The dataset consists of 55 soft X-ray tomography (SXT) reconstructions of INS-1E pancreatic beta cells acquired under multiple stimulation conditions. Cells were imaged in glass capillaries and reconstructed into three-dimensional tomograms for quantitative analysis of mitochondrial organization and network remodeling. Experimental conditions represented in the dataset include unstimulated controls and stimulated cells exposed to glucose, Exendin-4 (Ex-4) and glucose plus Ex-4 at multiple time points. Corresponding segmentation masks were generated for cellular and organelle structures, including the cell boundary, nucleus, and mitochondria. The dataset contains: - SXT tomograms (MRC format)- Organelle segmentation masks (MRC format)- Cell-level metadata including condition, timepoint, and voxel length This dataset supports the analyses reported in: Singh, A., Yadav, A., Deshmukh, A., Singh, A., Varma, R., White, K., & Singla, J. (2026). Morphotype-Resolved 3D Morphometry Reveals a Structure–Density–Location Coupling in Mitochondrial Networks. bioRxiv, 2026-03. The dataset was also used in following studies: White, K. L., Singla, J., Loconte, V., Chen, J. H., Ekman, A., Sun, L., ... & Stevens, R. C. (2020). Visualizing subcellular rearrangements in intact β cells using soft x-ray tomography. Science advances, 6(50), eabc8262. Loconte, V., Singla, J., Li, A., Chen, J. H., Ekman, A., McDermott, G., ... & Larabell, C. A. (2022). Soft X-ray tomography to map and quantify organelle interactions at the mesoscale. Structure, 30(4), 510-521. Yadav, A., Singh, A., Deshmukh, A., Bharadwaj, P., Baliyan, A., White, K., & Singla, J. (2026). Robust mitochondria segmentation and morphological profiling using soft X-ray tomography. Journal of Structural Biology, 108291. Li, A., Zhang, S., Loconte, V., Liu, Y., Ekman, A., Thompson, G. J., ... & Sun, L. (2022). An intensity-based post-processing tool for 3D instance segmentation of organelles in soft X-ray tomograms. PloS one, 17(9), e0269887. Li, A., Zhang, X., Singla, J., White, K., Loconte, V., Hu, C., ... & Stevens, R. C. (2022). Auto-segmentation and time-dependent systematic analysis of mesoscale cellular structure in β-cells during insulin secretion. Plos one, 17(3), e0265567.