Visible Monkey cerebrum dataset: sectioned images, segmented images, and 3D models

Overview This dataset accompanies the study “An interactive 2D/3D anatomical resource of the rhesus monkey cerebrum from high-resolution real-color sectioned images.” It provides 77 serial real-color sectioned images, 77 corresponding segmented images, two 3D cerebrum models, volumetric data, and the source code used for 3D reconstruction, color mapping, volumetric analysis, and the interactive web application. The data were derived from a single female rhesus monkey specimen from the Visible Monkey project. Seventy-seven images containing the cerebrum were selected at 0.5 mm intervals and used for manual segmentation of 35 major cerebral structures. An interactive 2D/3D viewer is available at: https://browsing-software.web.app Cite all versions DOI: https://doi.org/10.5281/zenodo.21756697 Included files 1. Sectioned images.zip 77 PNG images File names: 001.png–077.png Image matrix: 2312 × 1487 pixels Section interval: 0.5 mm Anatomical order: superior to inferior as the file number increases The deposited images were resized for public distribution and interactive viewing and do not retain the original image matrix. Their anatomical image content was derived from the original Visible Monkey sectioned images, which had an in-plane pixel size of 0.024 × 0.024 mm. 2. Segmented images.zip 77 PNG images File names: 001.png–077.png Image matrix: 2312 × 1487 pixels Section interval: 0.5 mm Anatomical order: superior to inferior as the file number increases Each image retains the corresponding real-color sectioned image as the background and displays the manually segmented structures using predefined solid colors. These files are visualization-ready composite images rather than machine-readable label maps. 3. 3D models.zip This archive contains: Cerebrum_RGB.glb: solid-colored 3D surface model Cerebrum_real_color.glb: real-color vertex-colored 3D surface model Both GLB files contain the 35 segmented cerebral structures described in the associated study. 4. Rhesus monkey cerebrum source code.zip This archive contains the custom Python scripts used for: Reconstruction of 3D surface models from segmented image stacks Vertex-color mapping from the real-color sectioned images Generation of solid-colored models Conversion and merging of vertex-colored models for web visualization Surface-model-based volumetric analysis The archive also contains the source files of the interactive web application: index.html style.css app.js 3d.html The Python scripts were developed for the directory organization used in this study. Local input and output paths may need to be adjusted before execution. 5. Supplementary Material.xlsx This spreadsheet contains the volumetric data for the whole cerebrum and the 35 segmented structures used in the associated study. Data generation The real-color sectioned images were used as the primary source for determining anatomical boundaries. The INIA19 atlas, the macaque Harvard-Oxford Atlas, a published cross-sectional atlas of the rhesus monkey head, and specimen-derived cerebrum volume models were used as anatomical references. Atlas labels were not directly transferred. The segmented image stack was reconstructed at an isotropic spacing of 0.5 × 0.5 × 0.5 mm. Surface models were generated using the marching cubes algorithm and refined with Taubin-based smoothing. Solid-colored and real-color vertex-colored models were prepared for interactive visualization, and structure volumes were calculated from the reconstructed surface models. Scope and limitations This is a specimen-specific anatomical resource based on one postmortem female rhesus monkey. The segmentation represents gross anatomical structures and does not include fine cytoarchitectural subdivisions. Right-left paired structures are not provided as separate labels. The deposited sectioned and segmented images were resized for public distribution and interactive viewing. The segmented PNG files are colored composite images rather than machine-readable label maps. License This dataset and source code are released under the Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0). Non-commercial sharing and adaptation are permitted with appropriate attribution, a link to the license, and an indication of any changes. Commercial use requires separate permission from the rights holder. Citation Kim, C. Y. (2026). Visible Monkey cerebrum dataset: sectioned images, segmented images, and 3D models. Zenodo. https://doi.org/10.5281/zenodo.21756697 Users should also cite the associated article and the original Visible Monkey publications when using the sectioned-image data. Keywords Rhesus monkey; Macaca mulatta; Cerebrum; Sectioned images; Comparative neuroanatomy; Visible Monkey