Supplemental Data: Rapid model-guided design of organ-scale synthetic vasculature for biomanufacturing

Supplemental Dataset: Synthetic Vascular Model Generation, Multiscale CFD Simulation, and In Vitro Viability Analysis This repository accompanies the article “Rapid, model-driven design of organ-scale vascular networks for perfused bioprinted tissues.”It contains every geometry, computational-fluid-dynamics (CFD) result, image analysis and post-processing script required to reproduce the figures in the main text and Supplementary Information. The data trace the complete workflow—from algorithmic vascular-tree construction with svv, through 0-D/3-D CFD analysis, to quantitative figure generation—and offer ready-to-use models for new design studies. Table of Contents 1. Data & File Structure2. Materials & Methods3. Sharing & Access 4. Code & Software Data & File Structure The archive unpacks into a single root folder:Selected folders a files (input files and python code) are shown here:adj6152_data/ Main/ Main Figures/ Figure 1/ cube/ heart/ Figure_1c.py Figure_1d.py Figure_1e.py Figure_1f.py Figure_1g.py Figure 2/ Fig. 2C/ Fig. 2F/ Fig. 2H-I/ Figure 3/ anulus_0d_simulation/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_at_slices.py plot_0d_results_to_3d.py run.py solver_0d.in wave.flow cube_0d_simulation/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_at_slices.py plot_0d_results_to_3d.py run.py solver_0d.in wave.flow gyrus_0d_simulation/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_at_slices.py plot_0d_results_to_3d.py run.py solver_0d.in wave.flow heart_0d_simulation/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_at_slices.py plot_0d_results_to_3d.py run.py solver_0d.in wave.flow Figure 4/ Figure (Data)/ Fig 4.A/ Model 10000/ Model 100000/ Model 1000000/ Fig 4.B/ Model 10000/ Model 100000/ Model 1000000/ Fig 4.C - Biventricular Model/ Processed/ Raw/ Fig 4.D - Annulus Model/ Processed/ Raw/ Figure 5/ Figure (Data)/ Fig. 5D-F/ raw data.zip Fig. 5G-J/ Vessel_Printing_65/ Images/ Meshes/ Models/ Paths/ ROMSimulations/ Segmentations/ Simulations/ cross_sections/ cross_sections_2/ cross_sections_3/ cross_sections_12/ cross_sections_22/ post_results_1/ post_results_2/ pulsatile_deformable_wall/ pulsatile_elastic_wall/ pulsatile_flow/ centerlines.txt color_branches.py create_graph.py read_centerlines.py slice_data.py visualize_deformation.py svFSI/ inflow.flow simvascular.proj multimaterial_test_network_65_vessels (1).txt Fig. 5K/ Photos/ Fig. 5L/ Processes/ Fig. 5M/ Analysis/ Data (Raw, Processed)/ Annulus/ Raw, Reconstructed/ Annulus_Vasculature/ Photos/ Vasculature/ Vascular 1/ Raw/ Reconstructed/ Vascular 2/ Fig. 5O/ Photos/ Renderings/ Fig. 5P/ Fig. 5P i/ Photos/ Fig. 5P ii/ Analysis/ MATLAB/ Processed Data/ Fig. 5P iii/ Analysis/ Fig. 5P iv/ Analysis/ Fig. 5P v/ Analysis/ MATLAB/ Processed Data/ Re-Scaled Data (per cell counts)/ Fig. 5P vi/ Analysis/ MATLAB/ Processed Data/ Supplement Materials/ Supplementary Figures/ Fig. S1/ cube_opposite_diagonal_source_sink/ cube_same_side_diagonal_source_sink/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_to_3d.py README.txt SF2.py solver_0d.in Fig. S2/ svcco/ array_vs_linked_list.py Fig. S3/ BFGS/ COBYLA/ L-BFGS-B/ Nelder-Mead/ Newton-CG/ Powell/ SLSQP/ TNC/ trust-ncg/ get_data.py test_optimizers.py Fig. S4/ svcco/ global_pu_time.py implicit_accuracy_number_patches.py implicit_condition_number.py Fig. S5/ brain_reconstructions/ brain_regions/ engineering_shapes/ svcco/ figure_code.py figure_writer.py Fig. S6/ svcco/ corner_recovery.py patch_functions.py Fig. S7/ svcco/ point_enclosure.py Fig. S8/ brain_data/ convex_data/ svcco/ build_times_figure.py Fig. S9/ Anterior Commissure/ output/ generate_tree.py Branchium of Left Inferior Colliculus/ output/ generate_tree.py Commissure of Fornix of Forebrain/ output/ generate_tree.py Fourth Ventricle/ output/ generate_tree.py Hypothalamus/ output/ generate_tree.py Lamina Terminalis/ output/ generate_tree.py Left Globus Pallidus/ output/ generate_tree.py Left Inferior Frontal Gyrus/ output/ generate_tree.py Left Internal Capsule/ output/ generate_tree.py Left Olfactory Tract/ output/ generate_tree.py Left Superior Frontal Gyrus/ output/ generate_tree.py Medulla Oblongata/ output/ generate_tree.py Midbrain/ output/ generate_tree.py Right Inferior Frontal Gyrus/ output/ generate_tree.py Right Internal Capsule/ output/ generate_tree.py Right Olfactory Tract/ output/ generate_tree.py Right Putamen/ output/ generate_tree.py Right Stria Medullaris of Thalamus/ output/ generate_tree.py Right Superior Fronal Gyrus/ output/ generate_tree.py Third ventricle/ output/ generate_tree.py Fig. S10/ Fig. S11/ Code/ S_Sample_Code_PIV.zip Fig. S12/ Vessel_Printing_65/ Images/ Meshes/ Models/ Paths/ ROMSimulations/ Segmentations/ Simulations/ cross_sections/ cross_sections_2/ cross_sections_3/ cross_sections_12/ cross_sections_22/ post_results_1/ post_results_2/ pulsatile_deformable_wall/ pulsatile_elastic_wall/ pulsatile_flow/ centerlines.txt color_branches.py create_graph.py read_centerlines.py slice_data.py visualize_deformation.py svFSI/ inflow.flow simvascular.proj Fig. S13/ Analysis/ Raw Data/ Fig. S14/ Other Files/ Photos/ Fig. S15/ Fig. S15 A/ Analysis/ Plots/ Processed Data/ Raw Data/ Fig. S15 C/ svcco/ docs/ examples/ scripts/ sv_interface/ svcco/ tests/ Supplementary Videos/ S Video 1/ svcco/ arbitrary_trees/ S Video 2/ anulus_0d_simulation/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_at_slices.py plot_0d_results_to_3d.py run.py solver_0d.in wave.flow cube_0d_simulation/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_at_slices.py plot_0d_results_to_3d.py run.py solver_0d.in wave.flow gyrus_0d_simulation/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_at_slices.py plot_0d_results_to_3d.py run.py solver_0d.in wave.flow heart_0d_simulation/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_at_slices.py plot_0d_results_to_3d.py run.py solver_0d.in wave.flow Inside each Figure directory Suffix File type Description ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ .vtp VTK **PolyData** Perfused tissue surface or vascular tree, Visualize with PyVista or Paraview .vtu VTK **Unstructured Grid** 3-D CFD solution fields (velocity, pressure, wall shear, etc.) Visualize with PyVista or Paraview .npy NumPy array Derived metrics (e.g., mean inter-vascular distance, resistances) .flow ASCII Inlet flow waveform for SimVascular 3-D/0-D solver .pkl Pickle Tree connectivity tables (nodes & edges) & data .py Python script Figure-generation & post-processing code .csv / .bmp CSV / image Processed viability assays or reconstructed micro-CT slices Relationships & Conventions All companion files share a common stem (e.g., tree_999.vtu, tree_999_metrics.npy). Units: mm (geometry), cm³ s⁻¹ (flow), dyn cm⁻² (pressure) unless noted. Missing values are encoded as nan. Live/dead assay CSVs give intensity-normalised counts; group statistics live in Analysis/ subfolders.补充数据集：人工血管模型生成、多尺度计算流体动力学（Computational Fluid Dynamics, CFD）模拟及体外活力分析 本数据集配套发表于论文《用于灌注式生物打印组织的器官级血管网络快速模型驱动设计》，包含复现正文及补充材料中所有图表所需的全部几何模型、计算流体动力学（CFD）结果、图像分析脚本与后处理脚本。本数据集完整覆盖从基于svv的算法式血管树构建、0维/3维CFD分析到定量图表生成的全流程，并可为新的设计研究提供现成可用的模型。 目录 1. 数据与文件结构 2. 材料与方法 3. 共享与获取 4. 代码与软件 ### 数据与文件结构 该压缩包解压后将生成一个单一根目录文件夹：此处展示了部分选定的文件夹与文件（包含输入文件及Python代码）： adj6152_data/ Main/ Main Figures/ Figure 1/ cube/ heart/ Figure_1c.py Figure_1d.py Figure_1e.py Figure_1f.py Figure_1g.py Figure 2/ Fig. 2C/ Fig. 2F/ Fig. 2H-I/ Figure 3/ anulus_0d_simulation/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_at_slices.py plot_0d_results_to_3d.py run.py solver_0d.in wave.flow cube_0d_simulation/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_at_slices.py plot_0d_results_to_3d.py run.py solver_0d.in wave.flow gyrus_0d_simulation/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_at_slices.py plot_0d_results_to_3d.py run.py solver_0d.in wave.flow heart_0d_simulation/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_at_slices.py plot_0d_results_to_3d.py run.py solver_0d.in wave.flow Figure 4/ Figure (Data)/ Fig 4.A/ Model 10000/ Model 100000/ Model 1000000/ Fig 4.B/ Model 10000/ Model 100000/ Model 1000000/ Fig 4.C - 双心室模型/ Processed/ Raw/ Fig 4.D - 瓣环模型/ Processed/ Raw/ Figure 5/ Figure (Data)/ Fig. 5D-F/ raw data.zip Fig. 5G-J/ Vessel_Printing_65/ Images/ Meshes/ Models/ Paths/ ROMSimulations/ Segmentations/ Simulations/ cross_sections/ cross_sections_2/ cross_sections_3/ cross_sections_12/ cross_sections_22/ post_results_1/ post_results_2/ pulsatile_deformable_wall/ pulsatile_elastic_wall/ pulsatile_flow/ centerlines.txt color_branches.py create_graph.py read_centerlines.py slice_data.py visualize_deformation.py svFSI/ inflow.flow simvascular.proj multimaterial_test_network_65_vessels (1).txt Fig. 5K/ Photos/ Fig. 5L/ Processes/ Fig. 5M/ Analysis/ Data (Raw, Processed)/ Annulus/ Raw, Reconstructed/ Annulus_Vasculature/ Photos/ Vasculature/ Vascular 1/ Raw/ Reconstructed/ Vascular 2/ Fig. 5O/ Photos/ Renderings/ Fig. 5P/ Fig. 5P i/ Photos/ Fig. 5P ii/ Analysis/ MATLAB/ Processed Data/ Fig. 5P iii/ Analysis/ Fig. 5P iv/ Analysis/ Fig. 5P v/ Analysis/ MATLAB/ Processed Data/ Re-Scaled Data (per cell counts)/ Fig. 5P vi/ Analysis/ MATLAB/ Processed Data/ Supplement Materials/ Supplementary Figures/ Fig. S1/ cube_opposite_diagonal_source_sink/ cube_same_side_diagonal_source_sink/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_to_3d.py README.txt SF2.py solver_0d.in Fig. S2/ svcco/ array_vs_linked_list.py Fig. S3/ BFGS/ COBYLA/ L-BFGS-B/ Nelder-Mead/ Newton-CG/ Powell/ SLSQP/ TNC/ trust-ncg/ get_data.py test_optimizers.py Fig. S4/ svcco/ global_pu_time.py implicit_accuracy_number_patches.py implicit_condition_number.py Fig. S5/ brain_reconstructions/ brain_regions/ engineering_shapes/ svcco/ figure_code.py figure_writer.py Fig. S6/ svcco/ corner_recovery.py patch_functions.py Fig. S7/ svcco/ point_enclosure.py Fig. S8/ brain_data/ convex_data/ svcco/ build_times_figure.py Fig. S9/ Anterior Commissure/ output/ generate_tree.py Branchium of Left Inferior Colliculus/ output/ generate_tree.py Commissure of Fornix of Forebrain/ output/ generate_tree.py Fourth Ventricle/ output/ generate_tree.py Hypothalamus/ output/ generate_tree.py Lamina Terminalis/ output/ generate_tree.py Left Globus Pallidus/ output/ generate_tree.py Left Inferior Frontal Gyrus/ output/ generate_tree.py Left Internal Capsule/ output/ generate_tree.py Left Olfactory Tract/ output/ generate_tree.py Left Superior Frontal Gyrus/ output/ generate_tree.py Medulla Oblongata/ output/ generate_tree.py Midbrain/ output/ generate_tree.py Right Inferior Frontal Gyrus/ output/ generate_tree.py Right Internal Capsule/ output/ generate_tree.py Right Olfactory Tract/ output/ generate_tree.py Right Putamen/ output/ generate_tree.py Right Stria Medullaris of Thalamus/ output/ generate_tree.py Right Superior Fronal Gyrus/ output/ generate_tree.py Third ventricle/ output/ generate_tree.py Fig. S10/ Fig. S11/ Code/ S_Sample_Code_PIV.zip Fig. S12/ Vessel_Printing_65/ Images/ Meshes/ Models/ Paths/ ROMSimulations/ Segmentations/ Simulations/ cross_sections/ cross_sections_2/ cross_sections_3/ cross_sections_12/ cross_sections_22/ post_results_1/ post_results_2/ pulsatile_deformable_wall/ pulsatile_elastic_wall/ pulsatile_flow/ centerlines.txt color_branches.py create_graph.py read_centerlines.py slice_data.py visualize_deformation.py svFSI/ inflow.flow simvascular.proj Fig. S13/ Analysis/ Raw Data/ Fig. S14/ Other Files/ Photos/ Fig. S15/ Fig. S15 A/ Analysis/ Plots/ Processed Data/ Raw Data/ Fig. S15 C/ svcco/ docs/ examples/ scripts/ sv_interface/ svcco/ tests/ Supplementary Videos/ S Video 1/ svcco/ arbitrary_trees/ S Video 2/ anulus_0d_simulation/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_at_slices.py plot_0d_results_to_3d.py run.py solver_0d.in wave.flow cube_0d_simulation/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_at_slices.py plot_0d_results_to_3d.py run.py solver_0d.in wave.flow gyrus_0d_simulation/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_at_slices.py plot_0d_results_to_3d.py run.py solver_0d.in wave.flow heart_0d_simulation/ timeseries/ timeseries_for_flow_gif/ timeseries_for_pressure_gif/ timeseries_for_wss_gif/ inflow.flow plot_0d_results_at_slices.py plot_0d_results_to_3d.py run.py solver_0d.in wave.flow ### 各图表目录内文件规范 | 后缀 | 文件类型 | 描述 | |------|----------|------| | .vtp | VTK 多面数据（PolyData） | 用于表示灌注组织表面或血管树，可通过PyVista或Paraview进行可视化 | | .vtu | VTK 非结构化网格（Unstructured Grid） | 存储三维CFD求解场（速度、压力、壁面切应力等），可通过PyVista或Paraview进行可视化 | | .npy | NumPy数组 | 存储衍生指标（如平均血管间距、阻力值） | | .flow | ASCII格式文件 | 用于SimVascular三维/零维求解器的入口流波形 | | .pkl | Pickle序列化文件 | 存储血管树连通性表（节点与边）及相关数据 | | .py | Python脚本 | 用于图表生成与后处理 | | .csv / .bmp | CSV文件/图像文件 | 存储已处理的活力检测结果或重建的显微CT切片 | ### 文件关联与通用规范 所有配套文件共享相同的文件名前缀（例如`tree_999.vtu`、`tree_999_metrics.npy`）。 单位：若无特殊说明，几何尺寸单位为毫米（mm），流量单位为立方厘米每秒（cm³ s⁻¹），压力单位为达因每平方厘米（dyn cm⁻²）。 缺失值以`nan`（非数字）进行编码。 活/死染色检测的CSV文件包含强度归一化后的细胞计数；分组统计数据存储于`Analysis/`子文件夹中。