Setting Up Smart Microscopy in a Facility Environment.

Session

Poster Session

Authors

Sara R. Roig (1), Alexia Ferrand (1), Kai Schleicher (1), Sébastien Herbert (1), Oliver Biehlmaier (1)

Affiliations

1. Biozentrum, University of Basel

Keywords

Smart microscopy, event-driven acquisition, microscopy facility

Abstract text

The need for complex multi-dimensional imaging experiments is increasing, and microscopy facilities are facing new challenges to provide users with innovative and robust solutions. At the Imaging Core Facility (IMCF), within the NCCR AntiResist* context, we were involved in implementing a versatile smart microscopy pipeline.  

The research group aimed to study small bacteria within an entire tissue section (up to cm). Tiled, high-resolution 3D imaging of the entire tissue sections had to be acquired, followed by extensive image analysis, re-acquisition, and complex image processing, which made it difficult to perform such studies in a timely manner and with reasonable data size. In addition, the tissue complexity, variety, number of bacteria, and their ability to form clusters added to the challenge of this project.

To provide the best possible solution to our users, we explored three different options: two proprietary (Evident and Nikon) and one open source (Event-Driven Acquisition, EDA). While still under investigation, the EDA open source tool, developed in the lab of Suliana Manley, seems to be the most flexible and with the highest potential to satisfy all requirements simultaneously. 

Here, we present the three smart imaging methods, how they compare, our progress in establishing EDA in a core facility environment, and the measures we are undertaking to make this innovative method stable and reproducible for multi-user cases. 

*National Centre of Competence in Research AntiResist https://www.nccr-antiresist.ch/