4D light sheet imaging, computational reconstruction, and cell tracking in mouse embryos -- example data (raw .czi and fused .klb light sheet images of mouse E7.5)

This dataset contains example .czi (Zeiss Z.1 Lightsheet format) image files and corresponding and multi-view fused .klb dataset, containing 3 hours of time lapse imaging of a mouse embryo at E7.5 / EHF, for processing and analysis. To be published with "4-dimension light sheet imaging and cell tracking in mouse embryos" in STAR Protocols. The dataset is intended for users to rehearse our comprehensive workflow for in toto capture, processing, and analysis of multi-view LSFM experiments using the ex vivo mouse embryo as a model system of development. Our protocol describes imaging on commercial LSFM instruments, and recites computational analysis in discrete and accessible chunks, using open source software.

Methods
Imaging was performed on a Lightsheet Z.1 (Zeiss) with incubation and dual pco.edge 4.2 cameras (PCO), with 20X/1.0 plan apochromat water-dipping detection objective (RI=1.34–1.35) and dual 10X/0.2 illumination objectives. The specimen tank was filled with culture medium and maintained at 37°C and 5% CO2. Mouse post-gastrulation embryos were subjected to 3 hours of LSFM imaging at 18-minute intervals, using our Zeiss Lightsheet Adaptive Position System (ZLAPS), linked in the key reagent table. The resulting .czi files were compressed with bzip2 and uploaded to Dryad. Following the protocol as published in "4-dimension light sheet imaging and cell tracking in mouse embryos" in ___ (2024), fused .klb dataset is included as well.