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Serial section images of Oikopleura dioica juvenile using SBF-SEM

Citation

Nishida, Hiroki (2021), Serial section images of Oikopleura dioica juvenile using SBF-SEM, Dryad, Dataset, https://doi.org/10.5061/dryad.d51c5b012

Abstract

The larvacean, Oikopleura dioica is a planktonic chordate, which is an emerging model organism with short life cycle of 5 days and belongs to tunicates (urochordates). Organ formation in the trunk proceeds in seven hours form hatching of tailbud larvae at three hours after fertilization (hpf) to completion of organ formation in fully functional juveniles that start feeding at 10 hpf and are just miniature of adult form. The dataset is serial section images of Oikopleura dioica juvenile that were obtained using SBF-SEM (Serial block face scanning electron microscopy). The 1961 TIFF images were compressed to a zip file.

The juveniles were fixed at 10.5 hours post fertilization, 30 min after the tail shift (Nishida, H., 2008 Development of the appendicularian Oikopleura dioica: culture, genome, and cell lineages. Dev. Growth Differ. 50, S239–S256.). The dataset would be used as a basic morphological data of this animal to explore organ structures and cellular composition at electron microscopic level.

This data is related to the paper, 3D reconstruction of structures of hatched larva and young juvenile of the larvacean Oikopleura dioica using SBF-SEM. (Scientific Reports, 2021, 11, 4833) (https://www.nature.com/articles/s41598-021-83706-y)

Methods

SBF-SEM observation was performed using a Merlin scanning electron microscope (Carl Zeiss Microscopy, Jena, Germany) equipped with a 3View in-chamber ultramicrotome system (Gatan, Pleasanton, CA). The serial slice thickness was 70 nm. Images were recorded with an accelerating voltage of 1.3 kV and a dwell time of 1.0 µs. The image size was 12,000 x 12,000 pixels, with a resolution of 8 nm, which covers an area of 96 µm x 96 µm. After 2 x 2 binning of the images to reduce noise, the image stack was automatically aligned using ‘Register Virtual Stack Slices’ in the Fiji/ImageJ software. For a 10.5 hr juvenile, 1967 images were acquired.

Usage Notes

To look at the image sequence, one can open the folder in ImageJ/Fiji software at Virtual stack mode. Each TIFF file in the folder is also ablke to be opened with conventional picture viewers.

Funding

The JSPS and MEXT Grants-in-Aid for Scientific Research (KAKENHI), Award: 26650079, 15H04377, 16K14735, 17KT0023, 19H03234

The MEXT Grants-in-Aid for Scientific Research (KAKENHI), Award: JP16H06280

Advanced Bioimaging Support (ABiS)

The JSPS and MEXT Grants-in-Aid for Scientific Research (KAKENHI), Award: 26650079, 15H04377, 16K14735, 17KT0023, 19H03234

The MEXT Grants-in-Aid for Scientific Research (KAKENHI), Award: JP16H06280

Advanced Bioimaging Support (ABiS)