├── .all-contributorsrc ├── .codecov.yaml ├── .codespellignore ├── .github ├── actions │ └── get-testing-dataset │ │ └── action.yaml ├── dependabot.yaml └── workflows │ ├── publish.yaml │ ├── pytest.yaml │ └── stubs.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── .prospector.yaml ├── .readthedocs.yaml ├── .yamllint.yaml ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── _static │ ├── img │ │ ├── inter_cluster_distance_dm.png │ │ ├── inter_cluster_distance_lm.png │ │ ├── intra_cluster_distance_dm.png │ │ └── intra_cluster_distance_lm.png │ ├── logos │ │ ├── FBMLAB_logo.png │ │ ├── Pycrostates_logo_black.png │ │ ├── Pycrostates_logo_white.png │ │ └── UNIGE_logo.png │ └── style.css ├── links.inc ├── make.bat ├── references.bib └── source │ ├── _templates │ ├── autosummary │ │ ├── class.rst │ │ └── function.rst │ └── paper.html │ ├── api │ ├── cluster.rst │ ├── datasets.rst │ ├── index.rst │ ├── io.rst │ ├── metrics.rst │ ├── most_used_classes.rst │ ├── preprocessing.rst │ ├── segmentation.rst │ └── viz.rst │ ├── conf.py │ ├── dev │ ├── changes │ │ ├── 0.2.0.rst │ │ ├── 0.3.0.rst │ │ ├── 0.4.0.rst │ │ ├── 0.5.0.rst │ │ ├── 0.6.0.rst │ │ ├── changelog.rst │ │ ├── latest.rst │ │ ├── latest.rst.template │ │ └── names.inc │ ├── development.rst │ └── index.rst │ ├── index.rst │ ├── install.rst │ └── microstates │ ├── bibliography.rst │ ├── glossary.rst │ ├── index.rst │ └── microstates.rst ├── paper ├── paper.bib └── paper.md ├── pycrostates ├── __init__.py ├── __init__.pyi ├── _typing.py ├── _typing.pyi ├── _version.py ├── cluster │ ├── __init__.py │ ├── __init__.pyi │ ├── _base.py │ ├── _base.pyi │ ├── aahc.py │ ├── aahc.pyi │ ├── kmeans.py │ ├── kmeans.pyi │ ├── tests │ │ ├── __init__.py │ │ ├── test_aahc.py │ │ ├── test_base.py │ │ └── test_kmeans.py │ └── utils │ │ ├── __init__.py │ │ ├── __init__.pyi │ │ ├── tests │ │ └── test_utils.py │ │ ├── utils.py │ │ └── utils.pyi ├── commands │ ├── __init__.py │ └── sys_info.py ├── conftest.py ├── datasets │ ├── __init__.py │ ├── __init__.pyi │ ├── lemon │ │ ├── __init__.py │ │ ├── __init__.pyi │ │ ├── data │ │ │ └── PREPROCESSED_LEMON_registry.txt │ │ ├── lemon.py │ │ └── lemon.pyi │ └── tests │ │ ├── __init__.py │ │ └── test_lemon.py ├── html_templates │ ├── __init__.py │ ├── _templates.py │ └── repr │ │ ├── AAHCluster.html.jinja │ │ ├── BaseCluster.html.jinja │ │ ├── BaseSegmentation.html.jinja │ │ ├── ChData.html.jinja │ │ └── ModKMeans.html.jinja ├── io │ ├── __init__.py │ ├── __init__.pyi │ ├── ch_data.py │ ├── ch_data.pyi │ ├── fiff.py │ ├── fiff.pyi │ ├── meas_info.py │ ├── meas_info.pyi │ ├── reader.py │ ├── reader.pyi │ └── tests │ │ ├── __init__.py │ │ ├── test_ch_data.py │ │ ├── test_fiff.py │ │ ├── test_meas_info.py │ │ └── test_reader.py ├── metrics │ ├── __init__.py │ ├── __init__.pyi │ ├── calinski_harabasz.py │ ├── calinski_harabasz.pyi │ ├── davies_bouldin.py │ ├── davies_bouldin.pyi │ ├── dunn.py │ ├── dunn.pyi │ ├── silhouette.py │ ├── silhouette.pyi │ └── tests │ │ ├── __init__.py │ │ └── test_metrics.py ├── preprocessing │ ├── __init__.py │ ├── __init__.pyi │ ├── extract_gfp_peaks.py │ ├── extract_gfp_peaks.pyi │ ├── resample.py │ ├── resample.pyi │ ├── spatial_filter.py │ ├── spatial_filter.pyi │ └── tests │ │ ├── __init__.py │ │ ├── test_extract_gfp_peaks.py │ │ ├── test_resample.py │ │ └── test_spatial_filter.py ├── segmentation │ ├── __init__.py │ ├── __init__.pyi │ ├── _base.py │ ├── _base.pyi │ ├── entropy.py │ ├── entropy.pyi │ ├── segmentation.py │ ├── segmentation.pyi │ ├── tests │ │ ├── __init__.py │ │ ├── test_entropy.py │ │ ├── test_segmentation.py │ │ └── test_transitions.py │ ├── transitions.py │ └── transitions.pyi ├── utils │ ├── __init__.py │ ├── __init__.pyi │ ├── _checks.py │ ├── _checks.pyi │ ├── _config.py │ ├── _config.pyi │ ├── _docs.py │ ├── _docs.pyi │ ├── _fixes.py │ ├── _fixes.pyi │ ├── _imports.py │ ├── _imports.pyi │ ├── _logs.py │ ├── _logs.pyi │ ├── mixin.py │ ├── mixin.pyi │ ├── sys_info.py │ ├── sys_info.pyi │ ├── tests │ │ ├── __init__.py │ │ ├── test_checks.py │ │ ├── test_config.py │ │ ├── test_docs.py │ │ ├── test_imports.py │ │ ├── test_logs.py │ │ ├── test_mixin.py │ │ ├── test_sys_info.py │ │ └── test_utils.py │ ├── utils.py │ └── utils.pyi └── viz │ ├── __init__.py │ ├── __init__.pyi │ ├── cluster_centers.py │ ├── cluster_centers.pyi │ ├── segmentation.py │ ├── segmentation.pyi │ └── tests │ ├── __init__.py │ ├── test_cluster_centers.py │ └── test_segmentation.py ├── pyproject.toml ├── setup.py ├── tools └── stubgen.py └── tutorials ├── README.rst ├── cluster ├── 00_modK.py ├── 10_subject_level_with_resampling.py └── README.rst ├── group_level_analysis ├── 00_group_level_with_individual_clusters.py ├── 10_group_level_with_individual_gfp_peaks.py └── README.rst ├── metrics ├── 00_metrics.py └── README.rst ├── preprocessing ├── 00_extract_gfp_peaks.py ├── 10_resampling.py ├── 20_spatial_filter.py └── README.rst └── segmentation ├── 00_segmentation.py 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