├── .gitattributes ├── .github └── workflows │ ├── python-package.yml │ └── python-publish.yml ├── .gitignore ├── LICENSE ├── README.md ├── data ├── C4.swc ├── EC3-60126.CNG.swc ├── EC3-80604.CNG.rotated.swc ├── EC3-80604.CNG.swc ├── Image001-005-01.CNG.swc ├── Image001-005_01_CNenhance_latest_LXS.swc ├── V1_Layer23_Chat-IRES-Cre-neo_Ai14-299537.04.02.01_614430666_m.swc ├── density.conf ├── empty_file.swc ├── sample.swc ├── sample_doublet_point.swc ├── sample_no_root.swc ├── sample_three_soma_points.swc ├── sm090918b1-3_idA_-_Scale_x1.000_y1.025_z1.000_commata_in_swc.swc ├── test_neuron.swc ├── test_neuron2.swc ├── test_neuron_disconnected.swc └── test_neuron_undefined_type.swc ├── docs ├── Makefile ├── command.rst ├── computation.rst ├── conf.py ├── feature_presentation.rst ├── file_manager.rst ├── index.rst ├── make.bat ├── morphopy.rst ├── neuron.rst ├── neurontree.rst ├── persistence_functions.rst ├── plotting.rst └── utils.rst ├── morphopy ├── MorphoPy.py ├── __init__.py ├── about │ └── __init__.py ├── computation │ ├── __init__.py │ ├── feature_presentation.py │ ├── file_manager.py │ └── persistence_functions.py └── neurontree │ ├── NeuronTree.py │ ├── __init__.py │ ├── plotting.py │ └── utils.py ├── notebooks ├── Compare NeuroM and MorphoPy.ipynb ├── MORPHOPY Tutorial.ipynb └── persistence_test │ ├── Compare persistence implementations of TMD with MorphoPy.ipynb │ ├── create_persistence_diagrams_using_tmd.py │ ├── data │ ├── C010398B-P2.CNG.swc │ ├── C4.swc │ ├── ds_1_cell_390.swc │ ├── eNGC-j140908b_cell1.swc │ └── test_neuron.swc │ └── diagrams │ ├── C010398B-P2_path_distances.txt │ ├── C010398B-P2_projection.txt │ ├── C010398B-P2_radial_distances.txt │ ├── C010398B-P2_section_branch_orders.txt │ ├── C4_path_distances.txt │ ├── C4_projection.txt │ ├── C4_radial_distances.txt │ ├── C4_section_branch_orders.txt │ ├── ds_1_cell_390_path_distances.txt │ ├── ds_1_cell_390_projection.txt │ ├── ds_1_cell_390_radial_distances.txt │ ├── ds_1_cell_390_section_branch_orders.txt │ ├── eNGC-j140908b_cell1_path_distances.txt │ ├── eNGC-j140908b_cell1_projection.txt │ ├── eNGC-j140908b_cell1_radial_distances.txt │ ├── eNGC-j140908b_cell1_section_branch_orders.txt │ ├── test_neuron2_path_distances.txt │ ├── test_neuron2_projection.txt │ ├── test_neuron2_radial_distances.txt │ ├── test_neuron2_section_branch_orders.txt │ ├── test_neuron_path_distances.txt │ ├── test_neuron_projection.txt │ ├── test_neuron_radial_distances.txt │ └── test_neuron_section_branch_orders.txt ├── paper ├── figures │ ├── 2D_morph_dist.png │ ├── 2D_morph_dist_small.png │ ├── Fig1_attributes_small.png │ ├── density_map_smoothing.png │ ├── fig_morphometrics.png │ └── threeview_dendrites.png ├── morphopy.bib └── paper.md ├── pyproject.toml ├── tests ├── test_data │ ├── C4.swc_density.mat │ ├── EC3-80604.CNG.rotated.swc_density.mat │ ├── Image001-005_01_CNenhance_latest_LXS.swc_density.mat │ ├── 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