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 divides his time between the Francis Crick Institute in London, where he develops image analysis and registration software for large-scale microscopy research, and NL-BioImaging in the Netherlands, where he works on FAIR bioimaging data infrastructure, OME-Zarr conversion and metadata standards across the national network. He has extensive experience developing automated and reproducible solutions across biomedical research, healthcare and AI, with a particular interest in open standards, open science and translating complex scientific challenges into practical computational solutions.

Bioimaging data & FAIR

NL-BioImaging

fair-metadata-integration

Integrate and package all metadata into a Workflow RO-Crate

Python★ 0

NL-BioImaging

imaging-metadata-converter

Convert acquisition metadata to custom model

Python★ 0Docs

NL-BioImaging

napari-meta-tiff

napari tiff reader with extended metadata

Python★ 0

NL-BioImaging

biomero

BIOMERO.analyzer - A python library for easy connecting between OMERO (jobs) and a Slurm cluster

Python★ 29Docs

NL-BioImaging

NL-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.

Python★ 13Docs

folterj

zarr-memory-loader

Zarr in-memory compressed data loader

Python★ 0

NL-BioImaging

biomero-converter

Convert db image format to Ome-Tiff and Ome-Zarr

Python★ 1Docs

FrancisCrickInstitute

OmeSliCC

Ome(ro) SLide Image Conversion and Compression pipline (OmeSliCC)

Python★ 7

Microscopy & image analysis

NL-BioImaging

fair-segmentation

FAIR organelle segmentation pipeline

Python★ 0Docs

FrancisCrickInstitute

napari-isbem

Multimodal SBEM acquistion targeting

Python★ 0Docs

ccp-volume-em

muvis-align

Image registration using multiview-stitcher

Python★ 9Docs

SBEMimage

SBEMimage

Versatile acquisition software for serial block-face electron microscopy

Python★ 27Docs

folterj

BioImageOperation

Image processing tool focusing on biological applications

C++★ 14

Contributions to open standards

fideus-labs

ngff-zarr

A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.

Python★ 75Docs

ome

ngff

Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

Python★ 181Docs

Earlier work

FrancisCrickInstitute

Etch-a-Cell-Nuclear-Envelope

Deep learning segmentation of the nuclear envelope in electron microscopy, trained on citizen science annotations

Python★ 10

folterj

IEEE11073Analyser

Analyses and validates binary IEEE 11073 messages in explorable formats

C++★ 0

folterj

ProMISE2

Probabilistic Model for Immiscible Separations and Extractions 2

C#★ 0

Organisations

The Francis Crick InstituteSBEMimageCellular Imaging, Amsterdam UMCNL-BioImaging AMBioImageToolsCCP-volumeEM