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.

Methods
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.