LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements/requirements.txt
requirements/requirements_convnext.txt
requirements/requirements_dev.txt
requirements/requirements_docs.txt
requirements/requirements_plotting.txt
requirements/requirements_stitching.txt
requirements/requirements_test.txt
src/scportrait/__init__.py
src/scportrait.egg-info/PKG-INFO
src/scportrait.egg-info/SOURCES.txt
src/scportrait.egg-info/dependency_links.txt
src/scportrait.egg-info/requires.txt
src/scportrait.egg-info/top_level.txt
src/scportrait/data/__init__.py
src/scportrait/data/_dataloader.py
src/scportrait/data/_datasets.py
src/scportrait/data/_single_cell_images.py
src/scportrait/io/__init__.py
src/scportrait/io/_convert.py
src/scportrait/io/daskmmap.py
src/scportrait/io/h5sc.py
src/scportrait/pipeline/__init__.py
src/scportrait/pipeline/_base.py
src/scportrait/pipeline/extraction.py
src/scportrait/pipeline/featurization.py
src/scportrait/pipeline/project.py
src/scportrait/pipeline/selection.py
src/scportrait/pipeline/_utils/constants.py
src/scportrait/pipeline/_utils/helper.py
src/scportrait/pipeline/_utils/sdata_io.py
src/scportrait/pipeline/_utils/segmentation.py
src/scportrait/pipeline/_utils/spatialdata_helper.py
src/scportrait/pipeline/mask_filtering/__init__.py
src/scportrait/pipeline/mask_filtering/filter_segmentation.py
src/scportrait/pipeline/mask_filtering/workflows.py
src/scportrait/pipeline/segmentation/__init__.py
src/scportrait/pipeline/segmentation/segmentation.py
src/scportrait/pipeline/segmentation/workflows/__init__.py
src/scportrait/pipeline/segmentation/workflows/_base_segmentation_workflow.py
src/scportrait/pipeline/segmentation/workflows/_cellpose.py
src/scportrait/pipeline/segmentation/workflows/_wga_segmentation.py
src/scportrait/plotting/__init__.py
src/scportrait/plotting/_utils.py
src/scportrait/plotting/h5sc.py
src/scportrait/plotting/sdata.py
src/scportrait/plotting/vis.py
src/scportrait/processing/__init__.py
src/scportrait/processing/images/__init__.py
src/scportrait/processing/images/_image_processing.py
src/scportrait/processing/images/_zstack_compression.py
src/scportrait/processing/masks/__init__.py
src/scportrait/processing/masks/mask_filtering.py
src/scportrait/tools/__init__.py
src/scportrait/tools/h5sc/__init__.py
src/scportrait/tools/h5sc/operations.py
src/scportrait/tools/ml/__init__.py
src/scportrait/tools/ml/callback.py
src/scportrait/tools/ml/datasets.py
src/scportrait/tools/ml/metrics.py
src/scportrait/tools/ml/models.py
src/scportrait/tools/ml/plmodels.py
src/scportrait/tools/ml/pretrained_models.py
src/scportrait/tools/ml/transforms.py
src/scportrait/tools/ml/utils.py
src/scportrait/tools/parse/__init__.py
src/scportrait/tools/parse/_parse_phenix.py
src/scportrait/tools/sdata/__init__.py
src/scportrait/tools/sdata/filter/__init__.py
src/scportrait/tools/sdata/processing/__init__.py
src/scportrait/tools/sdata/processing/_image_processing.py
src/scportrait/tools/sdata/processing/_subset.py
src/scportrait/tools/sdata/read/__init__.py
src/scportrait/tools/sdata/write/__init__.py
src/scportrait/tools/sdata/write/_helper.py
src/scportrait/tools/sdata/write/_write.py
src/scportrait/tools/stitch/__init__.py
src/scportrait/tools/stitch/_stitch.py
src/scportrait/tools/stitch/_utils/__init__.py
src/scportrait/tools/stitch/_utils/alignment.py
src/scportrait/tools/stitch/_utils/ashlar_plotting.py
src/scportrait/tools/stitch/_utils/filereaders.py
src/scportrait/tools/stitch/_utils/filewriters.py
src/scportrait/tools/stitch/_utils/graphs.py
src/scportrait/tools/stitch/_utils/parallelilzation.py
src/scportrait/tools/stitch/_utils/parallelized_ashlar.py