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AUTHORS.md
CHANGELOG.md
CITATION.cff
CONTRIBUTING.md
LICENSE.txt
MANIFEST.in
README.md
codecov.yml
commitlint.config.js
package.json
pyproject.toml
requirements.txt
setup.py
tox.ini
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axon_synthesis/__init__.py
axon_synthesis/atlas.py
axon_synthesis/base_path_builder.py
axon_synthesis/constants.py
axon_synthesis/typing.py
axon_synthesis/utils.py
axon_synthesis/version.py
axon_synthesis/white_matter_recipe.py
axon_synthesis.egg-info/PKG-INFO
axon_synthesis.egg-info/SOURCES.txt
axon_synthesis.egg-info/dependency_links.txt
axon_synthesis.egg-info/entry_points.txt
axon_synthesis.egg-info/requires.txt
axon_synthesis.egg-info/top_level.txt
axon_synthesis/cli/__init__.py
axon_synthesis/cli/common.py
axon_synthesis/cli/input_creation.py
axon_synthesis/cli/scripts.py
axon_synthesis/cli/synthesis.py
axon_synthesis/cli/utils.py
axon_synthesis/cli/validation.py
axon_synthesis/data/tuft_distributions.json
axon_synthesis/data/tuft_parameters.json
axon_synthesis/inputs/__init__.py
axon_synthesis/inputs/create.py
axon_synthesis/inputs/pop_neuron_numbers.py
axon_synthesis/inputs/trunk_properties.py
axon_synthesis/inputs/clustering/__init__.py
axon_synthesis/inputs/clustering/extract_terminals.py
axon_synthesis/inputs/clustering/from_barcodes.py
axon_synthesis/inputs/clustering/from_brain_regions.py
axon_synthesis/inputs/clustering/from_sphere_parents.py
axon_synthesis/inputs/clustering/from_spheres.py
axon_synthesis/inputs/clustering/plot.py
axon_synthesis/inputs/clustering/utils.py
axon_synthesis/synthesis/__init__.py
axon_synthesis/synthesis/add_tufts.py
axon_synthesis/synthesis/outputs.py
axon_synthesis/synthesis/plot.py
axon_synthesis/synthesis/source_points.py
axon_synthesis/synthesis/target_points.py
axon_synthesis/synthesis/tuft_properties.py
axon_synthesis/synthesis/main_trunk/__init__.py
axon_synthesis/synthesis/main_trunk/post_process.py
axon_synthesis/synthesis/main_trunk/steiner_morphology.py
axon_synthesis/synthesis/main_trunk/steiner_tree.py
axon_synthesis/synthesis/main_trunk/create_graph/__init__.py
axon_synthesis/synthesis/main_trunk/create_graph/plot.py
axon_synthesis/synthesis/main_trunk/create_graph/utils.py
axon_synthesis/validation/__init__.py
axon_synthesis/validation/atlas_utils.py
axon_synthesis/validation/mimic.py
axon_synthesis/validation/projection_intensity.py
axon_synthesis/validation/statistics.py
axon_synthesis/validation/utils.py
docs/Makefile
docs/environment.yml
docs/source/api_ref.rst
docs/source/changelog.rst
docs/source/cli.rst
docs/source/conf.py
docs/source/config_file.rst
docs/source/contributing.rst
docs/source/general_principles.rst
docs/source/index.rst
docs/source/input_files.rst
docs/source/scripts/create_graph_figure.py
docs/source/scripts/graph_creation.svg
docs/source/scripts/graph_creation_preferred_regions.svg
docs/source/scripts/graph_creation_solution.png
docs/source/scripts/graph_creation_solution.svg
docs/source/scripts/graph_creation_solution_preferred_regions.png
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examples/axon_grafting_points.h5
examples/config.cfg
examples/input_cells.mvd3
examples/run.sh
examples/morphologies/dataset.csv
examples/morphologies/logging.conf
examples/morphologies/luigi.cfg
examples/morphologies/neuromorpho_config.json
examples/morphologies/run.sh
examples/morphologies/raw_morphologies/165421.swc
examples/morphologies/raw_morphologies/172992.swc
examples/morphologies/raw_morphologies/172993.swc
examples/morphologies/raw_morphologies/172994.swc
examples/morphologies/raw_morphologies/172995.swc
examples/morphologies/raw_morphologies/172996.swc
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examples/morphologies/raw_morphologies/173000.swc
examples/morphologies/raw_morphologies/metadata.csv
examples/morphologies/repair_release/asc/172992.asc
examples/morphologies/repair_release/asc/172993.asc
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tests/__init__.py
tests/conftest.py
tests/data_factories.py
tests/test_atlas.py
tests/test_cli.py
tests/test_clustering.py
tests/test_examples.py
tests/test_statistics.py
tests/test_trunk_post_process.py
tests/data/.gitignore
tests/data/atlas_metadata.json
tests/data/logging.conf
tests/data/luigi.cfg
tests/data/luigi_mimic.cfg
tests/data/region_structure.yaml
tests/data/score_matrix.pdf
tests/data/tuft_distributions.json
tests/data/tuft_parameters.json
tests/data/white_matter_recipe.yaml
tests/data/input_morphologies/morph_0001.swc
tests/data/input_morphologies/morph_0002.swc
tests/data/input_morphologies/morph_0003.swc
tests/data/mimic_example/inputs/circuit.h5
tests/data/mimic_example/inputs/metadata.json
tests/data/mimic_example/inputs/population_probabilities.csv
tests/data/mimic_example/inputs/projection_probabilities.csv
tests/data/mimic_example/inputs/Clustering/clustered_morphologies_paths.csv
tests/data/mimic_example/inputs/Clustering/clustered_terminals.csv
tests/data/mimic_example/inputs/Clustering/clustering_configurations.json
tests/data/mimic_example/inputs/Clustering/trunk_properties.json
tests/data/mimic_example/inputs/Clustering/tuft_properties.json
tests/data/mimic_example/inputs/Clustering/clustered_morphologies/172992_big_spheres_0.asc
tests/data/mimic_example/inputs/Clustering/clustered_morphologies/172993_big_spheres_0.asc
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tests/data/mimic_example/synthesis_basic_172992/GraphCreationData/172992_0.h5
tests/data/mimic_example/synthesis_basic_172992/MainTrunkMorphologies/172992_0.h5
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tests/data/mimic_example/synthesis_basic_172993/GraphCreationData/172993_0.h5
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