DOI: 10.5061/dryad.hmgqnk9dw
title: Interactive 3D PDF file for the structures 10 hr juvenile of Oikopleura dioica and supplementary movie S1-20 with high resolution

description: 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
 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 data would be used as a basic morphological data of
 this animal to explore organ structures and cellular composition. This PDF
 file allows one to view 3D juvenile of O. dioica in any desired
 directions. One can show or hide the organs and rotate them by mouse. Open
 this PDF file and activate it as described in Adobe Acrobat User Guide
 (https://helpx.adobe.com/acrobat/using/displaying-3d-models-pdfs.html).
 Click Toggle “Model Tree button” with three small rectangulars in the tool
 bar. Then in the left panel, one can select the organs and nuclei you want
 to see. Select lighting as “daylight”. Select solid or transparency mode.
 The Juvenile 3D image was reconstructed with Amira software using 1967
 serial section images of SBF-SEM (Serial block face scanning electron
 microscopy) that are available at https://doi.org/10.5061/dryad.d51c5b012.
 The Zip file also contains supplementary movie S1-20 (avi file) with high
 resolution and the legends (PDF file). 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.
 (https://www.nature.com/articles/s41598-021-83706-y).
description: 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.
description: This PDF file allows one to view 3D juvenile of O. dioica in any
 desired directions. One can show or hide the organs and rotate them by
 mouse. Open this PDF file and activate it as described in Adobe Acrobat
 User Guide
 (https://helpx.adobe.com/acrobat/using/displaying-3d-models-pdfs.html).
 Click Toggle “Model Tree button” with three small rectangulars in the tool
 bar. Then in the left panel, one can select the organs and nuclei you want
 to see. Select lighting as “daylight”. Select solid or transparency
 mode. The Zip file also contains Supplementary movie
 S1-20 (avi file) with high resolution and the legends (PDF
 file).