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mkdocs.yml
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mkdocs.yml
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site_name: 'infer_subc'
nav:
- Home: 'index.md'
- frameworks:
- 'reproducible imaging': 'framework.md'
- 'general workflow': 'pipeline.md'
- getting started:
- 'install + config' : 'config.md'
- 'example notebooks' : 'nbs/overview.md'
- Napari:
- 'infer_subc/napari/plugin.md'
- 'infer_subc/napari/organelle_config.md'
- 'infer_subc module':
- 'overview': 'infer_subc/overview.md'
- 'organelles':
- 'Overview' : 'infer_subc/organelles.md'
- 'cellmask' : 'infer_subc/organelles/cellmask.md'
- 'nuclei' : 'infer_subc/organelles/nuclei.md'
- 'cytoplasm' : 'infer_subc/organelles/cytoplasm.md'
- 'lysosome' : 'infer_subc/organelles/lysosome.md'
- 'mitochondria' : 'infer_subc/organelles/mitochondria.md'
- 'golgi' : 'infer_subc/organelles/golgi.md'
- 'peroxisome' : 'infer_subc/organelles/peroxisome.md'
- 'ER' : 'infer_subc/organelles/er.md'
- 'LD' : 'infer_subc/organelles/lipid.md'
- 'core':
- 'file_io' : 'infer_subc/core/file_io.md'
- 'img' : 'infer_subc/core/img.md'
- 'utils':
- 'Overview' : 'infer_subc/utils/utils.md'
- 'stats' : 'infer_subc/utils/stats.md'
- 'batch': 'infer_subc/utils/batch.md'
- 'etc' : 'infer_subc/utils/etc.md'
- 'workflow': 'infer_subc/workflow.md'
# - Notebooks:
# - 'Overview' : notebooks/nbs_overview.md
# - '00_setup' : 'notebooks/nbs/00.1_pipeline_setup.ipynb'
# - '00_choose_Z' : 'notebooks/nbs/00.2_extract_optimal_Z.ipynb'
# - '01_cellmask' : 'notebooks/nbs/01_infer_cellmask.ipynb'
# - '02_nuclei' : 'notebooks/nbs/02_infer_nuclei.ipynb'
# - '03_cytoplasm' : 'notebooks/nbs/03_infer_cytoplasm.ipynb'
# - '04_lysosome' : 'notebooks/nbs/04_infer_lysosome.ipynb'
# - '05_mitochondria' : 'notebooks/nbs/05_infer_mitochondria.ipynb'
# - '06_golgi' : 'notebooks/nbs/06_infer_golgi.ipynb'
# - '07_peroxisome' : 'notebooks/nbs/07_infer_peroxisome.ipynb'
# - '08_endoplasmic_reticulum' : 'notebooks/nbs/08_infer_endoplasmic_reticulum.ipynb'
# - '09_lipid_body' : 'notebooks/nbs/09_infer_lipid_body.ipynb'
# # - 'batch processing' : 'notebooks/nbs/10_batch_processing.ipynb'
# # # - 'workflows' : 'notebooks/nbs/11_workflows.ipynb'
# # # - 'QC' : 'notebooks/nbs/12_QC.ipynb'
plugins:
# - mkdocs-jupyter:
# theme: dark
- search
- mkdocstrings
theme:
name: material
palette:
scheme: slate