Journal article Open Access

Tribolium castaneum embryo development as seen with lightsheet microscopy ("Lund" sample, first 36h)

Daniela Vorkel; Robert Haase; Eugene Myers

We here present an excerpt of a 3D+time lightsheet microscopy dataset. We acquired this developing Tribolium castaneum embryo (sample line provided by Akanksha Jain, Tomancak lab, MPI CBG Dresden, Germany) for about one week with variable temporal resolution. To simplify post-processing, we exported individual timepoints of this dataset with a frame delay of approximal 5 minutes. The actual acquisition time and image-index are given in the metadata.csv file. For example, the image with the filename "lund_i000002_oi_000007.tif" has index 2 and original index 7, according to metadata.csv, it was acquired 780s after start of acquisition. It is the 8th (index 7) image stack that was acquired from this sample. Furthermore, some datasets such as "lund_i000398_oi_002374.tif" and "lund_i000399_oi_002374.tif" are obviously the same dataset because the microscope was acquiring just one stack every 10 minutes. Additionally, we provide the original metadata files ("C0opticsprefused*" files) written by the microscope control / image acquisition software ClearControl [1]. The script for exporting the dataset ("export_dclij.py") is also provided. It uses the beetlesafari library [2, 3]. A quick overview as animated gif ("Lund.gif") is also provided. It shows a maximum intensity projection along Z over the whole one-week timelapse.

More details:

Duration: 36 h

Frame delay 5 min (except duplicated frames)

Voxel size: 0.6934 x 0.6934 x 3.0 microns^3 (x, y, z)

 

[1] https://github.com/clearcontrol

[2] https://github.com/haesleinhuepf/beetlesafari

[3] https://doi.org/10.5281/zenodo.5863867

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metadata.csv
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10.4 kB Download
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