High-throughput, high-fidelity reconstruction of whole mouse-heart cytoarchitecture at cellular scale: dataset

This dataset accompanies the publication:Giardini F., Palandri C., et al. "High-throughput, high-fidelity reconstruction of whole mouse-heart cytoarchitecture at cellular scale." The Journal of Physiology (2026). The dataset contains four components: 1. Whole_hearts_tomograms/ (9 tomograms, D1.tif – D9.tif, plus a parameters file)Fused autofluorescence tomograms of 9 adult wild-type mouse hearts (CTRL), acquired using a custom dual-camera selective plane-illumination microscope (dual-mesoSPIM) after CUBIC tissue clearing. Each tomogram was generated by automated dual-view fusion combining the highest-contrast information from two opposing detection arms. Files are 8-bit TIFF stacks. Voxel size: 6.0 × 6.0 × 6.0 µm³ (isotropic, resampled from the raw acquisition voxel size of 3.25 × 3.25 × 3.0 µm³). These tomograms were used for Structure Tensor Analysis (STA) of cardiomyocyte fibre orientations and laminar sheetlet organisation. The folder also includes parameters_DualMesoSPIM.txt, reporting the acquisition parameters. Naming convention: D1.tif – D9.tif. 2. Anatomical_meshes/ (5 files, N1.vtu – N5.vtu)Volumetric tetrahedral meshes of the ventricular myocardium for 5 hearts (subset of the above, selected on the basis of >95% analysable fibre orientation coverage). Each mesh integrates locally prevailing cardiomyocyte fibre orientation vectors mapped onto mesh elements, derived from STA applied within non-overlapping macrovoxels of 96 × 96 × 96 µm³ (FA threshold ≥ 0.25). Files are in VTK format. Naming convention: N1.vtu – N5.vtu. 3. AntiTH_tomogram/ (1 file)Fused whole-heart tomogram from anti-tyrosine hydroxylase (TH) immunofluorescence imaging of the cardiac sympathetic nervous system, acquired at full acquisition resolution. Voxel size: 3.25 × 3.25 × 3.0 µm³. The tomogram was used for machine-learning-based segmentation of sympathetic axons (Trainable Weka 3D, Fiji) to reconstruct innervation density throughout the intact ventricular myocardium. File: AntiTH_fused_ps_zyx_3.0_3.25_3.25_um.tif. 4. Source data for Figure 5d (2 files)Raw, paired measurements underlying the fluorescence-preservation quantification shown in Figure 5d, assessing the effect of CUBIC clearing on endogenous fluorescent reporters in 300-µm sections from postnatal day 7 R26R-Confetti mouse hearts (n = 4 sections from N = 2 hearts; 40 RFP cells and 40 GFP nuclei). The spreadsheet contains six worksheets (RFP and GFP signal intensity, their adjacent background intensity, and the corresponding signal-to-background ratios), each with paired Pre/Post-clearing values. A companion README describes the file structure. Files: Fig5d_data_RFP_GFP_confetti_fluorescence.xlsx and Fig5d_data_RFP_GFP_confetti_fluorescence_README.txt. Microscope control and fusion software are available at: https://github.com/giardini-iekm/dual-mesospim.git