Streamlining Operation and Data Processing for the Zeiss Lattice Light Sheet 7 Microscope

Session

Poster Session

Authors

Nicolas Chiaruttini (1), José Artacho (1), Thierry Laroche (1), Arne Seitz (1)

Affiliations

1. School of Life Sciences, EPFL, BioImaging and Optics Platform

Keywords

Microscopy, Lattice Light Sheet 7, BigDataViewer, Image Processing

Abstract text

The Zeiss Lattice Light Sheet 7 brings new 3D live-imaging capabilities in a user-friendly and standard platform. Despite the machine's user-friendly inverted geometry and responsive software, we encountered certain challenges. We share our experience on managing this machine in a core facility and detail the in-house advancements made to streamline its usage, focusing on hardware and software aspects.

We present our strategies for achieving reliable stability during extended (> 24 hours) acquisitions and the hardware adaptations to the system to allow operation at temperatures below its original design specifications (18°C). Additionally, we provide a comparative analysis of Point Spread Functions (PSFs) obtained based on different light-sheet shapes and aberration controls, offering valuable insights for users when designing their acquisition strategy.

Dealing with substantial data volumes (>1TB) is a common challenge for such machines. While the Zeiss software efficiently processes entire datasets, not all data may be relevant. Leveraging the BigDataViewer ecosystem in ImageJ/Fiji, we have developed a suite of tools that enables efficient visualization, cropping, and processing of the multi-terabyte datasets generated. This approach ensures that only pertinent data is processed, accelerating the extraction of valuable biological insights.

Together, these advancements optimize the Zeiss LLS7 machine, improving accessibility and usability for enhanced 3D live imaging.