├── .gitignore ├── .travis.yml ├── CONTRIBUTING.md ├── LICENSE ├── Makefile ├── README.md ├── apt.txt ├── environment.yml ├── notebooks ├── intro │ ├── DashSynapseExplorer.ipynb │ ├── ImageAndSegmentationDownload.ipynb │ ├── MeshExample.ipynb │ ├── MostSynapsesInAndOut.ipynb │ ├── Render3DScaleBar.ipynb │ └── img │ │ ├── dash_screenshot.png │ │ └── synapse_figure.png ├── mm3_intro │ ├── CAVEsetup.ipynb │ ├── MeshAccess.ipynb │ ├── SynapseAndAnnotationQuery.ipynb │ └── VisualizingSynapsesWithMeshes.ipynb └── vignette_analysis │ ├── function │ ├── README.md │ ├── datajoint_usage_example.ipynb │ ├── dj_conf.json │ ├── figures │ │ ├── function_flowchart.png │ │ └── pinky_schema.png │ ├── lib │ │ ├── __init__.py │ │ ├── calcium.py │ │ ├── data.py │ │ ├── datajoint.py │ │ ├── plot.py │ │ ├── tuning.py │ │ └── utils.py │ ├── orientation_direction_tuning.ipynb │ ├── scripts │ │ ├── compute_degree.py │ │ └── compute_neurite_length.py │ ├── spatial_organization.ipynb │ ├── structure_function_analysis.ipynb │ └── visualize_response.ipynb │ ├── mitochondria │ ├── README.md │ ├── assets │ │ ├── mito.png │ │ └── mito_flowchart.png │ ├── compartment_comparison.ipynb │ ├── distance_to_soma.ipynb │ ├── lib │ │ ├── __init__.py │ │ ├── compartment.py │ │ ├── mesh.py │ │ ├── modelling.py │ │ ├── ngl.py │ │ ├── plot.py │ │ ├── skel.py │ │ └── u.py │ ├── scripts │ │ ├── README.md │ │ ├── assemblemitotoskel.py │ │ ├── branchdiameter.py │ │ ├── branchproximity.py │ │ ├── computebasicbranchstats.py │ │ ├── computedensitystats.py │ │ ├── computeextramitostats.py │ │ ├── computemitolengths.py │ │ ├── derivedata.sh │ │ ├── downloadNeuronMeshes.sh │ │ └── mitotoskel.py │ └── visualize.ipynb │ ├── motifs │ ├── figures │ │ ├── full │ │ │ ├── full_2_scatter.pdf │ │ │ ├── full_2_violin.pdf │ │ │ ├── full_3_scatter.pdf │ │ │ ├── full_3_scatter_CGE.pdf │ │ │ ├── full_3_scatter_GE.pdf │ │ │ ├── full_3_violin.pdf │ │ │ ├── full_3_violin_CGE.pdf │ │ │ ├── full_3_violin_GE.pdf │ │ │ ├── full_3_violin_diff.pdf │ │ │ ├── full_3_violin_diff_GE.pdf │ │ │ ├── full_cnr.pdf │ │ │ ├── full_cnr_CGE.pdf │ │ │ ├── full_cnr_GE.pdf │ │ │ ├── full_degree_distribution.pdf │ │ │ ├── full_degree_distribution_ge.pdf │ │ │ ├── proximity_full_2_violin.pdf │ │ │ ├── proximity_full_somadist_bi_uni.pdf │ │ │ ├── proximity_full_somadist_count.pdf │ │ │ ├── proximity_full_somadist_p.pdf │ │ │ └── proximity_full_somadist_p_bi_uni.pdf │ │ ├── motif_flowchart.png │ │ ├── th0 │ │ │ ├── .ipynb_checkpoints │ │ │ │ └── th0_2_violin-checkpoint.pdf │ │ │ ├── th0_2_scatter.pdf │ │ │ ├── th0_2_violin.pdf │ │ │ ├── th0_3_scatter.pdf │ │ │ ├── th0_3_scatter_CGE.pdf │ │ │ ├── th0_3_scatter_GE.pdf │ │ │ ├── th0_3_violin.pdf │ │ │ ├── th0_3_violin_CGE.pdf │ │ │ ├── th0_3_violin_GE.pdf │ │ │ ├── th0_3_violin_diff.pdf │ │ │ ├── th0_3_violin_diff_GE.pdf │ │ │ ├── th0_cnr.pdf │ │ │ ├── th0_cnr_CGE.pdf │ │ │ ├── th0_cnr_GE.pdf │ │ │ ├── th0_degree_distribution.pdf │ │ │ ├── th0_degree_distribution_ge.pdf │ │ │ └── th0_loc.pdf │ │ ├── th100 │ │ │ ├── .ipynb_checkpoints │ │ │ │ ├── proximity_th100_degree_distribution-checkpoint.pdf │ │ │ │ ├── proximity_th100_somadist_count-checkpoint.pdf │ │ │ │ ├── proximity_th100_somadist_p-checkpoint.pdf │ │ │ │ ├── th100_3_scatter_C-GC-checkpoint.pdf │ │ │ │ └── th100_degree_distribution_ge-checkpoint.pdf │ │ │ ├── proximity_th100_2_violin.pdf │ │ │ ├── proximity_th100_3_scatter.pdf │ │ │ ├── proximity_th100_3_scatter_CGE.pdf │ │ │ ├── proximity_th100_3_violin.pdf │ │ │ ├── proximity_th100_3_violin_CGE.pdf │ │ │ ├── proximity_th100_3_violin_diff.pdf │ │ │ ├── proximity_th100_cnr.pdf │ │ │ ├── proximity_th100_cnr_GE.pdf │ │ │ ├── proximity_th100_degree_distribution.pdf │ │ │ ├── proximity_th100_degree_distribution_ge.pdf │ │ │ ├── proximity_th100_somadist_bi_uni.pdf │ │ │ ├── proximity_th100_somadist_count.pdf │ │ │ ├── proximity_th100_somadist_p.pdf │ │ │ ├── proximity_th100_somadist_p_bi_uni.pdf │ │ │ ├── th100_2_scatter.pdf │ │ │ ├── th100_2_violin.pdf │ │ │ ├── th100_3_scatter.pdf │ │ │ ├── th100_3_scatter_C-GC.pdf │ │ │ ├── th100_3_scatter_CGE.pdf │ │ │ ├── th100_3_scatter_E-GE.pdf │ │ │ ├── th100_3_scatter_GC-GE.pdf │ │ │ ├── th100_3_scatter_GE.pdf │ │ │ ├── th100_3_violin.pdf │ │ │ ├── th100_3_violin_CGE.pdf │ │ │ ├── th100_3_violin_GE.pdf │ │ │ ├── th100_3_violin_GEER.pdf │ │ │ ├── th100_3_violin_GRE.pdf │ │ │ ├── th100_3_violin_diff.pdf │ │ │ ├── th100_3_violin_diff_GE.pdf │ │ │ ├── th100_3_violin_diff_GEER.pdf │ │ │ ├── th100_cnr.pdf │ │ │ ├── th100_cnr_CGE.pdf │ │ │ ├── th100_cnr_GE.pdf │ │ │ ├── th100_degree_distribution.pdf │ │ │ ├── th100_degree_distribution_ge.pdf │ │ │ └── th100_loc.pdf │ │ └── th300 │ │ │ ├── th300_2_scatter.pdf │ │ │ ├── th300_2_violin.pdf │ │ │ ├── th300_3_scatter.pdf │ │ │ ├── th300_3_scatter_CGE.pdf │ │ │ ├── th300_3_scatter_GE.pdf │ │ │ ├── th300_3_violin.pdf │ │ │ ├── th300_3_violin_CGE.pdf │ │ │ ├── th300_3_violin_GE.pdf │ │ │ ├── th300_3_violin_diff.pdf │ │ │ ├── th300_3_violin_diff_GE.pdf │ │ │ ├── th300_cnr.pdf │ │ │ ├── th300_cnr_CGE.pdf │ │ │ ├── th300_cnr_GE.pdf │ │ │ ├── th300_degree_distribution.pdf │ │ │ ├── th300_degree_distribution_ge.pdf │ │ │ └── th300_loc.pdf │ ├── full-2-and-3-neuron-motifs.ipynb │ ├── full-common-neighbor-rule.ipynb │ ├── full-degree-dist.ipynb │ ├── proxy-th100-2-and-3-neuron-motifs.ipynb │ ├── proxy-th100-common-neighbor-rule.ipynb │ ├── proxy-th100-degree-dist.ipynb │ ├── readme.md │ ├── th0-2-and-3-neuron-motifs.ipynb │ ├── th0-common-neighbor-rule.ipynb │ ├── th0-degree-dist.ipynb │ ├── th100-2-and-3-neuron-motifs.ipynb │ ├── th100-common-neighbor-rule.ipynb │ ├── th100-degree-dist.ipynb │ ├── th300-2-and-3-neuron-motifs.ipynb │ ├── th300-common-neighbor-rule.ipynb │ ├── th300-degree-dist.ipynb │ └── utils │ │ ├── .ipynb_checkpoints │ │ ├── common_neighbor_rule-checkpoint.py │ │ ├── graph_creation-checkpoint.py │ │ ├── motif_counts-checkpoint.py │ │ ├── proximity-checkpoint.py │ │ ├── skel-checkpoint.py │ │ ├── utils-checkpoint.py │ │ └── visualization-checkpoint.py │ │ ├── __pycache__ │ │ ├── common_neighbor_rule.cpython-37.pyc │ │ ├── graph_creation.cpython-37.pyc │ │ ├── motif_counts.cpython-37.pyc │ │ ├── proximity.cpython-37.pyc │ │ ├── skel.cpython-37.pyc │ │ ├── utils.cpython-37.pyc │ │ └── visualization.cpython-37.pyc │ │ ├── common_neighbor_rule.py │ │ ├── graph_creation.py │ │ ├── motif_counts.py │ │ ├── proximity.py │ │ ├── skel.py │ │ ├── utils.py │ │ └── visualization.py │ └── resource_statistics │ ├── README.md │ ├── assets │ └── dendritelength.png │ ├── lib │ ├── __init__.py │ ├── modelling.py │ ├── plot.py │ ├── skel.py │ ├── string2list.py │ └── u.py │ ├── neurite_lengths.ipynb │ └── scripts │ ├── README.md │ ├── compute_compartment_lengths.py │ ├── compute_dist_to_leaf.py │ └── derivedata.sh └── postBuild /.gitignore: -------------------------------------------------------------------------------- 1 | *-checkpoint.ipynb 2 | notebooks/*.png 3 | .DS_Store 4 | 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