├── .editorconfig ├── .gitignore ├── .prospector.yml ├── CHANGELOG.rst ├── CODE_OF_CONDUCT.rst ├── CONTRIBUTING.rst ├── LICENSE ├── MANIFEST.in ├── NOTICE ├── README.rst ├── demos ├── equalization_demo.ipynb ├── feature_extraction_demo.ipynb ├── params.yml ├── preprocessing_demo.ipynb └── segmentation_demo.ipynb ├── docs ├── Makefile ├── _static │ └── theme_overrides.css ├── conf.py ├── index.rst └── make.bat ├── environment.yml ├── requirements.txt ├── setup.cfg ├── setup.py ├── stapl3d ├── __init__.py ├── __version__.py ├── backproject.py ├── blocks.py ├── equalization.py ├── future.py ├── imarisfiles.py ├── pipelines │ ├── .stapl3d.ini │ ├── __init__.py │ ├── functions.sh │ ├── params.yml │ ├── pipeline.py │ ├── pipeline.sh │ ├── pipeline_dualres.sh │ ├── pipeline_equalization.md │ ├── pipeline_equalization.py │ ├── pipeline_preprocessing.md │ ├── pipeline_preprocessing.py │ ├── pipeline_stitching_zen.md │ ├── plantseg_config.yml │ ├── plantseg_predict.yml │ ├── stardist_testing_library.py │ ├── unet3d_memb_predict.yml │ ├── unet3d_memb_train.yml │ ├── unet3d_nucl_predict.yml │ └── unet3d_nucl_train.yml ├── preprocessing │ ├── __init__.py │ ├── biasfield.py │ ├── masking.py │ ├── registration.py │ ├── shading.py │ ├── stitching.ijm │ └── stitching.py ├── profiling │ ├── scanpy_functions.py │ └── umap_plotting.py ├── reporting.py └── segmentation │ ├── __init__.py │ ├── enhance.py │ ├── features.py │ ├── scoring.py │ ├── segment.py │ ├── stardist_nuclei.py │ └── zipping.py └── tests ├── __init__.py ├── test_lint.py └── test_stapl3d.py /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/.editorconfig -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/.gitignore -------------------------------------------------------------------------------- /.prospector.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/.prospector.yml -------------------------------------------------------------------------------- /CHANGELOG.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/CHANGELOG.rst -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/CODE_OF_CONDUCT.rst -------------------------------------------------------------------------------- /CONTRIBUTING.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/CONTRIBUTING.rst -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /NOTICE: -------------------------------------------------------------------------------- 1 | This product includes STAPL3D, software developed by 2 | . 3 | -------------------------------------------------------------------------------- /README.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/README.rst -------------------------------------------------------------------------------- /demos/equalization_demo.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/demos/equalization_demo.ipynb -------------------------------------------------------------------------------- /demos/feature_extraction_demo.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/demos/feature_extraction_demo.ipynb -------------------------------------------------------------------------------- /demos/params.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/demos/params.yml -------------------------------------------------------------------------------- /demos/preprocessing_demo.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/demos/preprocessing_demo.ipynb -------------------------------------------------------------------------------- /demos/segmentation_demo.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/demos/segmentation_demo.ipynb -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/_static/theme_overrides.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/docs/_static/theme_overrides.css -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/docs/index.rst -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/docs/make.bat -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/environment.yml -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/requirements.txt -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/setup.cfg -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/setup.py -------------------------------------------------------------------------------- /stapl3d/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/__init__.py -------------------------------------------------------------------------------- /stapl3d/__version__.py: -------------------------------------------------------------------------------- 1 | __version__ = '1.0.0-beta' 2 | -------------------------------------------------------------------------------- /stapl3d/backproject.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/backproject.py -------------------------------------------------------------------------------- /stapl3d/blocks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/blocks.py -------------------------------------------------------------------------------- /stapl3d/equalization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/equalization.py -------------------------------------------------------------------------------- /stapl3d/future.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/future.py -------------------------------------------------------------------------------- /stapl3d/imarisfiles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/imarisfiles.py -------------------------------------------------------------------------------- /stapl3d/pipelines/.stapl3d.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/.stapl3d.ini -------------------------------------------------------------------------------- /stapl3d/pipelines/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /stapl3d/pipelines/functions.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/functions.sh -------------------------------------------------------------------------------- /stapl3d/pipelines/params.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/params.yml -------------------------------------------------------------------------------- /stapl3d/pipelines/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/pipeline.py -------------------------------------------------------------------------------- /stapl3d/pipelines/pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/pipeline.sh -------------------------------------------------------------------------------- /stapl3d/pipelines/pipeline_dualres.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/pipeline_dualres.sh -------------------------------------------------------------------------------- /stapl3d/pipelines/pipeline_equalization.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/pipeline_equalization.md -------------------------------------------------------------------------------- /stapl3d/pipelines/pipeline_equalization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/pipeline_equalization.py -------------------------------------------------------------------------------- /stapl3d/pipelines/pipeline_preprocessing.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/pipeline_preprocessing.md -------------------------------------------------------------------------------- /stapl3d/pipelines/pipeline_preprocessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/pipeline_preprocessing.py -------------------------------------------------------------------------------- /stapl3d/pipelines/pipeline_stitching_zen.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/pipeline_stitching_zen.md -------------------------------------------------------------------------------- /stapl3d/pipelines/plantseg_config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/plantseg_config.yml -------------------------------------------------------------------------------- /stapl3d/pipelines/plantseg_predict.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/plantseg_predict.yml -------------------------------------------------------------------------------- /stapl3d/pipelines/stardist_testing_library.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/stardist_testing_library.py -------------------------------------------------------------------------------- /stapl3d/pipelines/unet3d_memb_predict.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/unet3d_memb_predict.yml -------------------------------------------------------------------------------- /stapl3d/pipelines/unet3d_memb_train.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/unet3d_memb_train.yml -------------------------------------------------------------------------------- /stapl3d/pipelines/unet3d_nucl_predict.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/unet3d_nucl_predict.yml -------------------------------------------------------------------------------- /stapl3d/pipelines/unet3d_nucl_train.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/pipelines/unet3d_nucl_train.yml -------------------------------------------------------------------------------- /stapl3d/preprocessing/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /stapl3d/preprocessing/biasfield.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/preprocessing/biasfield.py -------------------------------------------------------------------------------- /stapl3d/preprocessing/masking.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/preprocessing/masking.py -------------------------------------------------------------------------------- /stapl3d/preprocessing/registration.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/preprocessing/registration.py -------------------------------------------------------------------------------- /stapl3d/preprocessing/shading.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/preprocessing/shading.py -------------------------------------------------------------------------------- /stapl3d/preprocessing/stitching.ijm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/preprocessing/stitching.ijm -------------------------------------------------------------------------------- /stapl3d/preprocessing/stitching.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/preprocessing/stitching.py -------------------------------------------------------------------------------- /stapl3d/profiling/scanpy_functions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/profiling/scanpy_functions.py -------------------------------------------------------------------------------- /stapl3d/profiling/umap_plotting.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/profiling/umap_plotting.py -------------------------------------------------------------------------------- /stapl3d/reporting.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/reporting.py -------------------------------------------------------------------------------- /stapl3d/segmentation/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /stapl3d/segmentation/enhance.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/segmentation/enhance.py -------------------------------------------------------------------------------- /stapl3d/segmentation/features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/segmentation/features.py -------------------------------------------------------------------------------- /stapl3d/segmentation/scoring.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/segmentation/scoring.py -------------------------------------------------------------------------------- /stapl3d/segmentation/segment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/segmentation/segment.py -------------------------------------------------------------------------------- /stapl3d/segmentation/stardist_nuclei.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/segmentation/stardist_nuclei.py -------------------------------------------------------------------------------- /stapl3d/segmentation/zipping.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/stapl3d/segmentation/zipping.py -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | -------------------------------------------------------------------------------- /tests/test_lint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/tests/test_lint.py -------------------------------------------------------------------------------- /tests/test_stapl3d.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RiosGroup/STAPL3D/HEAD/tests/test_stapl3d.py --------------------------------------------------------------------------------