Niko Ehrenfeuchter
Bioimage Analyst @ University of Basel
IMCF: Imaging Core Facility lead by Oliver Biehlmaier
Niko has been working at the IMCF since 2012 after leaving the microscopy facility LIC at the University of Freiburg, Germany. He is responsible, along with Kai Schleicher, Laurent Guerard and Sébastien Herbert for the advice and follow up of any research projects involving light microscopy and image processing within the Biozentrum and occasionally other departments of the University of Basel.
On top of that, he is responsible for the group’s IT infrastructure including the microscope acquisition computers, analysis workstations, HRM and OMERO servers and the Virtualized Desktop Infrastructure VAMP. Additionally, he’s a big Linux enthusiast with more than two decades of experience on that and a strong advocate of versioning systems (he’s even having his phone’s address book in a git repo).
Background: Computer Science
Current interests:
- Surviving the strong decay in available (human) resources managing our not-so-small IT infrastructure.
- Pushing our Desktop Virtualization to the next generation.
- Providing a facility-suitable multi-user accessible heavy-GPU compute environment (read: not a cluster but something that an average non-computer-scientist can be instructed to use easily).
Areas of expertise:
- BioSample Preparation: If it can be scripted I might be of help here as well - otherwise you probably don’t want to let me near your lab bench…
- BioImage Acquisition: As soon as it’s Pixels, I’m all yours. As long as it’s still Photons, Filters, Mirrors and Lenses you don’t want me to touch it…
- BioImage Analysis: Stitching, Deconvolution, Time-lapse, WSI, 3D Analysis
Heavy user of: git, fish, bash, VS Code, Sublime Merge, Python, PowerShell, Grafana
Favorite BIA tools: Fiji, OMERO, Imaris, Huygens, (Jupyter) Notebooks, ZENODO
Languages:
- Human: German, English, French, (Spanish, Indonesian)
- Machine: Python, C#, Bash, ImageJMacro, PowerShell, Java, PHP
Online presence: