NL-BioImagingbiomero
BIOMERO.analyzer - A python library for easy connecting between OMERO (jobs) and a Slurm cluster
Dr Joost de Folter
Data scientist · Research Software Engineer
Dr Joost de Folter is a multidisciplinary data scientist and Research Software Engineer specialising in microscopy data science, machine learning, image analysis, modelling and visualisation. He has extensive experience developing automated and reproducible solutions across biomedical research, healthcare and AI. At the Francis Crick Institute and through international bioimaging collaborations, he works on data, ML and AI projects, large-scale microscopy analysis, deep learning and open science, with a particular interest in FAIR data, open standards and translating complex scientific challenges into practical computational solutions.
Bioimaging data & FAIR
NL-BioImaging
NL-BioImagingNL-BIOMERO
NL‑BIOMERO delivers a full containerized stack to run OMERO together with the BIOMERO 2.0 framework. It provides Docker/Podman configurations and Compose files to deploy OMERO + BIOMERO subsystems (importer, analyzer, OMERO.web plugin, databases, and auxiliary services) — the recommended starting point for a FAIR‑oriented bioimaging setup.
FrancisCrickInstituteOmeSliCC
Ome(ro) SLide Image Conversion and Compression pipline (OmeSliCC)
NL-BioImagingbiomero-converter
Convert db image format to Ome-Tiff and Ome-Zarr
NL-BioImagingimaging-metadata-converter
Convert acquisition metadata to custom model
NL-BioImagingfair-metadata-integration
Integrate and package all metadata into a Workflow RO-Crate
NL-BioImagingnapari-meta-tiff
napari tiff reader with extended metadata
folterjzarr-memory-loader
Zarr in-memory compressed data loader
Microscopy & image analysis
SBEMimageSBEMimage
Versatile acquisition software for serial block-face electron microscopy
FrancisCrickInstitutenapari-isbem
Multimodal SBEM acquistion targeting
ccp-volume-emmuvis-align
Image registration using multiview-stitcher
NL-BioImagingfair-segmentation
FAIR organelle segmentation pipeline
folterjBioImageOperation
Image processing tool focusing on biological applications
Contributions to open standards
ome
fideus-labsEarlier work
folterjProMISE2
Probabilistic Model for Immiscible Separations and Extractions 2
Publications
- 2026
- 2023
- 2023Nature Biomedical Engineering
- 2021
- 2021
- 2020
- 2018International Journal of Technology Assessment in Health Care
- 2017IEEE Transactions on Biomedical Engineering
- 2014BMC Medical Informatics and Decision Making
- 2013IEEE EMBS Special Topic Conference on Point-of-Care (POC) Healthcare Technologies: Synergy Towards Better Global Healthcare, PHT 2013
- 2012Journal of Visual Languages and Computing
- 2011Journal of Chromatography A
- 2011Journal of Chromatography A
- 2009Journal of Chromatography A
- 2003Journal of Liquid Chromatography and Related Technologies
