.gitignore
.pylintrc
AUTHORS.txt
CHANGELOG.rst
CONTRIBUTING.rst
LICENSE.txt
MANIFEST.in
README.rst
pyproject.toml
setup.py
tox.ini
.github/workflows/publish-sdist.yml
.github/workflows/run-tox.yml
atlas_densities/__init__.py
atlas_densities/exceptions.py
atlas_densities/utils.py
atlas_densities/version.py
atlas_densities.egg-info/PKG-INFO
atlas_densities.egg-info/SOURCES.txt
atlas_densities.egg-info/dependency_links.txt
atlas_densities.egg-info/entry_points.txt
atlas_densities.egg-info/requires.txt
atlas_densities.egg-info/top_level.txt
atlas_densities/app/__init__.py
atlas_densities/app/cell_densities.py
atlas_densities/app/cli.py
atlas_densities/app/combination.py
atlas_densities/app/mtype_densities.py
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atlas_densities/app/data/1.json
atlas_densities/app/data/__init__.py
atlas_densities/app/data/markers/README.rst
atlas_densities/app/data/markers/combine_markers_ccfv2_config.yaml
atlas_densities/app/data/markers/fit_average_densities_ccfv2_config.yaml
atlas_densities/app/data/markers/realigned_slices_bbp.json
atlas_densities/app/data/markers/realigned_slices_ccfv2.json
atlas_densities/app/data/measurements/README.rst
atlas_densities/app/data/measurements/gaba_papers.xlsx
atlas_densities/app/data/measurements/homogenous_regions.csv
atlas_densities/app/data/measurements/measurements.csv
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atlas_densities/app/data/measurements/mmc3.xlsx
atlas_densities/app/data/measurements/non_density_measurements.csv
atlas_densities/app/data/measurements/std_cells.json
atlas_densities/app/data/metadata/README.txt
atlas_densities/app/data/metadata/ca1_metadata.json
atlas_densities/app/data/metadata/excitatory-inhibitory-splitting.json
atlas_densities/app/data/metadata/group_ids.json
atlas_densities/app/data/metadata/isocortex_23_metadata.json
atlas_densities/app/data/metadata/isocortex_metadata.json
atlas_densities/app/data/metadata/metadata.json
atlas_densities/app/data/metadata/thalamus_metadata.json
atlas_densities/app/data/mtypes/mapping_cortex_all_to_exc_mtypes.csv
atlas_densities/app/data/mtypes/mtypes_probability_map_config.yaml
atlas_densities/app/data/mtypes/composition/README.rst
atlas_densities/app/data/mtypes/composition/composition.yaml
atlas_densities/app/data/mtypes/composition/neurons-mtype-taxonomy.tsv
atlas_densities/app/data/mtypes/density_profiles/README.rst
atlas_densities/app/data/mtypes/density_profiles/meta/layers.tsv
atlas_densities/app/data/mtypes/density_profiles/meta/mapping.tsv
atlas_densities/app/data/mtypes/density_profiles/profiles/BP.dat
atlas_densities/app/data/mtypes/density_profiles/profiles/BTC.dat
atlas_densities/app/data/mtypes/density_profiles/profiles/CHC.dat
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atlas_densities/app/data/mtypes/density_profiles/profiles/L1_LAC.dat
atlas_densities/app/data/mtypes/density_profiles/profiles/L1_NGC-DA.dat
atlas_densities/app/data/mtypes/density_profiles/profiles/L1_NGC-SA.dat
atlas_densities/app/data/mtypes/density_profiles/profiles/L1_SAC.dat
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atlas_densities/app/data/mtypes/density_profiles/profiles/L2_TPC-A.dat
atlas_densities/app/data/mtypes/density_profiles/profiles/L2_TPC-B.dat
atlas_densities/app/data/mtypes/density_profiles/profiles/L3_TPC-A.dat
atlas_densities/app/data/mtypes/density_profiles/profiles/L3_TPC-B.dat
atlas_densities/app/data/mtypes/density_profiles/profiles/L4_SSC.dat
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atlas_densities/app/data/mtypes/density_profiles/profiles/L5_TTPC-A.dat
atlas_densities/app/data/mtypes/density_profiles/profiles/L5_TTPC-B.dat
atlas_densities/app/data/mtypes/density_profiles/profiles/L5_UPC.dat
atlas_densities/app/data/mtypes/density_profiles/profiles/L6_BPC.dat
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atlas_densities/app/data/mtypes/density_profiles/profiles/L6_TPC-A.dat
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atlas_densities/app/data/mtypes/density_profiles/profiles/NBC.dat
atlas_densities/app/data/mtypes/density_profiles/profiles/NGC.dat
atlas_densities/app/data/mtypes/density_profiles/profiles/SBC.dat
atlas_densities/app/data/mtypes/probability_map/README.rst
atlas_densities/app/data/mtypes/probability_map/probability_map.csv
atlas_densities/combination/__init__.py
atlas_densities/combination/annotations_combinator.py
atlas_densities/combination/markers_combinator.py
atlas_densities/densities/__init__.py
atlas_densities/densities/cell_counts.py
atlas_densities/densities/cell_density.py
atlas_densities/densities/excel_reader.py
atlas_densities/densities/excitatory_inhibitory_splitting.py
atlas_densities/densities/fitting.py
atlas_densities/densities/glia_densities.py
atlas_densities/densities/inhibitory_neuron_densities_helper.py
atlas_densities/densities/inhibitory_neuron_densities_optimization.py
atlas_densities/densities/inhibitory_neuron_density.py
atlas_densities/densities/measurement_to_density.py
atlas_densities/densities/mtype_densities_from_composition.py
atlas_densities/densities/mtype_densities_from_profiles.py
atlas_densities/densities/refined_inhibitory_neuron_densities.py
atlas_densities/densities/utils.py
atlas_densities/densities/mtype_densities_from_map/__init__.py
atlas_densities/densities/mtype_densities_from_map/create.py
atlas_densities/densities/mtype_densities_from_map/utils.py
doc/Makefile
doc/source/bbpp82_628_linear_program.pdf
doc/source/cell_densities.rst
doc/source/changelog.rst
doc/source/cli.rst
doc/source/combination.rst
doc/source/conf.py
doc/source/index.rst
doc/source/mtype_densities.rst
doc/source/readme.rst
doc/source/static/atlas-densities.jpg
tests/1.json
tests/__init__.py
tests/markers_config.yaml
tests/mocking_tools.py
tests/test_utils.py
tests/utils.py
tests/app/__init__.py
tests/app/test_cell_densities.py
tests/app/test_combination.py
tests/app/test_mtype_densities.py
tests/app/test_refined_inhibitory_neuron_densities.py
tests/combination/__init__.py
tests/combination/test_annotations_combinator.py
tests/combination/test_markers_combinator.py
tests/densities/__init__.py
tests/densities/test_cell_counts.py
tests/densities/test_cell_density.py
tests/densities/test_excel_reader.py
tests/densities/test_excitatory_inhibitory_splitting.py
tests/densities/test_fitting.py
tests/densities/test_glia_densities.py
tests/densities/test_inhibitory_neuron_densities_helper.py
tests/densities/test_inhibitory_neuron_density.py
tests/densities/test_inhibitory_neuron_density_optimization.py
tests/densities/test_measurement_to_density.py
tests/densities/test_mtype_densities_from_composition.py
tests/densities/test_mtype_densities_from_map.py
tests/densities/test_mtype_densities_from_profiles.py
tests/densities/test_optimization_initialization.py
tests/densities/test_refined_inhibitory_neuron_density.py
tests/densities/test_utils.py
tests/densities/data/meta/layers.tsv
tests/densities/data/meta/mapping.tsv
tests/densities/data/meta/mapping_exc_only.tsv
tests/densities/data/mtypes/BP.dat
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tests/densities/data/mtypes/L3_TPC-A.dat
tests/densities/data/mtypes/L3_TPC-B.dat
tests/densities/data/mtypes/mtype-taxonomy.tsv