Light-sheet Imaging Atlas

Recent technological advancements in light-sheet microscopy have opened up exciting new opportunities for in toto imaging of whole developmental arcs at the cellular level. With the help of advanced fluorescent proteins, light-sheet microscopy enables the reconstruction of the entirety of embryonic development at a cellular level, allowing for image-based lineage reconstruction. We provide here a total of seven light-sheet microscopy time-lapse datasets together with cell tracking data acquired on two different instruments.

The two datasets listed below were acquired on our OpenSiMView light-sheet microscope. You can explore the full timelapse image data here:

The five datasets listed below were acquired on our DaXi light-sheet microscope. We also provide a smaller cropped dataset for timelapse 2 centered on the tail. You can explore the full timelapse image data online here:

You can find all corresponding imaging and tracking data for time-lapses here. For more information on the cell tracks format and how it was obtained, check the repository of Ultrack, the cell tracking tool used. Using our napari plugin for in silico, you can mark cells of interest and follow them over time. See video of demo below:

The main citation for our imaging datasets is:
Zebrahub - Multimodal Zebrafish Developmental Atlas Reveals the State Transition Dynamics of Late Vertebrate Pluripotent Axial Progenitors.

In terms of methods, the following are the papers for the light-sheet imaging and cell tracking:

DaXi - high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy

Ultrack: pushing the limits of cell tracking across biological scales

You can find the list of all Zebrahub-related papers here.