Assessing the importance of sex and disease-specific anatomy in electrophysiology and mechanical simulations with a newly developed public virtual cohort of four-chamber heart models.
The 11 matches
- [1] § 3. Methods › 3.2. Image to mesh stage › 3.2.1 Multi-stage segmentation. ↔ cemrg_heartbuilder/meshing/ModelCreationParameters.py, lines 1–29 · score 0.94 · venae cavae, pulmonary artery, pulmonary veins, blood pools, right atrial, left atrial
- [2] § 3. Methods › 3.2. Image to mesh stage › 3.2.1 Multi-stage segmentation. ↔ cemrg_heartbuilder/segmentation/process_handler.py, lines 273–319 · score 0.83 · pulmonary artery, right atrium, right ventricle, ventricle myocardium, right atrial, left atrial
- [3] § 3. Methods › 3.2. Image to mesh stage › 3.2.2. Conversion to mesh. ↔ cemrg_heartbuilder/meshing/MeshingParameters.py, lines 5–119 · score 0.75 · cell_size, facet_distance, facet_size, edge, smooth, segmentation
- [4] § 3. Methods › 3.5. Statistical tests and comparison of volume to clinical literature › 3.5.1. Effect sizes and statistical significance. ↔ examples/comprehensive_analysis.py, lines 262–330 · score 0.71 · post hoc, way ANOVA, pairwise, marginal, Tukey, Cohen
- [5] § 3. Methods › 3.3. Mesh processing and model creation ↔ cemrg_heartbuilder/simulation/toolbox.py, lines 248–325 · score 0.70 · Bachmann bundle, left atrium, right ventricular, fast, FEC, electrophysiology
- [6] § 3. Methods › 3.3. Mesh processing and model creation ↔ cemrg_heartbuilder/meshing/ModelCreationParameters.py, lines 1–29 · score 0.63 · vena cava, pulmonary veins, creation, Ventricular, tags, mesh
- [7] § 4. Results › 4.1. Geometric characterization and correlation with simulation outputs ↔ examples/comprehensive_analysis.py, lines 209–260 · score 0.63 · FDR correction, post hoc, way ANOVA, Cohen
- [8] § 3. Methods › 3.2. Image to mesh stage › 3.2.2. Conversion to mesh. ↔ cemrg_heartbuilder/meshing/scripts/get_meshing_parfile.py, lines 38–60 · score 0.59 · cell_size, facet_distance, facet_size, edge, segmentation, mesh
- [9] § 3. Methods › 3.5. Statistical tests and comparison of volume to clinical literature › 3.5.2. Left atrial and left ventricular volume. ↔ examples/plot_cardiac_distributions.py, lines 23–53 · score 0.55 · LV volume, right ventricles, females, atrial, cardiac, HF
- [10] § 2. Study population ↔ examples/plot_cardiac_distributions.py, lines 23–53 · score 0.52 · narrow QRS, wide QRS, Female, cardiac, HF
- [11] § 3. Methods › 3.3. Mesh processing and model creation ↔ cemrg_heartbuilder/simulation/scripts/basic_extract_ep_output.py, lines 23–34 · score 0.50 · Bachmann bundle, fast, EP, FEC, electrophysiology, atria
Paper
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The authors' code
Python · 340 lines · 9.1 KB · no license · 2 matches
- import os
- import json
- UNUSED_TAG = 200
- DEFAULT_ETAGS = {
- 'T_LV': 1,
- 'T_RV': 2,
- 'T_UNUSED' : UNUSED_TAG, # unused tag
- 'T_LA' : UNUSED_TAG, # left atrial wall
- 'T_LABP' : UNUSED_TAG, # left atrial blood pool
- 'T_LINFPULMVEINCUT' : UNUSED_TAG, # left inferior pulmonary vein (cut)
- 'T_LSUPPULMVEINCUT' : UNUSED_TAG, # left superior pulmonary vein (cut)
- 'T_RINFPULMVEINCUT' : UNUSED_TAG, # right inferior pulmonary vein (cut)
- 'T_RSUPPULMVEINCUT' : UNUSED_TAG, # right superior pulmonary vein (cut)
- 'T_RA' : UNUSED_TAG, # right atrial wall
- 'T_RABP' : UNUSED_TAG, # right atrial blood pool
- 'T_LVBP' : UNUSED_TAG, # left ventricular blood pool
- 'T_AORTA' : UNUSED_TAG, # aorta
- 'T_AORTABP' : UNUSED_TAG, # aortic blood pool
- 'T_MITRALVV' : UNUSED_TAG, # mitral valve
- 'T_AORTICVV' : UNUSED_TAG, # aortic valve
- 'T_RVBP' : UNUSED_TAG, # right ventricular blood pool
- 'T_VCINF' : UNUSED_TAG, # vena cava inferior
- 'T_VCSUP' : UNUSED_TAG, # vena cava superior
- 'T_PULMARTERY' : UNUSED_TAG, # pulmonary artery
- 'T_PULMARTERYBP' : UNUSED_TAG, # pulmonary artery blood pool
- 'T_TRICUSPVV' : UNUSED_TAG, # tricuspic valve
- 'T_PULMVV' : UNUSED_TAG # pulmonic valve
- }
- class ETagsParameters:
- def __init__(self, type='base') -> None:
- types = ['base', 'la', 'ra']
- if type not in types :
- raise ValueError(f'Invalid type for ETagsParameters. Must be one of {types}')
- self.type = type
- self.tags = DEFAULT_ETAGS.copy()
- self.update_tags()
- def update_type(self, type) :
- self.type = type
- self.update_tags()
- def update_tags(self) :
- tag_names = list(self.tags.keys())
- if self.type == 'base' :
- self.tags['T_LV'] = 1
- self.tags['T_RV'] = 2
- tag_names.remove('T_LV')
- tag_names.remove('T_RV')
- elif self.type == 'la' :
- self.tags['T_LV'] = 3
- tag_names.remove('T_LV')
- elif self.type == 'ra' :
- self.tags['T_LV'] = 4
- tag_names.remove('T_LV')
- for tag in tag_names :
- self.tags[tag] = UNUSED_TAG
- def save_to_file(self, filename) :
- filename += '.sh' if not filename.endswith('.sh') else ''
- # list tags different to UNUSED_TAG
- tags_used = {k:v for k,v in self.tags.items() if v != UNUSED_TAG}
- tags_unused = {k:v for k,v in self.tags.items() if v == UNUSED_TAG}
- with open(filename, 'w') as f :
- f.write('#!/bin/bash\n')
- f.write('\n')
- if self.type != 'base' :
- f.write(f'## CHANGE ONLY THIS LABEL SO THAT THE T_LV = THE LABELOF YOUR {self.type.upper()}')
- else :
- f.write('## ONLY CHANGE THESE LABELS TO MATCH YOUR MESH LABELS')
- f.write('\n\n')
- for k,v in tags_used.items() :
- f.write(f'{k}={v}\n')
- f.write('\n')
- for k,v in tags_unused.items() :
- f.write(f'{k}={v}\n')
- DEFAULT_ATRIA_MAP = {
- "la": {
- "phi_min_aorta_side": -3.15,
- "begin_interp_aorta_side": -2.09,
- "end_interp_aorta_side": -1.54,
- "phi_max": 0,
- "begin_interp_not_aorta": -0.1,
- "end_interp_not_aorta": 0.7,
- "phi_min_not_aorta": 3.15
- },
- "ra": {
- "phi_min_aorta_side": -3.15,
- "begin_interp_aorta_side": -1.0,
- "end_interp_aorta_side": -0.5,
- "phi_max": 0,
- "begin_interp_not_aorta": 0.5,
- "end_interp_not_aorta": 2,
- "phi_min_not_aorta": 3.15
- },
- "Iz": {
- "Iz_0": 0,
- "Iz_1": 0.4,
- "Iz_2": 0.7,
- "Iz_3": 1.0
- }
- }
- class AtriaMapSettings:
- def __init__(self) -> None:
- self.settings = DEFAULT_ATRIA_MAP.copy()
- def save_to_file(self, filename) :
- filename += '.json' if not filename.endswith('.json') else ''
- with open(filename, 'w') as f :
- json.dump(self.settings, f, indent=4)
- def load_from_file(self, filename) :
- filename += '.json' if not filename.endswith('.json') else ''
- with open(filename, 'r') as f :
- self.settings = json.load(f)
- def update_settings(self, settings) :
- self.settings = settings
- def change(self, atria, key, value) :
- if atria not in self.settings :
- raise ValueError(f'{atria} not found in the settings')
- if key not in self.settings[atria] :
- raise ValueError(f'{key} not found in the settings')
- self.settings[atria][key] = value
- DEFAULT_BACHMANN_BUNDLE = {
- "FEC_height": 0.8,
- "LA": {
- "phi_min": -0.54,
- "phi_max": 2,
- "z_min": 0.0,
- "z_max": 0.71
- },
- "RA": {
- "phi_min": -1.85,
- "phi_max": 1.4,
- "z_min": 0.0,
- "z_max": 0.46
- }
- }
- class BachmannBundleSettings:
- def __init__(self) -> None:
- self.settings = DEFAULT_BACHMANN_BUNDLE.copy()
- def save_to_file(self, filename) :
- filename += '.json' if not filename.endswith('.json') else ''
- with open(filename, 'w') as f :
- json.dump(self.settings, f, indent=4)
- def load_from_file(self, filename) :
- filename += '.json' if not filename.endswith('.json') else ''
- with open(filename, 'r') as f :
- self.settings = json.load(f)
- def update_settings(self, settings) :
- self.settings = settings
- def change(self, atria, key, value) :
- if atria not in self.settings :
- raise ValueError(f'{atria} not found in the settings')
- if key not in self.settings[atria] :
- raise ValueError(f'{key} not found in the settings')
- self.settings[atria][key] = value
- def change_la(self, key, value) :
- self.change('LA', key, value)
- def change_ra(self, key, value) :
- self.change('RA', key, value)
- def change_fec(self, value) :
- self.settings['FEC_height'] = value
- DEFAULT_MESH_TAGS = {
- "LV": 1,
- "RV": 2,
- "LA": 3,
- "RA": 4,
- "Ao": 5,
- "PArt": 6,
- "MV": 7,
- "TV": 8,
- "AV": 9,
- "PV": 10,
- "LSPV": 11,
- "LIPV": 12,
- "RSPV": 13,
- "RIPV": 14,
- "LAA": 15,
- "SVC": 16,
- "IVC": 17,
- "LAA_ring": 18,
- "SVC_ring": 19,
- "IVC_ring": 20,
- "LSPV_ring": 21,
- "LIPV_ring": 22,
- "RSPV_ring": 23,
- "RIPV_ring": 24,
- "FEC_LV": 25,
- "FEC": 25,
- "BB": 26,
- "AV_plane": 27,
- "FEC_RV": 28,
- "FEC_SV": 29
- }
- DEFAULT_FASCICLES_SETTINGS = {
- "LVsept" :{
- "z" : 0.61,
- "phi" : 0.73,
- "rho" : 0.0,
- "v" : -1.0,
- "radius": 2000.0,
- "radius_phi": 0.05,
- "radius_rho": 0.05
- },
- "LVpost" :{
- "z" : 0.47,
- "phi" : -1.36,
- "rho" : 0.0,
- "v" : -1.0,
- "radius": 2000.0,
- "radius_phi": 0.05,
- "radius_rho": 0.05
- },
- "LVant" :{
- "z" : 0.82,
- "phi" : 1.94,
- "rho" : 0.0,
- "v" : -1.0,
- "radius": 2000.0,
- "radius_phi": 0.05,
- "radius_rho": 0.05
- },
- "RVsept" :{
- "z" : 0.73,
- "phi" : -0.04,
- "rho" : 1.0,
- "v" : -1.0,
- "radius": 2000.0,
- "radius_phi": 0.05,
- "radius_rho": 0.05
- },
- "RVmod" :{
- "z" : 0.63,
- "phi" : 0.21,
- "rho" : 0,
- "v" : 1.0,
- "radius": 2000.0,
- "radius_phi": 0.05,
- "radius_rho": 0.05
- },
- "SAN" :{
- "radius": 2000.0
- }
- }
- ## EP SIMS
- DEFAULT_EP_TAGS = {
- "LV": 1,
- "RV": 2,
- "LA": 3,
- "RA": 4,
- "atria": [3,4],
- "FEC_LV": 25,
- "FEC_RV": 28,
- "FEC_SV": 29,
- "fast_endo": [25,28,29],
- "BB": 26,
- "AV_plane": [27],
- "aorta": [5],
- "pulmonary_artery": [6],
- "vein_rings": [18,19,20,21,22,23,24],
- "valve_planes": [7,8,9,10,11,12,13,14,15,16,17]
- }
- ##
- CV_F_V_SHARED = 0.407284
- CV_F_A_SHARED = 0.353259
- ANI_RATIO_V_SHARED = 0.272427
- ANI_RATIO_A_SHARED = 0.340049
- K_FEC_SHARED = 1.55631
- K_BB_SHARED = 1.65963
- DEFAULT_EP_VELOCITIES = {
- "EP": {
- "CV_f_v": CV_F_V_SHARED,
- "CV_ventricles": CV_F_V_SHARED,
- "ani_ratio_v": ANI_RATIO_V_SHARED,
- "k_ventricles": ANI_RATIO_V_SHARED,
- "k_FEC": K_FEC_SHARED,
- "CV_f_a": CV_F_A_SHARED,
- "CV_atria": CV_F_A_SHARED,
- "ani_ratio_a": ANI_RATIO_A_SHARED,
- "k_atria": ANI_RATIO_A_SHARED,
- "k_BB": K_BB_SHARED
- }
- }
- LAPLACE_FILE=[["experiment\t= 2",
- "bidomain\t= 1"],
- ["num_gregions\t= 1",
- "gregion[0].g_et\t= 1",
- "gregion[0].g_el\t= 1",
- "gregion[0].g_en\t= 1",
- "gregion[0].g_il\t= 1",
- "gregion[0].g_it\t= 1",
- "gregion[0].g_in\t= 1"],
- ["num_stim\t= 2",
- "stimulus[0].stimtype\t= 3",
- "stimulus[1].duration\t= 1",
- "stimulus[1].strength\t= 1",
- "stimulus[1].stimtype\t= 2"]]
- def write_laplace_carp_par(filename):
- with open(filename, 'w') as f :
- for i in range(len(LAPLACE_FILE)):
- for j in range(len(LAPLACE_FILE[i])):
- f.write(LAPLACE_FILE[i][j]+"\n")
- f.write("\n")
ModelCreationParameters.py at commit 9976818, no license · at the source
Overview
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiac Rhythm Management, Medtronic, London, United Kingdom
- School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- School of Engineering and Materials Science, Queen Mary University of London, London, United Kingdom
- Gottfried Schatz Research Center, Division of Medical Physics and Biophysics, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Food and Drug Administration, Silver Spring, Maryland, United States of America
- Alan Turing Institute, London, United Kingdom
Abstract
The abstract is not reproduced here: the paper's license (none stated) does not allow it. Read it in the paper, at the publisher or on Europe PMC.
Repositories
Its files are read in the Code ↔ Paper reader above, with 11 matches between paragraphs and lines of code.
OpenHeartDevelopers/cemrg-heartbuilder
9976818fe7e3baa573ddf3b28236057d6c081794, 28 August 2026Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
126 files
- cemrg_heartbuilder/
__init__.py , Python, 1 line - cemrg_heartbuilder/
common/ , Python, 139 linesCommandRunner.py - cemrg_heartbuilder/
common/ , Python, 87 linesFourChamberProject.py - cemrg_heartbuilder/
common/ , Python, 132 linesMeshtoolWrapper.py - cemrg_heartbuilder/
common/ , Python, 308 linesUAC_surface_utils.py - cemrg_heartbuilder/
common/ , Python, 1 line__init__.py - cemrg_heartbuilder/
common/ , Python, 48 linesconfig.py - cemrg_heartbuilder/
common/ , Python, 166 linesioutils.py - cemrg_heartbuilder/
common/ , Python, 55 linesjson_utils.py - cemrg_heartbuilder/
common/ , Python, 110 linesscripts/ export.py - cemrg_heartbuilder/
common/ , Python, 1 lineutilities.py - cemrg_heartbuilder/
meshing/ , Python, 136 lines, 1 matchMeshingParameters.py - cemrg_heartbuilder/
meshing/ , Python, 340 lines, 2 matchesModelCreationParameters. py - cemrg_heartbuilder/
meshing/ , Python, 1 line__init__.py - cemrg_heartbuilder/
meshing/ , Python, 41 lineshelpers/ identify_labels_in_mesh. py - cemrg_heartbuilder/
meshing/ , Python, 180 linesrelabel_utilities.py - cemrg_heartbuilder/
meshing/ , Python, 62 lines, 1 matchscripts/ get_meshing_parfile.py - cemrg_heartbuilder/
meshing/ , Python, 144 linesscripts/ get_model_creation_param s.py - cemrg_heartbuilder/
meshing/ , Python, 62 linesscripts/ mesh_postprocessing.py - cemrg_heartbuilder/
meshing/ , Python, 48 linesscripts/ mesh_preliminary_test.py - cemrg_heartbuilder/
meshing/ , Python, 52 linesscripts/ mesh_size_test.py - cemrg_heartbuilder/
meshing/ , Python, 30 linesscripts/ relabel_mesh.py - cemrg_heartbuilder/
meshing/ , Python, 97 linesscripts/ simple_relabel_mesh.py - cemrg_heartbuilder/
modeling/ , Python, 413 linesFourChamberModeler.py - cemrg_heartbuilder/
modeling/ , Python, 1 line__init__.py - cemrg_heartbuilder/
modeling/ , Python, 111 linescarp_wrapper.py - cemrg_heartbuilder/
modeling/ , Python, 806 linesdistance_utils.py - cemrg_heartbuilder/
modeling/ , Python, 309 linesfile_utils.py - cemrg_heartbuilder/
modeling/ , Python, 92 lineslinalg_utils.py - cemrg_heartbuilder/
modeling/ , Python, 894 linesmesh_utils.py - cemrg_heartbuilder/
modeling/ , Python, 1,306 linesmeshtools_utils.py - cemrg_heartbuilder/
modeling/ , Python, 186 linesmotion_volume.py - cemrg_heartbuilder/
modeling/ , Python, 389 linesprocess_handler.py - cemrg_heartbuilder/
modeling/ , Python, 16 linesscripts/ correct_fibres.py - cemrg_heartbuilder/
modeling/ , Python, 45 linesscripts/ main_UVCs.py - cemrg_heartbuilder/
modeling/ , Python, 287 linesscripts/ main_electrodes.py - cemrg_heartbuilder/
modeling/ , Python, 76 linesscripts/ main_fec.py - cemrg_heartbuilder/
modeling/ , Python, 153 linesscripts/ main_fibres.py - cemrg_heartbuilder/
modeling/ , Python, 80 linesscripts/ main_laplace.py - cemrg_heartbuilder/
modeling/ , Python, 36 linesscripts/ main_laplace_refact.py - cemrg_heartbuilder/
modeling/ , Python, 142 linesscripts/ main_mesh.py - cemrg_heartbuilder/
modeling/ , Python, 96 linesscripts/ main_surf_to_volume.py - cemrg_heartbuilder/
modeling/ , Python, 30 linesscripts/ main_surf_to_volume_refa ct.py - cemrg_heartbuilder/
modeling/ , Python, 34 linesscripts/ main_surfs.py - cemrg_heartbuilder/
modeling/ , Python, 108 linesscripts/ main_surfs_presim.py - cemrg_heartbuilder/
modeling/ , Python, 136 linesscripts/ main_tags.py - cemrg_heartbuilder/
modeling/ , Python, 37 linesscripts/ manual_mapping_from_indi ces.py - cemrg_heartbuilder/
modeling/ , Python, 36 linesscripts/ run_task.py - cemrg_heartbuilder/
modeling/ , Python, 361 linessimulation_utils.py - cemrg_heartbuilder/
modeling/ , Python, 121 linesuvc_landmarks.py - cemrg_heartbuilder/
segmentation/ , Python, 1,154 linesFourChamberProcess.py - cemrg_heartbuilder/
segmentation/ , Python, 868 linesImageAnalysis.py - cemrg_heartbuilder/
segmentation/ , Python, 1 line__init__.py - cemrg_heartbuilder/
segmentation/ , Python, 168 linescut_labels.py - cemrg_heartbuilder/
segmentation/ , Python, 626 linesparameters.py - cemrg_heartbuilder/
segmentation/ , Python, 192 linespost_slicer.py - cemrg_heartbuilder/
segmentation/ , Python, 387 lines, 1 matchprocess_handler.py - cemrg_heartbuilder/
segmentation/ , Python, 50 linesscripts/ 0_1_create_extra_veins.p y - cemrg_heartbuilder/
segmentation/ , Python, 26 linesscripts/ 0_2_add_extra_veins_to_s eg_refact.py - cemrg_heartbuilder/
segmentation/ , Python, 61 linesscripts/ 0_get_segmentation_param s.py - cemrg_heartbuilder/
segmentation/ , Python, 32 linesscripts/ 0_pad_image.py - cemrg_heartbuilder/
segmentation/ , Python, 37 linesscripts/ 1_create_cylinders.py - cemrg_heartbuilder/
segmentation/ , Python, 33 linesscripts/ 2_create_svc_ivc.py - cemrg_heartbuilder/
segmentation/ , Python, 41 linesscripts/ 3_cut_vessels.py - cemrg_heartbuilder/
segmentation/ , Python, 43 linesscripts/ 4_create_myo.py - cemrg_heartbuilder/
segmentation/ , Python, 51 linesscripts/ 5_create_valve_planes.py - cemrg_heartbuilder/
segmentation/ , Python, 35 linesscripts/ 6_clean_seg.py - cemrg_heartbuilder/
segmentation/ , Python, 109 linesscripts/ 7_smooth_segmentation.py - cemrg_heartbuilder/
segmentation/ , Python, 1 linescripts/ __init__.py - cemrg_heartbuilder/
segmentation/ , Python, 25 linesscripts/ extract_geometry.py - cemrg_heartbuilder/
segmentation/ , Python, 38 linesscripts/ o2_simple_pad_image.py - cemrg_heartbuilder/
segmentation/ , Python, 54 linesscripts/ relabel_segmentation.py - cemrg_heartbuilder/
segmentation/ , Python, 41 linesscripts/ reorient_image.py - cemrg_heartbuilder/
segmentation/ , Python, 42 linesscripts/ set_geometry.py - cemrg_heartbuilder/
segmentation/ , Python, 40 linesscripts/ world_to_index.py - cemrg_heartbuilder/
simulation/ , Python, 1 line__init__.py - cemrg_heartbuilder/
simulation/ , Python, 205 linesmechanics.py - cemrg_heartbuilder/
simulation/ , Python, 106 linesplot_tools.py - cemrg_heartbuilder/
simulation/ , Python, 39 lines, 1 matchscripts/ basic_extract_ep_output. py - cemrg_heartbuilder/
simulation/ , Python, 154 linesscripts/ basic_report.py - cemrg_heartbuilder/
simulation/ , Python, 53 linesscripts/ create_activation_video. py - cemrg_heartbuilder/
simulation/ , Python, 37 linesscripts/ create_submission_files. py - cemrg_heartbuilder/
simulation/ , Python, 26 linesscripts/ export_to_gif.py - cemrg_heartbuilder/
simulation/ , Python, 73 linesscripts/ extract_mechanics_output .py - cemrg_heartbuilder/
simulation/ , Python, 48 linesscripts/ extract_simulation_outpu t.py - cemrg_heartbuilder/
simulation/ , Python, 85 linesscripts/ simple_report.py - cemrg_heartbuilder/
simulation/ , Python, 325 lines, 1 matchtoolbox.py - examples/
calculate_summary_of_com , Python, 100 linesparisons.py - examples/
comprehensive_analysis.p , Python, 344 lines, 2 matchesy - examples/
plot_activation_times.py , Python, 76 lines - examples/
plot_cardiac_distributio , Python, 219 lines, 2 matchesns.py - examples/
plot_cardiac_effects.py , Python, 336 lines - examples/
plot_summary_of_results. , Python, 82 linespy - heartbuilder.py, Python, 37 lines
- helper_sh/
convert_to_inr.sh , Shell, 36 lines - helper_sh/
update_template_points.s , Shell, 56 linesh - optional_scripts.py, Python, 48 lines
- report-quick-run.sh, Shell, 44 lines
- segmt-quick-run.sh, Shell, 24 lines
- setup.sh, Shell, 24 lines
- shell_scripts/
00-segmt-pad_image.sh , Shell, 36 lines - shell_scripts/
01-segmt-create_cylinder , Shell, 33 liness.sh - shell_scripts/
02-segmt-create_svc_ivc. , Shell, 31 linessh - shell_scripts/
03-segmt-cut_vessels.sh , Shell, 31 lines - shell_scripts/
04-segmt-create_myocardi , Shell, 33 linesum.sh - shell_scripts/
05-segmt-create_valve_pl , Shell, 32 linesanes.sh - shell_scripts/
06-segmt-clean_segmentat , Shell, 36 linesion.sh - shell_scripts/
07-segmt-smooth_segmenta , Shell, 36 linestion.sh - shell_scripts/
08-meshg-cgal_meshing.sh , Shell, 48 lines - shell_scripts/
09-meshg-extract_myocard , Shell, 43 linesium.sh - shell_scripts/
10-meshg-mesh_verificati , Shell, 25 lineson.sh - shell_scripts/
11-meshg-setup_model_par , Shell, 21 linesameters.sh - shell_scripts/
12-model-extract_surfs.s , Shell, 32 linesh - shell_scripts/
13-model-calculate_UVCs. , Shell, 31 linessh - shell_scripts/
14-model-add_vent_fibres , Shell, 42 lines.sh - shell_scripts/
15-model-create_surfaces , Shell, 35 lines_endo_landmarks.sh - shell_scripts/
16-model-la_4ch_endo.sh , Shell, 96 lines - shell_scripts/
17-model-ra_4ch_endo.sh , Shell, 111 lines - shell_scripts/
18-model-map_2d_to_3d.sh , Shell, 86 lines - shell_scripts/
19-model-define_tags.sh , Shell, 31 lines - shell_scripts/
20-model-create_electrod , Shell, 21 lineses.sh - shell_scripts/
21-model-extract_surfs.s , Shell, 35 linesh - shell_scripts/
22-model-split_fec.sh , Shell, 27 lines - tests/
__init__.py , Python, 1 line - LICENSE, License, 1 line
- README.md, Text, 50 lines
Zenodo 4593739
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
- 27 September 2026: the link answers (HTTP 200)
The paper's code and data availability statement is in the Data section.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
- 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 124 scripts, each with its path and the digest of its content;
- 11 matches between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
No dataset and no data link were found in the paper.
Code and data availability statement
The paper has a code and data availability statement. Its license (none stated) does not allow reproducing it here; in short, from what the harvester recognized in it:
- it points to the authors' code: OpenHeartDevelopers/
cemrg-heartbuilder
Read it in the paper: doi.org/10.1371/journal.pcbi.1014325.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 17 authors, 12 MeSH terms, 2 funders, 63 references.
Cite
This paper
Solís-Lemus, J. A., Barrows, R. K., Rodero, C., Strocchi, M., Montarello, N., Lahoti, N., Corrado, C., Qayyum, A., Rahmani, S., Roney, C., Plank, G., Augustin, C., Xu, H., Young, A., Pathmanathan, P., Rajani, R., & Niederer, S. A. (2026). Assessing the importance of sex and disease-specific anatomy in electrophysiology and mechanical simulations with a newly developed public virtual cohort of four-chamber heart models. PLoS computational biology, 22(6), e1014325. https://
BibTeX
@article{solislemus2026a
author = {Solís-Lemus, José Alonso and Barrows, Rosie K and Rodero, Cristobal and Strocchi, Marina and Montarello, Natalie and Lahoti, Nishant and Corrado, Cesare and Qayyum, Abdul and Rahmani, Shahrokh and Roney, Caroline and Plank, Gernot and Augustin, Christoph and Xu, Hao and Young, Alistair and Pathmanathan, Pras and Rajani, Ronak and Niederer, Steven A},
title = {{Assessing the importance of sex and disease-specific anatomy in electrophysiology and mechanical simulations with a newly developed public virtual cohort of four-chamber heart models}},
journal = {PLoS computational biology},
year = {2026},
month = jun,
volume = {22},
number = {6},
pages = {e1014325},
publisher = {PLOS},
issn = {1553-734X},
doi = {10.1371/
url = {https://
pmid = {42228749},
pmcid = {PMC13252842}
}
RIS
TY - JOUR
AU - Solís-Lemus, José Alonso
AU - Barrows, Rosie K
AU - Rodero, Cristobal
AU - Strocchi, Marina
AU - Montarello, Natalie
AU - Lahoti, Nishant
AU - Corrado, Cesare
AU - Qayyum, Abdul
AU - Rahmani, Shahrokh
AU - Roney, Caroline
AU - Plank, Gernot
AU - Augustin, Christoph
AU - Xu, Hao
AU - Young, Alistair
AU - Pathmanathan, Pras
AU - Rajani, Ronak
AU - Niederer, Steven A
TI - Assessing the importance of sex and disease-specific anatomy in electrophysiology and mechanical simulations with a newly developed public virtual cohort of four-chamber heart models
T2 - PLoS computational biology
J2 - PLoS Comput Biol
PY - 2026
DA - 2026/
VL - 22
IS - 6
SP - e1014325
SN - 1553-734X
PB - PLOS
DO - 10.1371/
UR - https://
LA - en
ER -
CSL-JSON
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