LICENSE
Readme.md
_config.yml
_toc.yml
environment.yml
pyproject.toml
requirements.txt
setup.cfg
setup.py
tox.ini
.github/workflows/book.yml
.github/workflows/debug.yml
.github/workflows/python-package-conda.yml
.github/workflows/test_and_deploy.yml
images/logo.png
morphodynamics/__init__.py
morphodynamics/analysis_par.py
morphodynamics/correlation.py
morphodynamics/displacementestimation.py
morphodynamics/folders.py
morphodynamics/functionaldefinition.py
morphodynamics/morpho_segmentation.py
morphodynamics/segmentation.py
morphodynamics/splineutils.py
morphodynamics/syntheticdata.py
morphodynamics/utils.py
morphodynamics/version.py
morphodynamics/windowing.py
morphodynamics.egg-info/PKG-INFO
morphodynamics.egg-info/SOURCES.txt
morphodynamics.egg-info/dependency_links.txt
morphodynamics.egg-info/requires.txt
morphodynamics.egg-info/top_level.txt
morphodynamics/plots/__init__.py
morphodynamics/plots/animate_plots.py
morphodynamics/plots/show_plots.py
morphodynamics/plots/ui_wimage.py
morphodynamics/store/__init__.py
morphodynamics/store/dataset.py
morphodynamics/store/parameters.py
morphodynamics/store/results.py
morphodynamics/tests/test_analysis_par.py
mydocs/Analysis_with_morpho_segmentation.ipynb
mydocs/Analysis_without_UI.ipynb
mydocs/Data.ipynb
mydocs/Data_analysis.ipynb
mydocs/Installation.ipynb
mydocs/Introduction.ipynb
mydocs/Napari_Plugin.ipynb
mydocs/code_structure.ipynb
mydocs/generate_HTML_UI.ipynb
mydocs/segmentation.ipynb
mydocs/usage_step_by_step.ipynb
mydocs/images/UI.html
mydocs/images/UI.png
mydocs/images/ilastik.png
notebooks/Morpho_segmentation.ipynb
notebooks/Postprocessing.ipynb
notebooks/stitching_h5.ipynb
synthetic/simulate_data.ipynb
synthetic/synthetic_testUI.ipynb
synthetic/synthetic_test_cellpose.ipynb
synthetic/synthetic_test_ilastik.ipynb
synthetic/synthetic_test_postprocessing.ipynb
synthetic/data/synth_ch1.h5
synthetic/data/synth_ch2.h5
synthetic/data/synth_ch3.h5
synthetic/data/Ilastiksegmentation/segmented_k_00.tif
synthetic/data/Ilastiksegmentation/segmented_k_01.tif
synthetic/data/Ilastiksegmentation/segmented_k_02.tif
synthetic/data/Ilastiksegmentation/segmented_k_03.tif
synthetic/data/Ilastiksegmentation/segmented_k_04.tif
synthetic/data/Ilastiksegmentation/segmented_k_05.tif
synthetic/data/Ilastiksegmentation/segmented_k_06.tif
synthetic/data/Ilastiksegmentation/segmented_k_07.tif
synthetic/data/Ilastiksegmentation/segmented_k_08.tif
synthetic/data/Ilastiksegmentation/segmented_k_09.tif
synthetic/data/Ilastiksegmentation/segmented_k_10.tif
synthetic/data/Ilastiksegmentation/segmented_k_11.tif
synthetic/data/Ilastiksegmentation/segmented_k_12.tif
synthetic/data/Ilastiksegmentation/segmented_k_13.tif
synthetic/data/Ilastiksegmentation/segmented_k_14.tif
synthetic/data/Ilastiksegmentation/segmented_k_15.tif
synthetic/data/Ilastiksegmentation/segmented_k_16.tif
synthetic/data/Ilastiksegmentation/segmented_k_17.tif
synthetic/data/Ilastiksegmentation/segmented_k_18.tif
synthetic/data/Ilastiksegmentation/segmented_k_19.tif
synthetic/data/Ilastiksegmentation/segmented_k_20.tif
synthetic/data/Ilastiksegmentation/segmented_k_21.tif
synthetic/data/Ilastiksegmentation/segmented_k_22.tif
synthetic/data/Ilastiksegmentation/segmented_k_23.tif
synthetic/data/Ilastiksegmentation/segmented_k_24.tif
synthetic/data/Ilastiksegmentation/segmented_k_25.tif
synthetic/data/Ilastiksegmentation/segmented_k_26.tif
synthetic/data/Ilastiksegmentation/segmented_k_27.tif
synthetic/data/Ilastiksegmentation/segmented_k_28.tif
synthetic/data/Ilastiksegmentation/segmented_k_29.tif
synthetic/data/Ilastiksegmentation/segmented_k_30.tif
synthetic/data/Ilastiksegmentation/segmented_k_31.tif
synthetic/data/Ilastiksegmentation/segmented_k_32.tif
synthetic/data/Ilastiksegmentation/segmented_k_33.tif
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synthetic/data/Ilastiksegmentation/segmented_k_35.tif
synthetic/data/Ilastiksegmentation/segmented_k_36.tif
synthetic/data/Ilastiksegmentation/segmented_k_37.tif
synthetic/data/Ilastiksegmentation/segmented_k_38.tif
synthetic/data/Ilastiksegmentation/segmented_k_39.tif