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‎README.rst

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‎examples/01_atlases_and_parcellations/000_accessing_atlases.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/01_atlases_and_parcellations/001_accessing_parcellations.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/01_atlases_and_parcellations/002_explore_region_hierarchy.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/01_atlases_and_parcellations/003_find_regions.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/01_atlases_and_parcellations/004_brain_region_metadata.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");
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# we can access children with fuzzy string matching using "find"
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# as well as by their index
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v1l = v1.find("left")
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print(v1l)
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print(v1l)

‎examples/01_atlases_and_parcellations/005_brain_region_spatialprops.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/02_maps_and_templates/001_selecting_reference_spaces.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/02_maps_and_templates/002_accessing_templates.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/02_maps_and_templates/003_accessing_maps.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/02_maps_and_templates/004_access_bigbrain.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/02_maps_and_templates/005_access_surface_maps.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/02_maps_and_templates/006_bigbrain_cortical_layers.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");
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layers = [2, 4, 5]
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thicknesses = {}
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for layer in layers:
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upper_surf = layermap.fetch(f"layer {layer+1} left", format="mesh")
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upper_surf = layermap.fetch(f"layer {layer + 1} left", format="mesh")
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lower_surf = layermap.fetch(f"layer {layer} left", format="mesh")
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thicknesses[layer] = np.linalg.norm(upper_surf['verts'] - lower_surf['verts'], axis=1)
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plt.hist(thicknesses[layer], 200)

‎examples/03_data_features/000_matchings.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/03_data_features/001_receptor_densities.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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2020
EBRAINS provides transmitter receptor density measurements linked to a selection of cytoarchitectonic brain regions
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in the human brain (Palomero-Gallagher, Amunts, Zilles et al.). These can be accessed by calling the
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in the human brain (Palomero-Gallagher, Amunts, Zilles et al.). These can be accessed by calling the
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``siibra.features.get()`` method with feature types in ``siibra.features.molecular`` modality, and by
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specifying a cytoarchitectonic region. Receptor densities come as cortical profiles and regional fingerprints,
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both tabular style data features.

‎examples/03_data_features/002_colorize_map.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/03_data_features/003_cell_distributions.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/03_data_features/004_gene_expressions.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/03_data_features/005_ebrains_datasets.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/03_data_features/006_connectivity_matrices.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/03_data_features/008_functional_timeseries.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/03_data_features/009_compound_features.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/05_anatomical_assignment/001_coordinates.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎examples/05_anatomical_assignment/002_activation_maps.py

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# Copyright 2018-2021
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/__init__.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/commons.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/configuration/__init__.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/configuration/configuration.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/configuration/factory.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/core/__init__.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/core/assignment.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/core/atlas.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/core/concept.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/core/parcellation.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/core/region.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/core/space.py

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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/core/structure.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/exceptions.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/experimental/__init__.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/experimental/contour.py

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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/experimental/cortical_profile_sampler.py

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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/experimental/patch.py

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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/experimental/plane3d.py

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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/explorer/__init__.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/explorer/url.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/explorer/util.py

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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/features/__init__.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/features/anchor.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/features/connectivity/__init__.py

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# Copyright 2018-2024
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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/features/connectivity/functional_connectivity.py

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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/features/connectivity/regional_connectivity.py

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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/features/connectivity/streamline_counts.py

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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/features/connectivity/streamline_lengths.py

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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/features/connectivity/tracing_connectivity.py

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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/features/dataset/__init__.py

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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/features/dataset/ebrains.py

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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/features/feature.py

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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/features/image/__init__.py

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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/features/image/image.py

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# Copyright 2018-2025
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/features/image/sections.py

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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/features/image/volume_of_interest.py

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# Licensed under the Apache License, Version 2.0 (the "License");

‎siibra/features/tabular/__init__.py

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# Licensed under the Apache License, Version 2.0 (the "License");

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