.gitattributes
.gitignore
LICENSE
README.md
requirements.txt
setup.py
SyMBac/OPL_generation.py
SyMBac/PSF.py
SyMBac/Phase_PSF.png
SyMBac/__init__.py
SyMBac/cell.py
SyMBac/cell_colony.py
SyMBac/cell_geometry.py
SyMBac/general_drawing.py
SyMBac/interactive_kernel.py
SyMBac/misc.py
SyMBac/phase_contrast_drawing.py
SyMBac/plotting.py
SyMBac/pySHINE.py
SyMBac/scene_functions.py
SyMBac/scene_functions_colony.py
SyMBac/trench_geometry.py
SyMBac.egg-info/PKG-INFO
SyMBac.egg-info/SOURCES.txt
SyMBac.egg-info/dependency_links.txt
SyMBac.egg-info/requires.txt
SyMBac.egg-info/top_level.txt
SyMBac/image_manipulation/pySHINE.py
examples/Drawing_Bacillus.ipynb
examples/Drawing_DeLTA.ipynb
examples/Drawing_Narrow_Trench.ipynb
examples/Drawing_Phase_Contrast_100x_oil.ipynb
examples/Drawing_Phase_Contrast_100x_oil_stationary.ipynb
examples/Drawing_Phase_Contrast_Ph2_data.ipynb
examples/Untitled.ipynb
examples/__init__.py
examples/image_stack.tif
examples/true_mask_stack.tif
examples/deep_learning/DeLTA/LICENSE
examples/deep_learning/DeLTA/README.md
examples/deep_learning/DeLTA/all_mother_props_1.pickle
examples/deep_learning/DeLTA/all_mother_props_2.pickle
examples/deep_learning/DeLTA/bioformats2sequence.py
examples/deep_learning/DeLTA/bioformats_env.yml
examples/deep_learning/DeLTA/config.py
examples/deep_learning/DeLTA/data.py
examples/deep_learning/DeLTA/data_structure.txt
examples/deep_learning/DeLTA/delta_env.yml
examples/deep_learning/DeLTA/interactive_preprocess.ipynb
examples/deep_learning/DeLTA/interactive_segment.ipynb
examples/deep_learning/DeLTA/interactive_train_seg.ipynb
examples/deep_learning/DeLTA/interactive_train_seg_multi_training_amount.ipynb
examples/deep_learning/DeLTA/model.py
examples/deep_learning/DeLTA/pipeline.py
examples/deep_learning/DeLTA/segmentation.py
examples/deep_learning/DeLTA/segmentation_chambers.py
examples/deep_learning/DeLTA/tracking.py
examples/deep_learning/DeLTA/train_seg.py
examples/deep_learning/DeLTA/train_seg_chambers.py
examples/deep_learning/DeLTA/train_track.py
examples/deep_learning/DeLTA/utilities.py
examples/deep_learning/StarDist/stardist_data.ipynb
examples/deep_learning/StarDist/stardist_predict.ipynb
examples/deep_learning/StarDist/stardist_predict_100x_oil.ipynb
examples/deep_learning/StarDist/stardist_training_100x_oil.ipynb
examples/deep_learning/StarDist/stardist_training_Ph2.ipynb
examples/deep_learning/StarDist/test.pdf
examples/deep_learning/StarDist/test_1600_epoch.pdf
examples/deep_learning/StarDist/test_1600_epoch_50perc.pdf
examples/deep_learning/StarDist/test_mixed_cells.png
examples/deep_learning/StarDist/test_nohist.pdf
examples/deep_learning/StarDist/test_nohist.png
examples/old_tests/cell_class_dynamics_test.py
examples/old_tests/cell_dynamics_test.py
examples/old_tests/draw_cell_test.py
examples/old_tests/ipython_cell_input.py
examples/old_tests/morphologies_exponential.pickle
examples/old_tests/trench_creation.py
readme_files/example_comparison.jpeg
readme_files/image_generation.jpeg
readme_files/speed_comparison.png
readme_files/symbac_sliders.gif
readme_files/training.png
sample_images/sample_100x.tiff