Nicolas Chiaruttini
BioImage Analyst @ University of Geneva

Department of Biochemistry, University of Geneva

Nicolas is a BioImage Analyst and Scientific Developer with an interdisciplinary background at the intersection of physics, biology, and computer science. He obtained his PhD in biophysics in 2011, followed by postdoctoral research in biochemistry. He then joined the BioImaging and Optics Platform (BIOP) at EPFL in 2018, where he worked for several years before joining the Department of Biochemistry at the University of Geneva in 2026.

His work is dedicated to developing open-source image analysis tools and workflows for the scientific community.

Background: Biophysics (PhD), Postdoctoral research in Biochemistry

Current interests:

  • Supporting researchers in the Biochemistry Department with image analysis needs
  • Developing automated image analysis pipelines for optical microscopy data
  • Contributing to open-source tools for the bio-imaging community
  • Teaching image analysis to life scientists

Notable projects:

  • ABBA - Aligning Big Brains and Atlases: a Fiji + QuPath workflow for brain slice registration to the Allen Brain Atlas

Areas of expertise:

  • BioImage Acquisition: Optical microscopy (widefield, confocal, super-resolution)
  • BioImage Analysis: Segmentation, tracking, registration, quantification, pipeline automation
  • Scientific Software Development: Fiji plugins, QuPath extensions, Python workflows

Favorite BIA tools: Fiji, QuPath, ilastik, napari

Languages:

  • Human: French, English
  • Program: ImageJMacro, Java, Groovy, Python, C++, Matlab

Online presence: