.gitignore
CONTRIBUTING.md
Containerfile
HISTORY.md
LICENSE
MANIFEST.in
Makefile
README.md
env_create.sh
mkdocs.yml
pyproject.toml
requirements.txt
test.yaml
windows_notes.md
.github/workflows/ci.yml.disable
.github/workflows/publish.yml
docs/config.md
docs/framework.md
docs/index.md
docs/pipeline.md
docs/quantification.md
docs/segmentation.md
docs/infer_subc/organelles.md
docs/infer_subc/overview.md
docs/infer_subc/workflow.md
docs/infer_subc/core/file_io.md
docs/infer_subc/core/img.md
docs/infer_subc/napari/organelle_config.md
docs/infer_subc/napari/plugin.md
docs/infer_subc/organelles/cellmask.md
docs/infer_subc/organelles/cytoplasm.md
docs/infer_subc/organelles/er.md
docs/infer_subc/organelles/golgi.md
docs/infer_subc/organelles/lipid.md
docs/infer_subc/organelles/lysosome.md
docs/infer_subc/organelles/mitochondria.md
docs/infer_subc/organelles/nuclei.md
docs/infer_subc/organelles/peroxisome.md
docs/infer_subc/utils/batch.md
docs/infer_subc/utils/etc.md
docs/infer_subc/utils/stats.md
docs/infer_subc/utils/stats_helpers.md
docs/infer_subc/utils/utils.md
docs/nbs/overview.md
infer_subc/__init__.py
infer_subc/__main__.py
infer_subc/_version.py
infer_subc/cli.py
infer_subc/constants.py
infer_subc/exceptions.py
infer_subc.egg-info/PKG-INFO
infer_subc.egg-info/SOURCES.txt
infer_subc.egg-info/dependency_links.txt
infer_subc.egg-info/requires.txt
infer_subc.egg-info/top_level.txt
infer_subc/assets/0.7.LD.html
infer_subc/assets/0.7.LD.md
infer_subc/assets/0.7.LD.txt
infer_subc/assets/README.png
infer_subc/assets/diagrams/0.7.LD.png
infer_subc/core/__init__.py
infer_subc/core/file_io.py
infer_subc/core/img.py
infer_subc/core/zslice.py
infer_subc/organelles/__init__.py
infer_subc/organelles/cellmask.py
infer_subc/organelles/cytoplasm.py
infer_subc/organelles/er.py
infer_subc/organelles/golgi.py
infer_subc/organelles/lipid.py
infer_subc/organelles/lysosome.py
infer_subc/organelles/mitochondria.py
infer_subc/organelles/nuclei.py
infer_subc/organelles/peroxisome.py
infer_subc/organelles/qc.py
infer_subc/organelles_config/__init__.py
infer_subc/organelles_config/all_functions.json
infer_subc/organelles_config/conf_0.1.masks.json
infer_subc/organelles_config/conf_0.1.masks_A.json
infer_subc/organelles_config/conf_0.1.masks_B.json
infer_subc/organelles_config/conf_0.2.lyso.json
infer_subc/organelles_config/conf_0.3.mito.json
infer_subc/organelles_config/conf_0.4.golgi.json
infer_subc/organelles_config/conf_0.5.perox.json
infer_subc/organelles_config/conf_0.6.ER.json
infer_subc/organelles_config/conf_0.7.LD.json
infer_subc/organelles_config/function_guide.md
infer_subc/organelles_config/function_params.md
infer_subc/organelles_config/helper.py
infer_subc/utils/__init__.py
infer_subc/utils/_aicsimage_reader.py
infer_subc/utils/batch.py
infer_subc/utils/directories.py
infer_subc/utils/filesystem.py
infer_subc/utils/lazy.py
infer_subc/utils/stats.py
infer_subc/utils/stats_helpers.py
infer_subc/workflow/__init__.py
infer_subc/workflow/batch_workflow.py
infer_subc/workflow/segmenter_function.py
infer_subc/workflow/workflow.py
infer_subc/workflow/workflow_config.py
infer_subc/workflow/workflow_definition.py
infer_subc/workflow/workflow_engine.py
infer_subc/workflow/workflow_step.py
infer_subc/workflow/todelete/workflow_config.py
infer_subc/workflow/todelete/workflow_definition.py
notebooks/part_1_segmentation_workflows/1.0_image_setup.ipynb
notebooks/part_1_segmentation_workflows/1.1_infer_masks_from-composite_with_nuc.ipynb
notebooks/part_1_segmentation_workflows/1.1a_infer_masks_from-composite_single_cell.ipynb
notebooks/part_1_segmentation_workflows/1.1b_infer_masks_from-composite_multiple-cells.ipynb
notebooks/part_1_segmentation_workflows/1.2_infer_lysosome.ipynb
notebooks/part_1_segmentation_workflows/1.3_infer_mitochondria.ipynb
notebooks/part_1_segmentation_workflows/1.4_infer_golgi.ipynb
notebooks/part_1_segmentation_workflows/1.5_infer_peroxisome.ipynb
notebooks/part_1_segmentation_workflows/1.6_infer_ER.ipynb
notebooks/part_1_segmentation_workflows/1.7_infer_lipid_droplet.ipynb
notebooks/part_2_quantification/2.1_organelle_morphology.ipynb
notebooks/part_2_quantification/2.2_organelle_interactions.ipynb
notebooks/part_2_quantification/2.3_distribution_measurements.ipynb
notebooks/part_2_quantification/2.4_cell_region_morphology.ipynb
notebooks/part_2_quantification/2.5_combined_and_batch_processing.ipynb
notebooks/part_2_quantification/2.6_summary_stats.ipynb
notebooks/part_2_quantification/full_quantification_pipeline.ipynb
tests/__init__.py
tests/conftest.py
tests/test_base.py