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This dataset accompanies the manuscript “Quantitative comparison of laboratory-based diffraction contrast tomography (DCT) and serial-section three-dimensional electron backscatter diffraction (3D-EBSD) for microstructural characterization of pure Fe and a modified E309L stainless steel” by Mehdi Mosayebi, Pardis Mohammadpour, Pierre-Antony Deschênes, Laurent Tôn-Thât, Daniel Paquet, Andre B Phillion, and Nabil Bassim, submitted to Materials Characterization (In Review). The dataset provides the experimental data and processing workflows used to quantitatively compare non-destructive laboratory-based DCT with destructive serial-section 3D-EBSD for three-dimensional microstructural characterization. The dataset includes the complete 3D-EBSD and LabDCT data for a fully recrystallized pure iron and a chill-cast, modified E309L austenitic stainless steel, together with the Dream.3D processing pipelines used for segmentation, meshing, and quantitative grain- and grain-boundary–level analyses. These data support the evaluation of grain morphology, size and shape statistics, crystallographic orientation distributions, and five-degree-of-freedom (5DOF) grain boundary character distributions presented in the associated manuscript. Users of this dataset are kindly requested to cite the associated manuscript and acknowledge the authors if the data or processing workflows are used in their own research. The files include processed three-dimensional label volumes derived from both 3D-EBSD and LabDCT, Dream.3D pipeline files documenting the full data-processing workflow, and derived grain boundary datasets used for statistical analysis. The Dream.3D pipelines capture all key steps, including data import, segmentation, cleanup, surface meshing, and grain boundary character extraction. The software versions used in generating this dataset are: Dream3D v6.x. The dataset structure is as follows: Processed 3D-EBSD and LabDCT label volumes in HDF5 format Dream3D pipeline files (.json) documenting the complete processing workflow This dataset is intended to serve as a reproducible benchmark for researchers interested in three-dimensional crystallographic characterization and in assessing the capabilities and limitations of laboratory-based DCT relative to serial-section 3D-EBSD.