Published June 27, 2022 | Version v1
Dataset Open

3D+time nuclei tracking dataset of diSPIM lightsheet fluorescence microscopy time series of C. elegans embryos

Creators

  • 1. Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
  • 2. Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
  • 3. Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA and Marine Biological Laboratory, Woods Hole, MA, USA
  • 4. Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association

Description

The dataset consists of 3 diSPIM microscopy time series of C. elegans embryos, fully tracked.

  • 3 raw time-series and the corresponding tracks/lineage trees
  • temporal resolution: 1min
  • temporal extent: 350-400 frames, tracked for at least 330 frames
  • spatial resolution (zyx): 0.1625 x 0.1625 x 0.1625μm
  • spatial extent (zyx): 250 x 250 x 400px (average)
  • Microscope: dual-view ASI diSPIM (fused and deconvolved using the MIPAV GenerateFusion plugin)

The original raw data and annotations were part of the following publication (please also cite this if you use the dataset):

   Moyle, M.W., Barnes, K.M., Kuchroo, M. et al. Structural and developmental principles of neuropil assembly in C. elegans. Nature 591, 99–104 (2021). https://doi.org/10.1038/s41586-020-03169-5

Additionally the data was extended and slightly curated further by Peter Hirsch (MDC) and used for the development of a new tracking method in the following publication:

   Hirsch, P., Malin-Mayor, C., Santella, A., Preibisch, S., Kainmueller, D., Funke, J. Tracking by weakly-supervised learning and graph optimization for whole-embryo C. elegans lineages. MICCAI 2022

For questions please contact Peter Hirsch (peterhirsch@posteo.de).

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