2026-10-10T11:34:18Z https://www.scidb.cn/oai

10.57760/sciencedb.nb.00025 2026-09-03T08:24:24Z

2026-09-03 Whole-brain projectome map of Ventral Tegmental Area neuron types doi:10.57760/sciencedb.nb.00025 en This dataset comprises high-resolution imaging data from 15 adult mouse brains. The content includes:(1) Dual-color 3D volumetric images of 3 intact brains (TH-FlpO;GAD2-Cre, DAT-FlpO;vGlut2-Cre, and VGAT-FlpO;vGlut2-Cre) processed with the PEGASOS tissue clearing method, acquired via LiTone XL Light-sheet Microscope. (2) Single-color 3D volumetric images of 6 intact brains (three groups: TH-Cre, vGlut2-Cre, GAD2-Cre, 2 mice/group) processed with the PEGASOS tissue clearing method, acquired via LiTone XL Light-sheet Microscope.(3) Derived spatial registration datasets, including subject-aligned CCFv3 annotation maps (.tiff) and fully rendered interactive 3D surface files (allsurfaces-tree.ims), generated from the raw volumetric data of groups (1) and (2).(4) 2D coronal slice images from 6 mouse brains (three groups: TH-Cre, vGlut2-Cre, GAD2-Cre, 2 mice/group) acquired via Olympus VS120.Data generation method or processTo systematically map the whole-brain projections of VTA neuron subtypes, we established a comprehensive, cross-validated experimental and computational workflow encompassing viral tracing, tissue clearing, serial sectioning, high-resolution imaging, and atlas registration. Four weeks after virus injection, mice were transcardially perfused with 4% paraformaldehyde. For tissue clearing, 9 brains were rendered transparent using the standard PEGASOS protocol. The brains were imaged using LiTone XL Light-sheet Microscope (Objectives: Evident 4×, N.A. = 0.28, WD = 28 mm). The acquired datasets were registered to the CCFv3 atlas using Lit AiBot. For serial sectioning: 6 brains were sectioned coronally at 30 μm thickness using Leica CM1950; serial sections were collected at a sampling interval of 1:5. Sections were imaged using Olympus VS120 slide scanner (Objectives: UPLSAPO 2 10x N.A.= 0.40, WD = 3.1 mm). Data sample descriptionA total of 15 adult mice (aged 8-10 weeks, female) were utilized. For dual-color tissue clearing, 3 experimental groups (N = 1 per group) are included: TH-FlpO;GAD2-Cre, DAT-FlpO;vGlut2-Cre, and VGAT-FlpO;vGlut2-Cre. Single-color tissue clearing consists of 3 experimental groups (N = 2 per group): TH-Cre, GAD2-Cre, vGlut2-Cre. Serial Sectioning consists of 3 experimental groups (N = 2 per group): TH-Cre, GAD2-Cre, vGlut2-Cre.Data quality / Technical ValidationTo ensure the high fidelity and reproducibility of the dataset, rigorous quality control (QC) pipelines were implemented across all stages. The comprehensive QC status for each sample is summarized in the related data paper Table 3.Data volume and data formatThe total volume of this dataset is approximately 600 GB. The raw 3D volumetric images are stored in .ims format. The subject-aligned CCFv3 registration outputs are available in .tiff format. The rendered interactive 3D surface files are stored in .ims format. The 2D serial slice images are provided in .tiff format and archived in a .zip file.Data usage methods and suggestionsTo facilitate broad accessibility and efficient exploration of the dataset, we recommend using the free Imaris Viewer software (version 10.0.0 or later) for basic 3D visualization. Users can load the downsampled volumetric datasets (voxel size 5×5×5 µm) with the registered CCFv3 atlas rendered surfaces by opening the allsurface-tree.ims file. Within the AllSurface module, the Slicer tool enables real-time orthogonal viewing across coronal, sagittal, and horizontal planes. To navigate and examine specific brain regions, the root folder in the allsurface-tree.ims provides an interactive, hierarchical anatomical directory for all brain regions. Users can expand the CCFv3 brain tree within the interface to selectively search and highlight any desired brain region. For system requirements regarding basic visualization, we recommend a workstation equipped with at least an Intel Core i5-12400F processor, 16 GB of RAM, and a dedicated mid-range GPU (e.g., NVIDIA GeForce GTX 1660 SUPER).For advanced data utilization, researchers will require the full commercial version of Imaris (version 10.1.0 or later). By opening the provided allsurface-tree.ims file within this commercial software, users can leverage the Surface module for various sophisticated analytical workflows. For instance, to isolate projection signals within a specific target area, users can select the rendered CCFv3 surface of desired brain regions and apply the Mask All function. This operation effectively crops out signals from adjacent non-target areas, allowing for an unobstructed, 3D evaluation of axonal projections strictly within the selected anatomical boundary. Furthermore, by enabling the 'Statistics' function under the Surface module, users can rapidly compute and export comprehensive statistical parameters for the defined brain regions. To perform such computationally intensive masking and rendering tasks smoothly, a high-performance workstation is required, ideally configured with an Intel Xeon Silver 4214R multi-core processor (2.40 GHz), 256 GB of RAM, and a high-end GPU (e.g., NVIDIA RTX A6000). Whole-brain tissue clearing; Ventral tegmental area; Dopaminergic neuron; GABAergic neuron; Glutamatergic neuron Jiang Yunchun Lv Yanbo Zheng Jie Lin Ziru Wu Tianyang Li Yuan Le Qiumin Wang Feifei Ma Lan Xing Liu PUBLIC https://creativecommons.org/licenses/by/4.0/ dataset Science Data Bank