Day 3 – Open Hardware

Bio: The focus of my lab is two-fold: to apply cellular and physical biology-based approaches to problems in organismic biophysics and develop novel tools for measurements in biological systems. We also apply ideasfrom theoretical soft-condensed matter physics to understand material properties of active living systems. Future developments in microscopy and in particular SEM are a natural extension of my work actively seeking to improve accessibility of microscopy at all levels to scientists in a multitude of settings. One of the current themes in my lab is to  develop new microscopy mechanisms involving novel approaches to how such devices are constructed. Broadly, we invent new tools for studying non-model organisms with significant focus on life in the ocean – addressing fundamental questions of cell biology in context of its ecology. My lab is dedicated towards inventing, building and scaling-up “frugal science” tools to democratize access to science such as Foldscope, diagnostics of deadly diseases like malaria and convening global citizen science communities to tackle planetary scale environmental challenges such as mosquito or plankton surveillance by citizen sailors mapping the ocean in the age of Anthropocene.

Bio: GEORG E. FANTNER received his MS degree from the University of Technology Graz in 2003, and his PhD degree from UC Santa Barbara in 2006 (advisor: Paul K. Hansma). During his masters and PhD, he developed a number of high performance AFM instruments and applied them to the study of the molecular origin of bone fracture toughness. After a Postdoc in the biomolecular materials lab at the Massachusetts Institute of Technology (Advisor: Angela M. Belcher), he joined the École Polytechnique Fédéral de Lausanne as assistant professor in 2010. Now, as associate professor, he leads the laboratory for bio- and nano-instrumentation in the institute for bioengineering. His research, which has been funded by the European Research Council with an ERC starting grant and an ERC consolidator grant, focusses on the development of new technologies to measure and manipulate nanoscale structures in general, and the development of atomic force microscopy instrumentation in particular. He applies these instruments to answer questions in a variety of fields ranging from materials science and nanotechnology to biology and life science. His interdisciplinary work has been published in many high impact journals such as Nature Materials, Nature Nanotechnology, Nature Cell biology, Nature Microbiology, Nature Communications, Nano Letters, and Science, as well as featured in a number of popular science- and general-interest magazines. He serves as scanning probe microscopy editor for Microscopy and Microanalysis (CambridgeCore), and as editorial board member for Scientific Reports. His recent work focusses on the development of time resolved scanning probe microscopy imaging, encompassing new modes for high-speed AFM imaging of molecular processes, as well as long-term time lapse imaging of cellular processes using AFM and scanning ion conductance microscopy. Prof. Fantner hold several patents in the field of nanotechnology and is the co-founder of two nanotechnology companies. Recently he has become active in the field of open hardware, where he explores new avenues to foster free academic exchange of knowledge, particularly for the development of highly sophisticated custom instruments. He serves as the president of the EPFL open science strategic committee and the ETH-domain open research data steering committee.

Topic: The mesoSPIM project: a high-end DIY light-sheet microscope for cleared tissues. Challenges and solutions.

Bio: Nikita Vladimirov’s expertise is light-sheet microscopy, programming, and computational neuroscience. He did his PhD in computational biology at Heidelberg University and a postdoc in computational neuroscience at IBM Research. Interest in neuroscience led him to zebrafish brain imaging at HHMI Janelia Research Center. He then joined the BIMSB/MDC institute in Berlin where he received a Marie-Curie fellowship for his innovative project in light-sheet microscopy with adaptive optics. Tinkering with a mesoSPIM setup at the BIMSB Systems Biology Imaging core grew into a long-term commitment to this open-science project. In summer 2021 he joined the Helmchen Lab and the Center for Microscopy and Image Analysis (ZMB) at UZH to lead future development of mesoSPIM project as a staff scientist, supported by a multi-year grant URPP Adaptive Brain Circuits in Development and Learning (AdaBD)

Abstract: Over the last decade, light-sheet fluorescence microscopy (also known as selective-plane illumination microscopy, SPIM) has become one of the primary tools for imaging live and fixed organisms due to its low photo-toxicity, excellent optical sectioning, and high speed. A SPIM microscope typically uses two objectives orthogonal to each other: one creates a light sheet for sample illumination, the other detects light emitted by the fluorescent sample. This configuration allows optical sectioning of large samples (up to several cm) without physically cutting them, which minimizes manual preparation whereas imaging data is generated at unprecedented speed.
Chemical clearing of fixed tissues further augments the ability of SPIM microscopes to image entire organs and reveal finest anatomical details in 3D without destroying the samples. To meet the growing demand for SPIM imaging of cleared tissues, a custom light-sheet microscope (dubbed „mesoSPIM“) was recently developed in the Helmchen Lab at the University of Zurich (Voigt et al., Nat. Methods, 2019).
This open-source microscope rapidly gained popularity in research labs and imaging facilities, with currently 16 setups in operation across the world ( The mesoSPIM microscopes have become indispensable for many research projects. We further develop new versions of the system and support the growing bioimaging community that uses mesoSPIMs. In this talk we discuss challenges of the project and our current solutions.

Topic: Open Hardware at CERN 

Topic:  Open Science academia vs. industry & How to maintain an open science project 

Bio: Dr. Maximilian Strauss holds a research doctorate in physics and performed research at the University of Munich, Harvard University, and the Max Planck Institute,  with a track record of over 30 peer-reviewed publications. After his PostDoc, he led a bioinformatics team as the Head of Bioinformatics at a Startup company and later returned to academia. Currently, Maximilian is a researcher at the University of Copenhagen working on using artificial intelligence for biomarker discovery and the next generation of computational methods for proteomics. He likes coding and is a strong advocate of open science.


Open Source is transforming the scientific landscape with cutting-edge research powered by open software packages. This talk gives a broad overview of the different aspects when writing open-source software. Topics include why you should make your code open, the software lifecycle, how to maintain code, publication strategies, differences in academia and industry, and monetization.  Lessons learned will be highlighted with practical examples from academia and industry.

Topic: Introduction to rapid prototyping