arXiv subjects

Stefan Krauss

Publications and source records attributed to Stefan Krauss.

3 recordsLinked to original sources

arXiv2026

From OpenSPIM to FlowSPIM: Enhancing the versatility of a light sheet microscope through an iterative design process

Light sheet microscopy is ideal for the 3D imaging of large biological specimens, yet systematic documentation on adapting microscope designs to diverse experimental requirements remains limited. We present the iterative process used to design and build a modular light-sheet microscope and adapt it to different sample types and experimental conditions. Starting from a stripped-down OpenSPIM platform, we gradually make our microscope more versatile by implementing new hardware, such as additional laser channels and optical filters, and new protocols for sample handling. In its final iteration, FlowSPIM is a new flow-based incubation technique for 3D tissue culture.

physics.optics↗

arXiv2025

Spontaneous elongation of 3D gastruloids from local cell polarity alignment

Gastruloids are 3D stem cell aggregate models for early embryogenesis that provide a unique platform to study how collective cell dynamics drive tissue symmetry breaking and axial elongation. Using 3D light sheet imaging, we show that a pulse of Chiron, a Wnt activator, induces coherent alignment of cell polarity during elongation. While nuclear elongation occurs with or without treatment, only Chiron-treated gastruloids exhibit quasi-long-range alignment of nuclear axes, linking cell polarity coherence to tissue-scale remodeling. A minimal physical model of polarized cells, incorporating alignment-dependent torques and polarity-mediated adhesion, reproduces symmetry breaking and elongation, demonstrating that local cell polarity alignment alone can drive tissue-scale convergence-extension flows.

physics.bio-ph↗

arXiv2021

A decentralized FAIR platform to facilitate data sharing in the life sciences

The Hybrid Technology Hub and many other research centers work in cross-functional teams whose workflow is not necessarily linear and where in many cases technology advances are done through parallel work. The lack of proper tools and platforms for a collaborative environment can create time lags in coordination and limited sharing of research findings. To solve this, we have developed a simple, user-friendly platform built for academic and scientific research collaboration. To ensure FAIRness compliance, the platform consists of a metadata quality control based on blockchain technologies. The data is stored separately in a distributed object storage that functions as a cloud. The platform also implements a version control system; it provides a history track of the project along with the possibility of reviewing the project's development. This platform aims to be a standardized tool within the Hybrid Technology Hub to ease collaboration, speed research workflow and improve research quality.

cs.DC↗