├── .gitignore ├── AUTHORS.md ├── LICENSE ├── README.md ├── __init__.py ├── biovis24.cfg ├── data ├── em-spines-morphologies │ ├── 1.spine │ ├── 10.spine │ ├── 11.spine │ ├── 12.spine │ ├── 13.spine │ ├── 14.spine │ ├── 15.spine │ ├── 16.spine │ ├── 17.spine │ ├── 18.spine │ ├── 19.spine │ ├── 2.spine │ ├── 20.spine │ ├── 21.spine │ ├── 22.spine │ ├── 23.spine │ ├── 24.spine │ ├── 25.spine │ ├── 27.spine │ ├── 28.spine │ ├── 29.spine │ ├── 3.spine │ ├── 30.spine │ ├── 31.spine │ ├── 32.spine │ ├── 33.spine │ ├── 34.spine │ ├── 35.spine │ ├── 36.spine │ ├── 37.spine │ ├── 38.spine │ ├── 39.spine │ ├── 4.spine │ ├── 40.spine │ ├── 41.spine │ ├── 42.spine │ ├── 43.spine │ ├── 44.spine │ ├── 5.spine │ ├── 6.spine │ ├── 7.spine │ ├── 8.spine │ └── 9.spine ├── fonts │ ├── Arial.ttf │ ├── NimbusSanL-Bold.ttf │ ├── NimbusSanL-BoldCond.ttf │ ├── NimbusSanL-BoldCondItal.ttf │ ├── NimbusSanL-BoldItal.ttf │ ├── NimbusSanL-Regu.ttf │ ├── NimbusSanL-ReguCond.ttf │ ├── NimbusSanL-ReguCondItal.ttf │ └── NimbusSanL-ReguItal.ttf ├── images │ ├── bbp-logo.png │ ├── epfl-logo.png │ ├── github-logo.png │ └── nmv-logo.png ├── morphologies │ ├── h5 │ │ └── C010398B-I4_cor_-_Scale_x1.000_y1.050_z1.000_-_Clone_5.h5 │ └── swc │ │ ├── C031097B-I4.CNG.swc │ │ ├── C040600B3.CNG.swc │ │ ├── C080400A3.CNG.swc │ │ └── C220498B-I4.CNG.swc ├── nuclei-meshes │ ├── hq │ │ ├── nucleus-1.mtl │ │ ├── nucleus-1.obj │ │ ├── nucleus-2.mtl │ │ ├── nucleus-2.obj │ │ ├── nucleus-3.mtl │ │ ├── nucleus-3.obj │ │ ├── nucleus-4.mtl │ │ └── nucleus-4.obj │ └── lq │ │ ├── nucleus-1.mtl │ │ ├── nucleus-1.obj │ │ ├── nucleus-2.mtl │ │ ├── nucleus-2.obj │ │ ├── nucleus-3.mtl │ │ ├── nucleus-3.obj │ │ ├── nucleus-4.mtl │ │ └── nucleus-4.obj ├── nuclei-modeling │ └── nuclei-modeling.blend ├── simple-spines-morphologies │ ├── 1.spine │ ├── 2.spine │ ├── 3.spine │ ├── 4.spine │ ├── 5.spine │ ├── 6.spine │ ├── 7.spine │ ├── 8.spine │ └── 9.spine ├── spines-meshes │ ├── hq │ │ ├── nmv_spine_0.obj │ │ ├── nmv_spine_1.obj │ │ ├── nmv_spine_10.obj │ │ ├── nmv_spine_11.obj │ │ ├── nmv_spine_12.obj │ │ ├── nmv_spine_13.obj │ │ ├── nmv_spine_14.obj │ │ ├── nmv_spine_15.obj │ │ ├── nmv_spine_16.obj │ │ ├── nmv_spine_17.obj │ │ ├── nmv_spine_18.obj │ │ ├── nmv_spine_19.obj │ │ ├── nmv_spine_2.obj │ │ ├── nmv_spine_20.obj │ │ ├── nmv_spine_21.obj │ │ ├── nmv_spine_22.obj │ │ ├── nmv_spine_23.obj │ │ ├── nmv_spine_24.obj │ │ ├── nmv_spine_25.obj │ │ ├── nmv_spine_26.obj │ │ ├── nmv_spine_27.obj │ │ ├── nmv_spine_28.obj │ │ ├── nmv_spine_29.obj │ │ ├── nmv_spine_3.obj │ │ ├── nmv_spine_30.obj │ │ ├── nmv_spine_31.obj │ │ ├── nmv_spine_32.obj │ │ ├── nmv_spine_33.obj │ │ ├── nmv_spine_34.obj │ │ ├── nmv_spine_35.obj │ │ ├── nmv_spine_4.obj │ │ ├── nmv_spine_5.obj │ │ ├── nmv_spine_6.obj │ │ ├── nmv_spine_7.obj │ │ ├── nmv_spine_8.obj │ │ ├── nmv_spine_9.obj │ │ └── tip.obj │ └── lq │ │ ├── nmv_spine_0.obj │ │ ├── nmv_spine_1.obj │ │ ├── nmv_spine_10.obj │ │ ├── nmv_spine_11.obj │ │ ├── nmv_spine_12.obj │ │ ├── nmv_spine_13.obj │ │ ├── nmv_spine_14.obj │ │ ├── nmv_spine_15.obj │ │ ├── nmv_spine_16.obj │ │ ├── nmv_spine_17.obj │ │ ├── nmv_spine_18.obj │ │ ├── nmv_spine_19.obj │ │ ├── nmv_spine_2.obj │ │ ├── nmv_spine_20.obj │ │ ├── nmv_spine_21.obj │ │ ├── nmv_spine_22.obj │ │ ├── nmv_spine_23.obj │ │ ├── nmv_spine_24.obj │ │ ├── nmv_spine_25.obj │ │ ├── nmv_spine_26.obj │ │ ├── nmv_spine_27.obj │ │ ├── nmv_spine_28.obj │ │ ├── nmv_spine_29.obj │ │ ├── nmv_spine_3.obj │ │ ├── nmv_spine_30.obj │ │ ├── nmv_spine_31.obj │ │ ├── nmv_spine_32.obj │ │ ├── nmv_spine_33.obj │ │ ├── nmv_spine_34.obj │ │ ├── nmv_spine_35.obj │ │ ├── nmv_spine_4.obj │ │ ├── nmv_spine_5.obj │ │ ├── nmv_spine_6.obj │ │ ├── nmv_spine_7.obj │ │ ├── nmv_spine_8.obj │ │ ├── nmv_spine_9.obj │ │ └── tip.obj ├── spines-modeling │ ├── spines-modeling-1.blend │ └── spines-modeling-2.blend └── spines-morphologies │ ├── 1.spine │ ├── 10.spine │ ├── 11.spine │ ├── 12.spine │ ├── 13.spine │ ├── 14.spine │ ├── 15.spine │ ├── 16.spine │ ├── 17.spine │ ├── 18.spine │ ├── 19.spine │ ├── 2.spine │ ├── 20.spine │ ├── 21.spine │ ├── 22.spine │ ├── 23.spine │ ├── 24.spine │ ├── 25.spine │ ├── 27.spine │ ├── 28.spine │ ├── 29.spine │ ├── 3.spine │ ├── 30.spine │ ├── 31.spine │ ├── 32.spine │ ├── 33.spine │ ├── 34.spine │ ├── 35.spine │ ├── 36.spine │ ├── 37.spine │ ├── 38.spine │ ├── 39.spine │ ├── 4.spine │ ├── 40.spine │ ├── 41.spine │ ├── 42.spine │ ├── 43.spine │ ├── 44.spine │ ├── 5.spine │ ├── 6.spine │ ├── 7.spine │ ├── 8.spine │ └── 9.spine ├── deps └── omesh │ ├── CMakeLists.txt │ ├── README.md │ ├── setup.cfg │ ├── setup.py │ ├── setup.sh │ └── src │ ├── BMesh.hpp │ ├── Common.hh │ ├── EigenValue.hpp │ ├── EigenVector.hpp │ ├── NeighborPoint3.hpp │ ├── Neighbour.hpp │ ├── Normal.hpp │ ├── OptimizationMesh.cpp │ ├── OptimizationMesh.hh │ ├── PyInterface.cpp │ ├── Timer.hpp │ ├── Triangle.hpp │ └── Vertex.hpp ├── neuromorphovis.cfg ├── neuromorphovis.py ├── neuromorphovis.sh ├── nmv ├── __init__.py ├── analysis │ ├── __init__.py │ ├── analysis_distributions.py │ ├── analysis_items.py │ ├── kernels │ │ ├── __init__.py │ │ ├── arbor │ │ │ ├── __init__.py │ │ │ ├── angle_ops.py │ │ │ ├── area_ops.py │ │ │ ├── lengths_ops.py │ │ │ ├── samples_ops.py │ │ │ ├── structure_ops.py │ │ │ └── volume_ops.py │ │ ├── distributions.py │ │ ├── functional.py │ │ ├── morphology │ │ │ ├── __init__.py │ │ │ ├── angle_ops.py │ │ │ ├── area_ops.py │ │ │ ├── common.py │ │ │ ├── global_ops.py │ │ │ ├── lengths_ops.py │ │ │ ├── samples_ops.py │ │ │ ├── soma_ops.py │ │ │ ├── structure_ops.py │ │ │ └── volume_ops.py │ │ └── section │ │ │ ├── __init__.py │ │ │ ├── angle_ops.py │ │ │ ├── area_ops.py │ │ │ ├── lengths_ops.py │ │ │ ├── samples_ops.py │ │ │ └── volume_ops.py │ ├── plotting │ │ ├── __init__.py │ │ ├── distributions.py │ │ ├── ops.py │ │ └── options.py │ ├── stats │ │ ├── __init__.py │ │ ├── arbor.py │ │ ├── morphology.py │ │ └── section.py │ └── structs │ │ ├── __init__.py │ │ ├── analysis_data.py │ │ ├── analysis_distribution.py │ │ ├── analysis_item.py │ │ └── morphology_analysis_result.py ├── bbox │ ├── __init__.py │ ├── bounding_box.py │ └── ops.py ├── bbp │ ├── __init__.py │ ├── bbp_circuit.py │ ├── circuit.py │ ├── circuits.py │ ├── libsonata_circuit.py │ ├── neurons.py │ ├── spines.py │ ├── synapse_group.py │ ├── synapses.py │ ├── synapses_color_coding.py │ ├── synapses_generation.py │ ├── synapses_visualization.py │ └── transformations.py ├── bmeshi │ ├── __init__.py │ ├── objects │ │ ├── __init__.py │ │ └── bmesh_objects.py │ └── ops │ │ ├── __init__.py │ │ ├── bmesh_face_ops.py │ │ ├── bmesh_object_ops.py │ │ ├── bmesh_vertex_ops.py │ │ └── watertightness.py ├── bpys │ ├── __init__.py │ ├── curve_add.py │ ├── data_ops.py │ ├── mesh_add.py │ ├── mesh_ops.py │ └── object_ops.py ├── builders │ ├── __init__.py │ ├── mesh │ │ ├── __init__.py │ │ ├── base.py │ │ ├── common.py │ │ ├── meta_builder.py │ │ ├── piecewise_builder.py │ │ ├── skinning_builder.py │ │ ├── union_builder.py │ │ └── voxelization_builder.py │ ├── morphology │ │ ├── __init__.py │ │ ├── base.py │ │ ├── connected_sections_builder.py │ │ ├── dendrogram_builder.py │ │ ├── disconnected_sections_builder.py │ │ ├── disconnected_segments_builder.py │ │ ├── progressive_builder.py │ │ └── samples_builder.py │ ├── nucleus │ │ ├── __init__.py │ │ └── nucleus_builder.py │ ├── soma │ │ ├── __init__.py │ │ ├── soma_hybrid_builder.py │ │ ├── soma_meta_builder.py │ │ └── soma_softbody_builder.py │ └── spine │ │ ├── __init__.py │ │ ├── circuit_spine_builder.py │ │ ├── random_spine_builder.py │ │ ├── random_spine_builder_from_morphology.py │ │ └── spine_builder.py ├── consts │ ├── __init__.py │ ├── analysis_consts.py │ ├── circuit_consts.py │ ├── color_consts.py │ ├── dendrogram_consts.py │ ├── drawing_consts.py │ ├── geometry_conts.py │ ├── image_consts.py │ ├── math_consts.py │ ├── meshing_consts.py │ ├── messages_consts.py │ ├── meta_ball_consts.py │ ├── morphology_consts.py │ ├── mtypes_consts.py │ ├── paths_consts.py │ ├── simulation_consts.py │ ├── skeleton_consts.py │ ├── soft_body_consts.py │ ├── spines_consts.py │ ├── string_consts.py │ ├── suffix_consts.py │ └── synaptics_consts.py ├── edit │ ├── __init__.py │ └── morphology_editor.py ├── enums │ ├── __init__.py │ ├── analysis_enums.py │ ├── camera_enums.py │ ├── color_coding_enums.py │ ├── color_enums.py │ ├── colormaps_enums.py │ ├── dendrogram_enums.py │ ├── image_enums.py │ ├── input_enums.py │ ├── meshing_enums.py │ ├── morphology_enums.py │ ├── rendering_enums.py │ ├── shading_enums.py │ ├── skeleton_enums.py │ ├── soma_enums.py │ └── synaptics_enums.py ├── file │ ├── __init__.py │ ├── logger.py │ ├── ops │ │ ├── __init__.py │ │ └── file_ops.py │ ├── readers │ │ ├── __init__.py │ │ ├── configs │ │ │ ├── __init__.py │ │ │ └── rendere_config.py │ │ ├── mesh │ │ │ ├── __init__.py │ │ │ └── importers.py │ │ ├── morphology │ │ │ ├── __init__.py │ │ │ ├── bbp_reader.py │ │ │ ├── common.py │ │ │ ├── h5_reader.py │ │ │ ├── morphio_reader.py │ │ │ ├── morphology_reader.py │ │ │ └── swc_reader.py │ │ ├── nuclei │ │ │ ├── __init__.py │ │ │ └── nuclei_reader.py │ │ ├── spines │ │ │ ├── __init__.py │ │ │ └── spines_reader.py │ │ └── tetrahedal │ │ │ ├── __init__.py │ │ │ ├── quartet_reader.py │ │ │ └── tetgen_reader.py │ └── writers │ │ ├── __init__.py │ │ ├── mesh │ │ ├── __init__.py │ │ └── exporters.py │ │ ├── morphology │ │ ├── __init__.py │ │ ├── segments_writer.py │ │ └── swc_writer.py │ │ └── strings │ │ ├── __init__.py │ │ └── strings.py ├── geometry │ ├── __init__.py │ ├── object │ │ ├── __init__.py │ │ ├── curve.py │ │ ├── line.py │ │ ├── particle_system.py │ │ ├── poly_line.py │ │ ├── sphere.py │ │ └── vertex.py │ └── ops │ │ ├── __init__.py │ │ ├── clipping.py │ │ ├── intersection.py │ │ ├── line_ops.py │ │ ├── poly_line_ops.py │ │ └── sphere_ops.py ├── helpers │ └── rgb-to-hex.py ├── interface │ ├── __init__.py │ ├── cli │ │ ├── __init__.py │ │ ├── args_strings.py │ │ ├── arguments_parser.py │ │ ├── common.py │ │ ├── morphology_analysis.py │ │ ├── neuron_mesh_reconstruction.py │ │ ├── neuron_morphology_reconstruction.py │ │ ├── options_parser.py │ │ └── soma_reconstruction.py │ ├── common │ │ ├── __init__.py │ │ ├── file_ops.py │ │ ├── rendering_ops.py │ │ └── suffix_ops.py │ ├── ui │ │ ├── __init__.py │ │ ├── about │ │ │ ├── __init__.py │ │ │ ├── about_panel.py │ │ │ ├── layout_props.py │ │ │ ├── ops.py │ │ │ ├── panel.py │ │ │ └── registration.py │ │ ├── analysis │ │ │ ├── __init__.py │ │ │ ├── analysis_panel.py │ │ │ ├── analysis_panel_ops.py │ │ │ ├── analysis_panel_options.py │ │ │ ├── layout_props.py │ │ │ ├── ops_export.py │ │ │ ├── panel.py │ │ │ ├── panel_ops.py │ │ │ ├── panel_props.py │ │ │ └── registration.py │ │ ├── common.py │ │ ├── common │ │ │ ├── __init__.py │ │ │ ├── commonxx.py │ │ │ ├── file_system_ops.py │ │ │ ├── fonts_ops.py │ │ │ ├── icons_ops.py │ │ │ ├── layout_rendering_props.py │ │ │ ├── ops_documentation.py │ │ │ ├── rendering_operators.py │ │ │ ├── rendering_ops.py │ │ │ └── rendering_options.py │ │ ├── data.py │ │ ├── edit │ │ │ ├── __init__.py │ │ │ ├── edit_panel.py │ │ │ ├── layout_props.py │ │ │ ├── ops_documentation.py │ │ │ ├── ops_edit.py │ │ │ ├── ops_export.py │ │ │ ├── panel.py │ │ │ └── registration.py │ │ ├── globals.py │ │ ├── io │ │ │ ├── __init__.py │ │ │ ├── layout_props.py │ │ │ ├── ops.py │ │ │ ├── panel.py │ │ │ ├── panel_props.py │ │ │ └── registration.py │ │ ├── mesh │ │ │ ├── __init__.py │ │ │ ├── layout_buttons.py │ │ │ ├── layout_color_props.py │ │ │ ├── layout_reconstruction_props.py │ │ │ ├── layout_rendering_props.py │ │ │ ├── mesh_panel.py │ │ │ ├── mesh_panel_ops.py │ │ │ ├── mesh_panel_options.py │ │ │ ├── ops_documentation.py │ │ │ ├── ops_exports.py │ │ │ ├── ops_reconstruction.py │ │ │ ├── ops_render_360.py │ │ │ ├── ops_render_view.py │ │ │ ├── panel.py │ │ │ ├── panel_props.py │ │ │ └── registration.py │ │ ├── morphology │ │ │ ├── __init__.py │ │ │ ├── layout_buttons.py │ │ │ ├── layout_color_props.py │ │ │ ├── layout_reconstruction_props.py │ │ │ ├── layout_rendering_props.py │ │ │ ├── layout_skeleton_props.py │ │ │ ├── morphology_panel.py │ │ │ ├── morphology_panel_color_ops.py │ │ │ ├── morphology_panel_ops.py │ │ │ ├── morphology_panel_options.py │ │ │ ├── ops_documentation.py │ │ │ ├── ops_exports.py │ │ │ ├── ops_reconstruction.py │ │ │ ├── ops_render_360.py │ │ │ ├── ops_render_progressive.py │ │ │ ├── ops_render_view.py │ │ │ ├── panel.py │ │ │ ├── panel_props.py │ │ │ └── registration.py │ │ ├── soma │ │ │ ├── __init__.py │ │ │ ├── layout_buttons.py │ │ │ ├── layout_color_props.py │ │ │ ├── layout_reconstruction_props.py │ │ │ ├── layout_rendering_props.py │ │ │ ├── ops_documentation.py │ │ │ ├── ops_export.py │ │ │ ├── ops_reconstruction.py │ │ │ ├── ops_render_360.py │ │ │ ├── ops_render_progressive.py │ │ │ ├── ops_render_view.py │ │ │ ├── panel.py │ │ │ ├── panel_props.py │ │ │ ├── registration.py │ │ │ ├── soma_panel.py │ │ │ ├── soma_panel_ops.py │ │ │ └── soma_panel_options.py │ │ ├── synaptics │ │ │ ├── __init__.py │ │ │ ├── layout_neuron_props.py │ │ │ ├── layout_props.py │ │ │ ├── layout_rendering_props.py │ │ │ ├── layout_synapses_props.py │ │ │ ├── ops_reconstruction.py │ │ │ ├── ops_rendering.py │ │ │ ├── panel.py │ │ │ ├── panel_props.py │ │ │ └── registration.py │ │ └── ui_globals.py │ └── utilities │ │ ├── __init__.py │ │ ├── colormap.py │ │ ├── scale_bar.py │ │ └── text.py ├── mesh │ ├── __init__.py │ ├── objects │ │ ├── __init__.py │ │ └── mesh_objects.py │ └── ops │ │ ├── __init__.py │ │ ├── mesh_analysis.py │ │ ├── mesh_bounding_box.py │ │ ├── mesh_cleaning_ops.py │ │ ├── mesh_face_ops.py │ │ ├── mesh_object_ops.py │ │ ├── mesh_optimization.py │ │ └── mesh_vertex_ops.py ├── neurorender │ ├── __init__.py │ ├── neuron.py │ └── neurorender.py ├── options │ ├── __init__.py │ ├── io_options.py │ ├── mesh_options.py │ ├── morphology_options.py │ ├── neuromorphovis_options.py │ ├── rendering_options.py │ ├── shading_options.py │ ├── soma_options.py │ └── synaptics_options.py ├── physics │ ├── __init__.py │ ├── hook │ │ ├── __init__.py │ │ └── ops │ │ │ ├── __init__.py │ │ │ └── hook_ops.py │ ├── particel_system │ │ ├── __init__.py │ │ ├── drawing.py │ │ ├── field.py │ │ ├── particle.py │ │ ├── particle_remesher.py │ │ ├── spatial_hash.py │ │ ├── surface_particle_system.py │ │ └── utilities.py │ └── soft_body │ │ ├── __init__.py │ │ └── ops │ │ ├── __init__.py │ │ └── soft_body_ops.py ├── rendering │ ├── __init__.py │ ├── camera │ │ ├── __init__.py │ │ └── camera.py │ ├── ops │ │ ├── __init__.py │ │ └── rendering_ops.py │ ├── renderes │ │ ├── __init__.py │ │ ├── mesh_renderer.py │ │ ├── renderer.py │ │ ├── skeleton_renderer.py │ │ └── soma_renderer.py │ └── scale_bar.py ├── scene │ ├── __init__.py │ └── ops │ │ ├── __init__.py │ │ └── scene_ops.py ├── shading │ ├── __init__.py │ ├── illumination.py │ ├── materials.py │ └── shaders │ │ ├── background.blend │ │ ├── cracks.blend │ │ ├── diffuse.blend │ │ ├── eevee-sss.blend │ │ ├── electron-dark-material.blend │ │ ├── electron-light-material.blend │ │ ├── flat-material.blend │ │ ├── flat-transparent-material.blend │ │ ├── glossy-blending.blend │ │ ├── glossy-bumpy.blend │ │ ├── glossy.blend │ │ ├── granular.blend │ │ ├── grid.blend │ │ ├── neuron-shading.blend │ │ ├── plastic.blend │ │ ├── principled.blend │ │ ├── shadow-material.blend │ │ ├── super-electron-dark-material.blend │ │ ├── super-electron-light-material.blend │ │ ├── voronoi-cells.blend │ │ ├── wave.blend │ │ ├── wax.blend │ │ ├── wire-frame.blend │ │ ├── wireframe-electron.blend │ │ └── wireframe.blend ├── simulation │ ├── __init__.py │ ├── colormap.py │ └── simulation_mesh_renderer.py ├── skeleton │ ├── __init__.py │ ├── ops │ │ ├── __init__.py │ │ ├── skeleton_analysis_ops.py │ │ ├── skeleton_branching_ops.py │ │ ├── skeleton_coloring_ops.py │ │ ├── skeleton_connection_ops.py │ │ ├── skeleton_construction_ops.py │ │ ├── skeleton_dendrogram_ops.py │ │ ├── skeleton_drawing_ops.py │ │ ├── skeleton_generic_ops.py │ │ ├── skeleton_geometry_ops.py │ │ ├── skeleton_intersection_ops.py │ │ ├── skeleton_polylines_ops.py │ │ ├── skeleton_radius_alternation_ops.py │ │ ├── skeleton_repair_ops.py │ │ ├── skeleton_resampling_ops.py │ │ ├── skeleton_soma_ops.py │ │ ├── skeleton_spiny_ops.py │ │ ├── skeleton_style_ops.py │ │ └── skeleton_verification_ops.py │ └── structure │ │ ├── __init__.py │ │ ├── endfoot.py │ │ ├── morphology.py │ │ ├── random_spine.py │ │ ├── sample.py │ │ ├── section.py │ │ ├── soma.py │ │ ├── spine.py │ │ └── spine_morphology.py ├── slurm │ ├── slurm.py │ └── slurm_configuration.py └── utilities │ ├── __init__.py │ ├── auxiliary.py │ ├── collections.py │ ├── colors.py │ ├── get_pip.py │ ├── installation.py │ ├── parser.py │ ├── std_output.py │ ├── system.py │ ├── time_line.py │ ├── timer.py │ └── version.py ├── scripts ├── analysis-plots │ ├── analyze-morphology.py │ ├── analyze-morphology.sh │ └── create-aio-analysis-plots.py ├── astrocyte-collage │ ├── astrocytes-collage.py │ └── astrocytes-morphology-collage.py ├── astrocyte-reconstruction │ ├── README.md │ ├── astro_meta_builder.py │ ├── astrocyte_data.py │ ├── astrocyte_generator.py │ ├── gids │ ├── run.py │ └── run.sh ├── astrocytes-rendering │ ├── fonts │ │ ├── NimbusSanL-Bold.ttf │ │ ├── NimbusSanL-BoldCond.ttf │ │ ├── NimbusSanL-BoldCondItal.ttf │ │ ├── NimbusSanL-BoldItal.ttf │ │ ├── NimbusSanL-Regu.ttf │ │ ├── NimbusSanL-ReguCond.ttf │ │ ├── NimbusSanL-ReguCondItal.ttf │ │ └── NimbusSanL-ReguItal.ttf │ ├── plot-distribution.py │ ├── plot-distributions.py │ ├── plotting.py │ ├── render-astrocyte.py │ └── render-astrocyte.sh ├── brava-swc-to-h5 │ ├── BG001.CNG.swc │ └── converter.blend ├── circuit-renderer │ ├── circuit-overlaid-renderer.sh │ ├── circuit-renderer.py │ ├── circuit-renderer.sh │ ├── compose-images.py │ └── core │ │ ├── morphology.py │ │ ├── rendering.py │ │ ├── sonata.py │ │ └── utilities.py ├── efferent-synapses-on-axon │ └── efferent-synapses-on-axon.blend ├── mesh-analysis │ ├── analysis_input_vs_optimized.py │ ├── analysis_input_vs_watertight.py │ ├── analysis_step_by_step.py │ ├── analyze-mesh.py │ ├── create-analysis-plot.py │ ├── create-analysis-plot.sh │ ├── create-analysis-plots.py │ ├── create-analysis-plots.sh │ ├── create-input-vs-watertight-histograms.py │ ├── create-input-vs-watertight-histograms.sh │ ├── create-original-vs-optimized-histograms-for-mesh.py │ ├── create-original-vs-optimized-histograms-for-meshes.py │ ├── create-original-vs-optimized-histograms-for-meshes.sh │ ├── create-step-by-step-histograms.py │ ├── create-step-by-step-histograms.sh │ ├── examples │ │ ├── plot-heatmap.py │ │ └── plot-histogram.py │ ├── fact_sheet.py │ ├── fonts │ │ ├── 1H.otf │ │ ├── Arial.ttf │ │ ├── HelveticaLt.ttf │ │ ├── HelveticaLtObl.ttf │ │ ├── NimbusSanL-Bold.ttf │ │ ├── NimbusSanL-BoldCond.ttf │ │ ├── NimbusSanL-Bold_32889.ttf │ │ ├── NimbusSanL-Italic_32890.ttf │ │ ├── NimbusSanL-Regu.otf │ │ ├── NimbusSanL-Regu.ttf │ │ ├── NimbusSanL-ReguCond.ttf │ │ ├── NimbusSanL.ttf │ │ └── NimbusSanL_Bold_Italic.ttf │ ├── hausdorff │ │ ├── compute-hausdorff.py │ │ ├── hausdorff.mlx │ │ └── plot-hausdorff.py │ ├── plot-any-stats.py │ ├── plot-morphology-stats.py │ ├── plot-stats.py │ ├── render-meshes.py │ ├── render-meshes.sh │ └── utilities │ │ ├── data_utilities.py │ │ ├── file_utilities.py │ │ ├── geometry_utils.py │ │ ├── image_utilities.py │ │ ├── mesh_analysis.py │ │ ├── plotting_utils.py │ │ └── rendering_utilities.py ├── misc │ └── remove_vertices.py ├── morphology-collage │ └── render-morphology-collage.py ├── neuro-renderer │ ├── core │ │ ├── loading.py │ │ ├── neuron.py │ │ ├── parsing.py │ │ └── styling.py │ ├── neurorender.py │ ├── neurorender.sh │ └── style.config ├── optimize-meshes │ ├── optimize_mesh.py │ ├── optimize_mesh.sh │ ├── optimize_meshes.py │ └── optimize_meshes.sh ├── remesher │ ├── remesher.py │ ├── run.py │ └── run.sh ├── resampling-morphology │ ├── resample-morphology.py │ └── resample-morphology.sh ├── self-intersections-vs-iterations │ ├── count_self_intersections.py │ ├── count_self_intersections_for_meshes.py │ ├── count_self_intersections_for_meshes.sh │ └── plot_stats.py ├── skeletonization │ ├── analyze_input_mesh.py │ ├── analyze_input_mesh.sh │ ├── analyze_segmented_spines.py │ ├── analyze_segmented_spines.sh │ ├── analyze_skeletonization_artefacts.py │ ├── analyze_skeletonization_artefacts.sh │ ├── branching_artefacts.py │ ├── mesh_analysis.py │ ├── mesh_bounding_box.py │ ├── mesh_exporters.py │ ├── mesh_importers.py │ ├── mesh_partitioning.py │ ├── mesh_rendering.py │ ├── scene_utilities.py │ └── spine_artifacts.py ├── soma-rainbow │ ├── core │ │ ├── color.py │ │ ├── loading.py │ │ ├── neuron.py │ │ ├── parsing.py │ │ └── styling.py │ ├── soma-rainbow.py │ ├── soma-rainbow.sh │ └── style.config ├── synaptics-refactor │ ├── auxiliary │ │ ├── compositor.py │ │ ├── copy-synaptomes.py │ │ ├── create_portal_structure.py │ │ └── create_portal_structure_wo_directories.py │ ├── core │ │ ├── circuit_data.py │ │ ├── color_map.py │ │ ├── font.ttf │ │ ├── neuron_data.py │ │ ├── parsing.py │ │ ├── rendering.py │ │ ├── slurm.py │ │ ├── synaptic_pathways.py │ │ └── synaptome.py │ ├── create-synaptic-pathway.py │ ├── create-synaptic-pathways-cluster.py │ ├── create-synaptic-pathways-cluster.sh │ ├── create-synaptic-pathways.py │ ├── create-synaptic-pathways.sh │ ├── create-synaptic-projection.py │ ├── create-synaptic-projection.sh │ ├── create-synaptome.py │ ├── create-synaptome.sh │ ├── create-synaptomes-cluster-volta.sh │ ├── create-synaptomes-cluster.py │ ├── create-synaptomes-cluster.sh │ ├── create-synaptomes.py │ ├── create-synaptomes.sh │ ├── data │ │ └── ColorMap │ ├── visualize_exc_inh_synapses_on_neuron.py │ ├── visualize_exc_inh_synapses_on_neuron.sh │ ├── visualize_synapses_on_post_synaptic_neuron.py │ └── visualize_synapses_on_post_synaptic_neuron.sh └── synaptics │ ├── auxiliary │ ├── compositor.py │ ├── copy-synaptomes.py │ ├── create_portal_structure.py │ └── create_portal_structure_wo_directories.py │ ├── core │ ├── circuit_data.py │ ├── color_map.py │ ├── font.ttf │ ├── parsing.py │ ├── rendering.py │ ├── slurm.py │ ├── synaptic_pathways.py │ └── synaptome.py │ ├── create-synaptic-pathway.py │ ├── create-synaptic-pathways-cluster.py │ ├── create-synaptic-pathways-cluster.sh │ ├── create-synaptic-pathways.py │ ├── create-synaptic-pathways.sh │ ├── create-synaptic-projection.py │ ├── create-synaptic-projection.sh │ ├── create-synaptome.py │ ├── create-synaptome.sh │ ├── create-synaptomes-cluster-volta.sh │ ├── create-synaptomes-cluster.py │ ├── create-synaptomes-cluster.sh │ ├── create-synaptomes.py │ ├── create-synaptomes.sh │ ├── data │ └── ColorMap │ ├── etype │ ├── post-etypes.colors │ ├── pre-etypes.colors │ ├── visualize_synapses_color_coded_by_post_synaptic_etypes.sh │ ├── visualize_synapses_color_coded_by_pre_synaptic_etypes.sh │ └── visualize_synapses_color_coded_by_x_synaptic_etypes.py │ ├── exc_inh │ ├── visualize_exc_inh_synapses_on_neuron.py │ └── visualize_exc_inh_synapses_on_neuron.sh │ ├── mtype │ ├── post-mtypes.colors │ ├── pre-mtypes.colors │ ├── visualize_synapses_color_coded_by_post_synaptic_mtypes.sh │ ├── visualize_synapses_color_coded_by_pre_synaptic_mtypes.sh │ └── visualize_synapses_color_coded_by_x_synaptic_mtypes.py │ ├── post_synaptic │ ├── visualize_synapses_on_post_synaptic_neuron.py │ └── visualize_synapses_on_post_synaptic_neuron.sh │ └── synaptic_pathway │ ├── visualize_synaptic_pathway.py │ ├── visualize_synaptic_pathway.sh │ ├── visualize_synaptic_pathways.py │ └── visualize_synaptic_pathways.sh ├── setup.py ├── setup ├── deps.txt ├── setup-windows-blender-3.0.bat ├── setup-windows-blender-3.5.bat ├── setup-windows-blender-4.0.bat └── setup-windows-blender-4.2.bat ├── tests ├── bmeshi │ ├── __init__.py │ ├── input_data.py │ ├── test_bmesh_face_ops.py │ ├── test_bmesh_objects.py │ └── 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