Microscopy (meta)data management

Julio Mateos Langerak, Guillaume Gay

MiFoBio 2023

Julio Mateos Langerak	julio.mateos-langerak@igh.cnrs.fr
Guillaume Gay	guillaume.gay@lirmm.fr

Why bother?

You have to anyway

Publications will ask for raw data anyway
Funding bodies require it
It’s the law

«La recherche publique a pour objectifs : (…) e) L’organisation de l’accès libre aux données scientifiques.»

Open & FAIR science is good for you

Data is easier to search, longer term usefulness
Better traceability: recognition of your work (including facility personnel).
Articles with open data are more cited.
Easier collaborations, notably with image analysts.
Indirectly: Data re-use helps image analysis

Open science is good science

Peer pressure implies attention to metadata and data quality 😋
FAIR data eases reproducibilty
Clearer link between data and protocols

Ethical considerations

Highly performent, extremly sophisticated instruments
Highly trained operators (you 😉)
➡️ We are at a golden age for microscopy

the data you create is extremely valuable, and deserves some effort towards its long-term preservation as heritage.

Definitions

Data and Metadata

In computer science, data (treated as singular, plural, or as a mass noun) is any sequence of one or more symbols; datum is a single symbol of data. Data requires interpretation to become information. wikipedia

Metadata […] is “data that provides information about other data” wikipedia

As scientific data is complex, good metadata is essential to contextualize and interpret data.

Open Science

Open science is the movement to make scientific research (including publications, data, physical samples, and software) and its dissemination accessible to all levels of society, amateur or professional. wikipedia

Data Life Cycle

See RDM kit

Data Management Plan

The DMP is used to think about a project’s data
An occasion to discuss with the facility people & anticipate
An evolving document.

maDMP (machine actionable DMPs)

A DMP that can interact with software
Trigger resource booking
Harvest metadata

DMP edition tools

The FAIR principles

Findable
Accessible
Interoperable
Reusable

See meaning and details here: FAIR principles

PID

PID means Persistent Identifier
Unique “address” pointing to some data.
✅ An article DOI
✅ Someone’s ORCID
❌ An email
❌ personnal web page

Linked Data

From semantic web approaches

Licences

The copyright stays yours
The licence protects the use of the data:
- For code: open source and free software
- For other data: creative commons

Overview of the FAIR data management landscape

Internationaly

Resources

In France

Ouvrir la science
Le Plan™️
Recherche Data Gouv
L’IFB est Centre de Reference thématique pour la bio-santé
Ateliers de la donnée
Bibliothèques Universitaires

For microscopy

REMBI

What is “good enough” metadata for Biological Images?

Recommended Metadata for BioImages:

See the REMBI publication
And an overview spread sheet

QUAREP-LiMi

Exhaustive instrumental metadata - NBO-Q

ISA Framework

The Investigation Study Assay Framework is a spectification to organize research data hierarchically