LSH FAIR fellow: Joost de Folter

Bio

I work at the Francis Crick Institute (UK) for 50%, and also at NL-BioImaging for 50%. At Crick I’m working on a community-lead project providing best practice guiding for microscopy software and FAIR metadata.

At BioImaging, I help develop workflows for image analysis for life scientists in the Bio Imaging community. This contributes to open and transparent science by making the image analysis workflows compliant with the FAIR (Findable, Accessible, Interoperable, and Reusable) principles and promoting Open Science in general.

Besides this, I have a wide variety of research interests including animal tracking, deep learning, automation and visualisation.

Use Case Title 

Describing image acquisition and data analysis workflows using FAIR principles. 

Use Case Description

Making existing processes FAIRer:

  • FAIR Mapping workflows in Biomero: Describing image analysis tasks input parameters and output results using metadata. 
  • Automated segmentation of EM data: Currently there is no readily available software available able to take raw EM microscopy images and provide desired output including various statistic values. The second challenge is storing output using FAIR principles.
  1. Set up at AMC
  2. Reproduce at UMCG
  • FAIR Mapping EM acquisition metadata to NGFF/RO-Crate: The current version of NGFF / RO-Crate does not define how to store EM acquisition metadata, though there are some initiatives that point in this direction.
  • FAIR Mapping segmentation results in a more modular way using NGFF: Storing segmentation output in NGFF including metadata which describes the process and related metrics.

Matched FAIR Fellowship Coach

Coach: Team BioImaging & ACDC. Visit the profile here!

What are the biggest challenges you anticipate facing in your use case over the next months? 

Finding readily available, compatible metadata and ontology standards within the limited time.

What specific skills or knowledge do you hope to gain through the fellowship programme?

Insight into practical application of FAIR principles.

What motivated you to apply for this TDCC LSH fellowship?

The funding opportunity to improve FAIRness into our BioImaging project.   

In one compelling sentence, why does your project matter? 

To establish a workflow that links metadata integration with automated analysis in a FAIR-compliant manner. 

Want to connect with Joost? Use LinkedIn or view the research profile on ORCID.