Benjamin Pavie

From Abandoned Scripts to FAIR Community Pipelines: Rescuing Orphan Bioinformatics Workflows with nf-core - Lessons from Light-Sheet Fluorescence Microscopy

The paper re-engineers an abandoned MATLAB-based image analysis toolkit into a sustainable, FAIR-compliant Nextflow workflow for light-sheet microscopy.

A high-performance end-to-end 3D CLEM processing workflow for facilities

This paper presents an end-to-end 3D CLEM processing pipeline that integrates existing and new tools to streamline analysis, improve reproducibility, and support facility-scale use.

Human motor units in microfluidic devices are impaired by FUS mutations and improved by HDAC6 inhibition

This study uses a microfluidic model of human motor units to show that FUS mutations impair neurite outgrowth and NMJ formation, which can be mitigated by HDAC6 inhibition.

Spatial and temporal transcriptomics reveal microglia-astroglia crosstalk in the amyloid-β plaque cell niche of Alzheimer’s disease

The paper uses spatial transcriptomics and in situ sequencing to study gene networks in the amyloid-β plaque niche of AD, revealing microglia-astroglia interactions and myelination abnormalities.

BIAFLOWS: A collaborative framework to reproducibly deploy and benchmark bioimage analysis workflows

BIAFLOWS provides a framework to document, deploy, and benchmark bioimage analysis workflows, enabling reproducible and fair comparisons of image analysis methods.