Insights into the zebrafish left-right organizer's centrosomes and cilia via volume electron microscopy

This dataset contains the source volumetric electron microscopy (vEM) image data and derived 3D segmentations used to generate Figure 4D in Ononiwu et al. (2026). Figure 4D depicts a KV mother–daughter centriole pair with ultrastructurally resolved distal appendages (DAs), subdistal appendages (SDAs), and a rootlet, shown as representative 2D serial slices and as a 3D segmented reconstruction. The image data are derived from serial ultrathin sections imaged by SEM and exported as an aligned, contrast/brightness–adjusted image stack with voxel sampling reported for the aligned dataset as 10 nm.
, Three-dimensional segmentation of KV structures was performed manually using Dragonfly software. Image stacks, acquired from vEM, were imported into Dragonfly to create a volumetric dataset. Each structure of interest was then manually traced across serial sections using the software’s segmentation tools. After each structure’s three-dimensional model was generated, a contour mesh was applied with a single sampling (for x, y, and z coordinates) and a threshold of 50. Each structure was smoothed using two to four iterations, with the number of iterations adjusted until pixelated edge artifacts were eliminated, as confirmed by visual inspection. The final reconstructed volume was generated by aligning individual segmented axis providing a detailed three-dimensional representation of the sample.
, # Data from: Insights into the zebrafish left-right organizer's centrosomes and cilia via volume electron microscopy

Dataset DOI: [10.5061/dryad.8kprr4z2z](https://doi.org/10.5061/dryad.8kprr4z2z)

## Description of the data and file structure

Volumetric Electron Microscopy data, in .tiff format, of a centrosome (including both mother and daughter centriole, appendages, subdistal appendages, centrosome-associated dense region, and rootlet) and its corresponding KV cilia.

README — Protocol: Manual 3D segmentation of KV structures in Dragonfly (from vEM stacks)\
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Purpose: This protocol describes how three-dimensional (3D) segmentations and surface meshes of Kupffer’s vesicle (KV) structures were generated from volumetric electron microscopy (vEM) image stacks using Dragonfly software.\
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Software: Dragonfly (Object Research Systems)\
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Input data: vEM image stacks (serial sections) representing the region of interest.\
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Protocol\
1\) Import vEM image stacks\
\- Import vEM-acquired im..., , , **Changes after Mar 6, 2026:** Added the second Concatenated_Stack1_Stack2.tif