├── .gitignore ├── README.md ├── code ├── helper │ ├── __init__.py │ ├── callbacks.py │ ├── contours_to_labels.ipynb │ ├── data_provider.py │ ├── metrics.py │ ├── model_builder.py │ ├── objectives.py │ └── visualize.py ├── predict.py ├── predict_generator-boundary.py ├── predict_generator.py ├── predict_manual.py ├── preprocessing │ ├── archive │ │ ├── preprocessing_BBBC022_01_labels_to_one_hot.ipynb │ │ ├── preprocessing_BBBC022_02_split_up.ipynb │ │ ├── preprocessing_BBBC022_03_window.ipynb │ │ ├── preprocessing_set01.py │ │ ├── preprocessing_set02_step01.ipynb │ │ ├── preprocessing_set02_step02.ipynb │ │ ├── preprocessing_set02_step03.py │ │ ├── preprocessing_set03_step01.ipynb │ │ ├── preprocessing_set03_step02.ipynb │ │ └── preprocessing_set03_step03.ipynb │ └── preprocessing_BBBC022.ipynb ├── run_jobs.sh ├── segmentation.cppipe ├── training_DL_on_CP.py ├── training_DL_on_Hand.py ├── training_DL_on_Hand_boundary.py └── training_DL_on_Hand_boundary_augment.py ├── data └── BBBC022 │ ├── raw │ └── get_raw_images.ipynb │ ├── setup_dirs.sh │ ├── test.txt │ ├── training.txt │ └── validation.txt ├── experiments ├── CP │ ├── CP_vs_GT.ipynb │ ├── results_table_CP.txt │ └── visualize_errors.ipynb ├── DL_on_CP │ ├── DL_on_CP_2_label.ipynb │ ├── DL_on_CP_vs_GT.ipynb │ ├── results_table_DL_on_CP.txt │ ├── results_table_DL_on_CP_bb.txt │ └── visualize_errors.ipynb ├── DL_on_Hand │ ├── DL_on_Hand_2 │ │ └── results_table_DL_on_Hand_2.txt │ ├── DL_on_Hand_2_label.ipynb │ ├── DL_on_Hand_4 │ │ └── results_table_DL_on_Hand_4.txt │ ├── DL_on_Hand_6 │ │ └── results_table_DL_on_Hand_6.txt │ ├── DL_on_Hand_8 │ │ └── results_table_DL_on_Hand_8.txt │ ├── DL_on_Hand_vs_GT.ipynb │ └── visualize_errors.ipynb ├── DL_on_Hand_boundary │ ├── DL_on_Hand_boundary_2 │ │ └── results_table_DL_on_Hand_boundary_2.txt │ ├── DL_on_Hand_boundary_2_label.ipynb │ ├── DL_on_Hand_boundary_4 │ │ └── results_table_DL_on_Hand_boundary_4.txt │ ├── DL_on_Hand_boundary_6 │ │ └── results_table_DL_on_Hand_boundary_6.txt │ ├── DL_on_Hand_boundary_8 │ │ └── results_table_DL_on_Hand_boundary_8.txt │ ├── DL_on_Hand_boundary_soft │ │ └── results_table_DL_on_Hand_boundary_soft.txt │ ├── DL_on_Hand_boundary_vs_GT.ipynb │ └── visualize_errors.ipynb ├── DL_on_Hand_boundary_augment │ ├── DL_on_Hand_boundary_augment │ │ └── results_table_DL_on_Hand_boundary_augment.txt │ ├── DL_on_Hand_boundary_augment_2_label.ipynb │ ├── DL_on_Hand_boundary_augment_vs_GT.ipynb │ └── visualize_errors.ipynb ├── GT_segmentations │ └── get_gt_segmentations.ipynb ├── results_analysis │ └── bootstrap.R └── timing │ ├── prediction_analysis.ipynb │ ├── summary_timing.txt │ └── time_measurement.ipynb ├── poster ├── demo.ipynb └── visualizations.ipynb ├── thesis_final.compressed.pdf └── visualization ├── CellArt.ipynb ├── vis_benchmark_hand.ipynb ├── vis_merge.ipynb ├── vis_merge_annot_boundaries.eps ├── vis_merge_img.eps └── vis_merge_merge.eps /.gitignore: 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