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mkdocs.yml
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site_name: 'infer_subc'
nav:
- Home: 'index.md'
- Getting Started:
- 'Setup' : 'config.md'
- 'Segmentation Workflows' : 'segmentation.md'
- 'Quantification Pipeline' : 'quantification.md'
- Napari:
- 'infer_subc/napari/plugin.md'
- 'organelles_config' : 'infer_subc/napari/organelle_config.md'
- 'infer_subc module':
- 'overview': 'infer_subc/overview.md'
- 'core':
- 'file_io' : 'infer_subc/core/file_io.md'
- 'img' : 'infer_subc/core/img.md'
- 'organelles':
- 'cellmask' : 'infer_subc/organelles/cellmask.md'
- 'cytoplasm' : 'infer_subc/organelles/cytoplasm.md'
- 'ER' : 'infer_subc/organelles/er.md'
- 'golgi' : 'infer_subc/organelles/golgi.md'
- 'lipid' : 'infer_subc/organelles/lipid.md'
- 'lysosome' : 'infer_subc/organelles/lysosome.md'
- 'mitochondria' : 'infer_subc/organelles/mitochondria.md'
- 'nuclei' : 'infer_subc/organelles/nuclei.md'
- 'peroxisome' : 'infer_subc/organelles/peroxisome.md'
- 'utils':
- 'batch' : 'infer_subc/utils/batch.md'
- 'stats_helpers' : 'infer_subc/utils/stats_helpers'
- 'stats' : 'infer_subc/utils/stats.md'
- 'workflow': 'infer_subc/workflow.md'
- Notebooks: 'nbs/overview.md'
- '1.0_image_setup' : 'notebooks/part_1_segmentation_workflows/1.0_image_setup.ipynb'
- '1.1_infer_masks_from-composite_with_nuc' : 'notebooks/part_1_segmentation_workflows/1.1_infer_masks_from-composite_with_nuc.ipynb'
- '1.1a_infer_masks_from-composite_single_cell' : 'notebooks/part_1_segmentation_workflows/1.1a_infer_masks_from-composite_single_cell.ipynb'
- '1.1b_infer_masks_from-composite_multiple-cells' : 'notebooks/part_1_segmentation_workflows/1.1b_infer_masks_from-composite_multiple-cells.ipynb'
- '1.2_infer_lysosome' : 'notebooks/part_1_segmentation_workflows/1.2_infer_lysosome.ipynb'
- '1.3_infer_mitochondria' : 'notebooks/part_1_segmentation_workflows/1.3_infer_mitochondria.ipynb'
- '1.4_infer_golgi' : 'notebooks/part_1_segmentation_workflows/1.4_infer_golgi.ipynb'
- '1.5_infer_peroxisome' : 'notebooks/part_1_segmentation_workflows/1.5_infer_peroxisome.ipynb'
- '1.6_infer_ER' : 'notebooks/part_1_segmentation_workflows/1.6_infer_ER.ipynb'
- '1.7_infer_lipid_droplet' : 'notebooks/part_1_segmentation_workflows/1.7_infer_lipid_droplet.ipynb'
- '2.1_organelle_morphology' : 'notebooks/part_2_quantification/2.1_organelle_morphology.ipynb'
- '2.2_organelle_interactions' : 'notebooks/part_2_quantification/2.2_organelle_interactions.ipynb'
- '2.3_distribution_measurements' : 'notebooks/part_2_quantification/2.3_distribution_measurements.ipynb'
- '2.4_cell_region_morphology' : 'notebooks/part_2_quantification/2.4_cell_region_morphology.ipynb'
- '2.5_combined_and_batch_processing' : 'notebooks/part_2_quantification/2.5_combined_and_batch_processing.ipynb'
- '2.6_summary_stats' : 'notebooks/part_2_quantification/2.6_summary_stats.ipynb'
- 'full_quantification_pipeline' : 'notebooks/part_2_quantification/full_quantification_pipeline.ipynb'
plugins:
# - mkdocs-jupyter:
# theme: light
- search
- mkdocstrings
theme:
name: material
palette:
scheme: slate