIMAGE from A to Z: X as in XML. Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. Source: https://en.wikipedia.org/wiki/XML

#NFDI4BIOIMAGEfromAtoZ - X as in XML.
Encouraging the use of standards like XML is important to @nfdi4bioimage.bsky.social, as it guarantees interoperability between softwares and labs.
More about the specific file format OME-XML for biological image data:
👉 docs.openmicroscopy.org/ome-model/5....

#NFDI4BIOIMAGEfromAtoZ - W as in Workflow

If your research involves working with large amounts of data, it is important to plan your data workflow beforehand. A planned #workflow makes your data easy to process and reproduce, from the first image to publication.

NFDI4BIOIMAGE from A to Z. U as in Usability. Usability, or user friendliness, describes how effectively a system supports users in completing intended tasks with a high level of safety, efficiency, and reliability, while promoting a smooth and intuitive workflow. Applied to research data, usability refers to how easily other people (or even your future self) can find, understand, access, and correctly use the data.

#NFDI4BIOIMAGEfromAtoZ - U as in Usability.
Usability is closely linked to the #FAIR data principles that we at @nfdi4bioimage.bsky.social strive for. To improve the usability of your data, you need to document it well, add metadata and store data in common, non-proprietary formats.

#NFDI4BIOIMAGEfromAtoZ - T as in TIFF
When working with microscopy data, you often need image formats that preserve every detail of your measurements. #TIFF (Tagged Image File Format) is a raster image format particularly suited for high-quality, multidimensional microscopy data.

#NFDI4BioImageFromAtoZ - S for semantic annotation

Would you like to create #FAIR bioimage data with your research? Then, you can’t ignore semantic annotation: Data only becomes reusable, interoperable, and thus FAIR, through standardized annotation using shared vocabularies and ontologies.

NFDI4BIOIMAGE from A to Z: R as in REMBI. Recommended Metadata for Biological Images (REMBI) provides guidelines for metadata for biological images to enable the FAIR sharing of scientific data. REMBI is the result of the bioimaging community coming together to develop a metadata checklist to describe the imaging data itself, together with supporting metadata such as those describing the biological study and sample. It will also help enable automated data harvesting leveraging machine accessibility. Source: https://www.ebi.ac.uk/bioimage-archive/rembi-help-overview/

#NFDI4BIOIMAGEfromAtoZ - R as in REMBI.
REMBI was developed by the light, electron, and X-ray microscopy communities to increase the likelihood that image data will be reused by their own reserachers, but also by other users of archived image material.
Read more:
👉 www.nature.com/articles/s41...

NFDI4BIOIMAGE from A to Z: Q as in QUAREP-LiMi. QUAREP-LiMi (Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy) is an international initiative with a multifaceted aim to enhance the quality, reliability, and reproducibility of light microscopy data across the life and material sciences. Source: https://quarep.org/about/

#NFDI4BIOIMAGEfromAtoZ - Q as in QUAREP-LiMi.
Quarep-LiMi is one of @NFDI4BIOIMAGE's partners with whom we exchange regularly and work together to develop internationally coordinated standards and processes for quality controll and assessment.
Have a look at the initiative:
👉 quarep.org

#NFDI4BIOIMAGEfromAtoZ - P as in Pixels.
In biological microscopy, #pixels are more than just image dots – they are quantitative measurements that encode spatial and intensity information at the core of high-dimensional bioimaging data.

NFDI4BIOIMAGE A-Z. M as in Metadata Standards. Community-driven metadata checklists make it easier for third-party users of original data to understand the dataset. Such standards depend on the research field and the technology used. Peer groups and communities of specialists determine what information is important and should always accompany publicly available data. (https://gerbi-gmb.de/i3dbio/i3dbio-resources/metadata-guide/)

#NFDI4BIOIMAGEfromAtoZ - M as in Metadata Standards.
Standards developed by the bioimaging community emphasize that metadata should contain information relevant to microscopists, computer vision researchers, and imaging scientists - e.g. the imaging method.
👉 gerbi-gmb.de/2024/12/05/m...

Graphic showing the NFDI4BIOIMAGE A-Z logo and five creative commons lincensing stickers. The text reads: L as in License. Legal instrument that defines the terms under which research data can be accessed, used, and shared. Published research data have limited potential for re-use if re-use is not clearly defined. It is, therefore, crucial to assign a license to a dataset. Community standards and good scientific practice should still be observed even if not enforced by licenses. (Link: https://rdm.mpdl.mpg.de/after-research/licenses/)

#NFDI4BIOIMAGEfromAtoZ - L as in License.
An important aspect of making your research data #FAIR is to make it #reusable.
We at @NFDI4BIOIMAGE encourage you to make your data publicly available under an appropriate license to increase its potential for reuse.

#NFDI4BIOIMAGEfromAtoZ - I for Interoperability

Interoperability is the most important prerequisite for standardizing biological image data. Therefore, @nfdi4bioimage.bsky.social creates standards, interoperable formats, and a common foundation for the description and exchange of bioimage data.

#NFDI4BIOIMAGEfromAtoZ - H as in Help Desk.
If you have questions about metadata annotations, suitable repositories, and other topics related to image analysis and software integration, then the Help Desk is your starting point.
You can contact the Help Desk here:
👉 nfdi4bioimage.de/help-desk/

#NFDI4BIOIMAGEfromAtoZ - G as in Galaxy.
The platform Galaxy is designed for data-intensive scientific analysis and provides access to virtual workstations for analysing, visualising and training bioimage data, in order to create and manage reproducible image analysis workflows.
👉 galaxyproject.org

#NFDI4BIOIMAGEfromAtoZ: F as in FAIR.
Creating data in accordance with the #FAIR principles can be achieved by documenting it, including the associated metadata in a suitable repository, using consistent identifiers and standardized vocabulary.
Read more:
👉 www.go-fair.org/fair-princip...

#NFDI4BIOIMAGEfromAtoZ: Experimental Metadata.
Much of the technical metadata in microscopy is captured automatically, but the story behind the image – how the experiment was designed, performed, and controlled – needs to be added by the researchers themselves.
Our Helpdesk is here to support you!

The third letter in our #NFDI4BIOIMAGEfromAtoZ calendar is C for Community Standards. Common standards for high-dimensional image data, like the FAIR-IO concept, are being developed by NFDI4BIOIMAGE together with the bioimaging community.

👉 Find out more nfdi4bioimage.de/about-us/goa...

The 2nd term of our #NFDI4BIOIMAGEfromAtoZ calendar is @bioimagearchive.bsky.social, an international data repository for biological image data provided by @ebi.embl.org. It accepts data linked to a publication and promotes measures to increase the reusability of data 👉 www.ebi.ac.uk/bioimage-arc...

Our campaign #NFDI4BIOIMAGEfromAtoZ starts with the word 'Annotation' - an important step to not only making your image data #FAIR, but also enriching it with information that goes beyond technical details. If you have questions on the topic, you can contact us:
👉 nfdi4bioimage.de/help-desk/