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mkdocs.yml
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mkdocs.yml
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site_name: cellseg_gsontools
site_description: A Python package for analyzing cell and tissue segmentation maps
site_author: Oskari Lehtonen
site_url: https://okunator.github.io/cellseg_gsontools/
theme:
name: "material"
logo: img/logo.png
favicon: img/logo.png
palette:
primary: black
accent: cyan
font:
text: Raleway
icon:
repo: fontawesome/brands/github
features:
- content.code.copy
- content.tabs.link
- navigation.indexes
repo_url: https://github.com/okunator/cellseg_gsontools
repo_name: cellseg_gsontools
plugins:
- search
- social
- autorefs
- mkdocstrings:
default_handler: python
handlers:
python:
rendering:
show_source: true
- mkdocs-jupyter:
include: ["*.ipynb"]
markdown_extensions:
- pymdownx.highlight:
anchor_linenums: true
line_spans: __span
pygments_lang_class: true
- pymdownx.arithmatex:
generic: true
- codehilite
- markdown.extensions.def_list
- pymdownx.inlinehilite
- pymdownx.snippets
- pymdownx.emoji
- pymdownx.superfences
- pymdownx.magiclink
- pymdownx.keys
- admonition
- attr_list
- tables
- toc:
permalink: true
extra_javascript:
- javascripts/katex.js
- https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.js
- https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/contrib/auto-render.min.js
extra_css:
- https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.css
nav:
- Home: index.md
- Getting Started:
- Installation: "getting_started/installation.md"
- Quick Start: "getting_started/quick_start.ipynb"
- User Guide:
- Cell Morphology: "user_guide/cell_morphology.ipynb"
- Cell Neighborhoods: "user_guide/cell_neighborhoods.ipynb"
- Cell Neighborhood Characteristics: "user_guide/cell_neighborhood_characteristics.ipynb"
- Cell Neighborhood Diversity: "user_guide/cell_neighborhood_diversity.ipynb"
- Spatial Grids: "user_guide/spatial_grids.ipynb"
- Global Spatial Autocorrelation: "user_guide/global_spatial_autocorrelation.ipynb"
- Local Spatial Autocorrelation: "user_guide/local_spatial_autocorrelation.ipynb"
- Cell Clustering: "user_guide/cell_clustering.ipynb"
- Cell Regionalization: "user_guide/cell_regionalization.ipynb"
- Merging Segmentation Maps:
- "user_guide/merging/index.ipynb"
- Merging WSI-level Segmenation: "user_guide/merging/WSI_merge.ipynb"
- Spatial Contexts:
- "user_guide/spatial_contexts/index.md"
- Within Context: "user_guide/spatial_contexts/within_context.ipynb"
- Interface Context: "user_guide/spatial_contexts/interface_context.ipynb"
- Point Cluster Context: "user_guide/spatial_contexts/point_cluster_context.ipynb"
- API Reference:
- Spatial Contexts:
- WithinContext: "reference/spatial_contexts/within_context_ref.md"
- InterfaceContext: "reference/spatial_contexts/iface_context_ref.md"
- PointClusterContext: "reference/spatial_contexts/point_cluster_context_ref.md"
- Merging:
- CellMerger: "reference/merging/cell_merger_ref.md"
- AreaMerger: "reference/merging/area_merger_ref.md"
- I/O:
- read_gdf: "reference/io/read_gdf_ref.md"
- gdf_to_file: "reference/io/gdf_to_file_ref.md"
- Data:
- cervix_cells: "reference/data/cervix_cells_ref.md"
- cervix_tissue: "reference/data/cervix_tissue_ref.md"
- gland_cells: "reference/data/gland_cells_ref.md"
- gland_tissue: "reference/data/gland_tissue_ref.md"
- tumor_stroma_interface_cells: "reference/data/tumor_stroma_interface_cells_ref.md"
- tumor_stroma_interface_tissue: "reference/data/tumor_stroma_interface_tissue_ref.md"
- Geometry:
- shape_metric: "reference/geometry/shape_metric_ref.md"
- major_axis_len: "reference/geometry/major_axis_len_ref.md"
- minor_axis_len: "reference/geometry/minor_axis_len_ref.md"
- major_axis_angle: "reference/geometry/major_axis_angle_ref.md"
- minor_axis_angle: "reference/geometry/minor_axis_angle_ref.md"
- convexity: "reference/geometry/convexity_ref.md"
- compactness: "reference/geometry/compactness_ref.md"
- circularity: "reference/geometry/circularity_ref.md"
- rectangularity: "reference/geometry/rectangularity_ref.md"
- squareness: "reference/geometry/squareness_ref.md"
- shape_index: "reference/geometry/shape_index_ref.md"
- sphericity: "reference/geometry/sphericity_ref.md"
- solidity: "reference/geometry/solidity_ref.md"
- fractal_dimension: "reference/geometry/fractal_dimension_ref.md"
- eccentricity: "reference/geometry/eccentricity_ref.md"
- elongation: "reference/geometry/elongation_ref.md"
- equivalent_rectangular_index: "reference/geometry/equivalent_rectangular_index_ref.md"
- Lines:
- medial_lines: "reference/lines/medial_lines_ref.md"
- voronoi_medial: "reference/lines/voronoi_medial_ref.md"
- perpendicular_lines: "reference/lines/perpendicular_lines_ref.md"
- perependicular_line: "reference/lines/perpendicular_line_ref.md"
- line_branches: "reference/lines/line_branches_ref.md"
- equal_interval_points: "reference/lines/equal_interval_points_ref.md"
- Cell Neighbors:
- neighborhood: "reference/cell_neighbors/neighborhood_ref.md"
- nhood_vals: "reference/cell_neighbors/nhood_vals_ref.md"
- nhood_type_count: "reference/cell_neighbors/nhood_type_count_ref.md"
- nhood_counts: "reference/cell_neighbors/nhood_counts_ref.md"
- nhood_dists: "reference/cell_neighbors/nhood_dists_ref.md"
- Cell Neighborhoods:
- local_character: "reference/cell_neighborhoods/local_character_ref.md"
- local_distances: "reference/cell_neighborhoods/local_distances_ref.md"
- local_diversity: "reference/cell_neighborhoods/local_diversity_ref.md"
- Diversity:
- simpson_index: "reference/diversity/simpson_index_ref.md"
- shannon_index: "reference/diversity/shannon_index_ref.md"
- gini_index: "reference/diversity/gini_index_ref.md"
- theil_index: "reference/diversity/theil_index_ref.md"
- Graph:
- fit_graph: "reference/graph/fit_graph_ref.md"
- get_border_crosser_links: "reference/graph/get_border_crosser_links_ref.md"
- dist_thresh_weights_sequential: "reference/graph/dist_thresh_weights_sequential_ref.md"
- Clustering:
- cluster_points: "reference/clustering/cluster_points_ref.md"
- cluster_cells: "reference/clustering/cluster_cells_ref.md"
- find_lisa_clusters: "reference/clustering/find_lisa_clusters_ref.md"
- connected_components: "reference/clustering/connected_components_ref.md"
- label_connected_components: "reference/clustering/label_connected_components_ref.md"
- Links:
- weights2gdf: "reference/links/weights2gdf_ref.md"
- link_counts: "reference/links/link_counts_ref.md"
- get_link_combinations: "reference/links/get_link_combinations_ref.md"
- Grid:
- fit_spatial_grid: "reference/grid/fit_spatial_grid_ref.md"
- hexgrid_overlay: "reference/grid/hexgrid_overlay_ref.md"
- grid_overlay: "reference/grid/grid_overlay_ref.md"
- grid_classify: "reference/grid/grid_classify_ref.md"
- Tools:
- gdf_apply: "reference/tools/gdf_apply_ref.md"
- clip_gdf: "reference/tools/clip_gdf_ref.md"
- pre_proc_gdf: "reference/tools/pre_proc_gdf_ref.md"
- set_uid: "reference/tools/set_uid_ref.md"
- xy_to_lonlat: "reference/tools/xy_to_lonlat_ref.md"
- lonlat_to_xy: "reference/tools/lonlat_to_xy_ref.md"
- Plotting:
- plot_gdf: "reference/plotting/plot_gdf_ref.md"
- plot_all: "reference/plotting/plot_all_ref.md"