Details on imaging

Imaging timeline

The first images included in the dataset were acquired on August 10th, 2021.
The last images included in the dataset were acquired on March 29th, 2022.
Imaging spanned 7.5 calendar months, but 96.5% of the images were acquired during the 4 months of November 2021 to February 2022. (The remainder of the time was spent upgrading or fixing the microscope, either its hardware or the control software.)

This is unlikely to be interesting to most readers but is provided for completeness.

Because the neck connective is much much thinner than the brain and the VNC, the neck connective was visible in only ~500 out of the 7010 tissue sections. In the remaining sections, the brain and VNC were separated by a large amount of empty space. To not waste time imaging the empty space between the brain and VNC, the two separate islands of brain and VNC tissue were imaged in separate imaging runs, and then stitched together later. In total, 12050 imaging runs were performed to generate the data that was included in the final dataset: ~5700 brain-only runs, ~5850 VNC-only runs, and ~500 brain + neck connective + VNC runs.
An additional ~500 to ~1000 imaging runs were performed that did not produce usable data, e.g. images were out of focus, images were too dark, or hardware or software errors occurred that interrupted the run. We did not keep an exact count of these unused imaging runs but we estimate that ~5-10% of imaging runs ended up being discarded.
Of the 12050 imaging runs, 6 of them captured 2 separate regions of tissue that were processed independently during alignment, and 1 of them captured 3 separate regions of tissue that were processed independently during alignment. Taking these into account, there were 12058 separate regions of tissue that were stitched independently. In rendering the final 7010 section dataset, any regions that were part of the same physical tissue section (e.g. a brain and VNC for the same section) were recombined.