(15)-Kraemer2026A – SLICE-2 – Tribolium castaneum AGOC{ATub'H2A/H2B°NB-mEmerald} #1 subline fused/deconvolved datasets with segmentation of blastodermal and serosa nuclei

The second Systematic Live Imaging Collection of Embryogenesis (SLICE-2) is a collection of sixteen isotropic 3D fluorescence live imaging datasets documenting gastrulation and early germband elongation in the red flour beetle Tribolium castaneum. Imaging was performed using light sheet fluorescence microscopy (LSFM) in combination with the transgenic AGOC{ATub’H2A/H2B°NB-mEmerald} #1 subline, which expresses mEmerald-labeled nanobodies against histone H2A/H2B under the control of the constitutively and ubiquitously active tubulin alpha 1-like protein promoter.

This entry contains the accompanying nuclei segmentation data for selected SLICE-2 datasets. The archive includes (i) copies of the axis-aligned, cropped, and intensity-adjusted 3D images from the fusion-deconvolution branch used for segmentation, including the time-merged 3D images and “helper” images where applicable; (ii) the corresponding segmentation SIS files together with their associated resources; and (iii) machine-readable XLSX files containing nuclei coordinates based on the intensity-weighted center of mass and sorted according to the center of the bounding box, first by y (primary), then x (secondary), and finally z (tertiary).

Blastodermal nuclei were segmented in fourteen datasets, excluding the two datasets in which imaging commenced after the embryos had progressed beyond the uniform blastoderm stage. Serosa nuclei were segmented in the seven datasets in which the germband underwent sufficient rotation around the anterior-posterior axis after serosa window closure. Segmentation was performed manually in Arivis Pro and systematically reviewed by a second researcher to ensure accuracy and reproducibility.

Detailed descriptions of the segmentation workflow, validation procedures, image-processing workflow, and file organization are provided in the associated Data Descriptor manuscript.

Please note that we strongly recommend using the current dataset version (v2) instead of the previous version (v1) that was originally published alongside the preprint of the associated study. Certain segmentations in v1 contained duplicated nuclei positions, which were identified and corrected during the revision process. If you previously downloaded the v1 dataset, we kindly ask you to replace it with the updated v2 release.