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# Table of contents
# Learn more at https://jupyterbook.org/customize/toc.html
format: jb-book
root: intro
parts:
- caption: Course Preparation
chapters:
- file: day0_preparation/readme.md
- caption: Monday
chapters:
- file: day1.1_python_basics/readme.md
sections:
- file: day1.1_python_basics/01_jupyter_notebooks.ipynb
- file: day1.1_python_basics/02_basic_terms_and_types.ipynb
- file: day1.1_python_basics/03_notebook_pitfalls.ipynb
- file: day1.1_python_basics/04_math_in_python.ipynb
- file: day1.1_python_basics/05_sequence_types.ipynb
- file: day1.1_python_basics/05a_indexing_sequences.ipynb
- file: day1.1_python_basics/05b_masking_arrays.ipynb
- file: day1.1_python_basics/06_dictionaries_and_tables.ipynb
- file: day1.1_python_basics/07_conditions.ipynb
- file: day1.1_python_basics/08_loops.ipynb
- file: day1.1_python_basics/09_custom_functions.ipynb
- file: day1.2_file_handling/readme.md
sections:
- file: day1.2_file_handling/01_list_files_in_a_folder.ipynb
- file: day1.2_file_handling/02_interactive_image_visualization.ipynb
- file: day1.2_file_handling/03_opening_images_using_aicsimageio.ipynb
- file: day1.2_file_handling/04_nextcloud.ipynb
- file: day1.2_file_handling/05_bia_bob.ipynb
- file: day1.3_image_processing_basics/readme.md
sections:
- file: day1.3_image_processing_basics/00_images_as_arrays.ipynb
- file: day1.3_image_processing_basics/01_opening_visualizing_images.ipynb
- file: day1.3_image_processing_basics/02_Brightness_and_Contrast.ipynb
- file: day1.3_image_processing_basics/03_Cropping_images.ipynb
- file: day1.3_image_processing_basics/04_Image_Filters.ipynb
- file: day1.3_image_processing_basics/05_Binarization.ipynb
- file: day1.3_image_processing_basics/06_Morphological_operations.ipynb
- file: day1.3_image_processing_basics/bonus_simulated_dataset_remove_noise_and_background.ipynb
- caption: Tuesday
chapters:
- file: day2.1_image_segmentation/readme.md
sections:
- file: day2.1_image_segmentation/10_napari-assistant.md
- file: day2.1_image_segmentation/11_notebook_export.md
- file: day2.1_image_segmentation/12_voronoi_otsu_labeling.ipynb
- file: day2.1_image_segmentation/13_watershed.ipynb
- file: day2.1_image_segmentation/22_napari_intro.ipynb
- file: day2.1_image_segmentation/30_Segmentation_3D.ipynb
- file: day2.2_feature_extraction/readme.md
sections:
- file: day2.2_feature_extraction/01_count_blobs.ipynb
- file: day2.2_feature_extraction/02_statistics_with_scikit_image.ipynb
- file: day2.2_feature_extraction/03_statistics_with_simpleitk.ipynb
- file: day2.2_feature_extraction/04_roundness_circularity.ipynb
- file: day2.3_machine_learning/readme.md
sections:
- file: day2.3_machine_learning/interaction/pixel_classification/sources/pixel_classification
- file: day2.3_machine_learning/interaction/object_classification/sources/readme
- file: day2.3_machine_learning/notebooks/03_apoc_object_segmenter
- file: day2.4_tabular_data_wrangling/readme.md
sections:
- file: day2.4_tabular_data_wrangling/01_introduction_dataframes.ipynb
- file: day2.4_tabular_data_wrangling/02_selecting_dataframes.ipynb
- file: day2.4_tabular_data_wrangling/03_appending_dataframes.ipynb
- file: day2.4_tabular_data_wrangling/04_handle_missing_data.ipynb
- file: day2.4_tabular_data_wrangling/05_group_by.ipynb
- file: day2.4_tabular_data_wrangling/06_tidy_data.ipynb
- caption: Wednesday
chapters:
- file: day3.1_explorative_data_science/readme.md
sections:
- file: day3.1_explorative_data_science/0_raw_data_preparation.ipynb
- file: day3.1_explorative_data_science/1_data_prep_segment_dapi_batch_process.ipynb
- file: day3.1_explorative_data_science/2_data_prep_segment_actin_batch_process.ipynb
- file: day3.1_explorative_data_science/3_data_prep_segment_tubulin_batch_process.ipynb
- file: day3.1_explorative_data_science/4_data_prep_quantitative_measurements_extraction.ipynb
- file: day3.1_explorative_data_science/5_Interactive_features_exploration_dim_red_one_compound.ipynb
- file: day3.1_explorative_data_science/6_Interactive_dim_red_and_clustering_comparing_compounds.ipynb
- file: day3.2_data_visualization/readme.md
- file: day3.3a_basic_plotting/readme.md
sections:
- file: day3.3a_basic_plotting/01_Introduction_to_Seaborn.ipynb
- file: day3.3a_basic_plotting/02_Plotting_distributions.ipynb
- file: day3.3a_basic_plotting/03_BONUS_Multivariate_views.ipynb
- file: day3.3b_advanced_plotting/readme.md
sections:
- file: day3.3b_advanced_plotting/00_getdata.ipynb
# - file: day3.3b_advanced_plotting/01_seabornobj_open.ipynb
- file: day3.3b_advanced_plotting/01_seabornobj_solution.ipynb
# - file: day3.3b_advanced_plotting/02_dataviz_MLunsupervised_open.ipynb
- file: day3.3b_advanced_plotting/02_dataviz_MLunsupervised_solution.ipynb
# - file: day3.3b_advanced_plotting/03_dataviz_MLsupervised_open.ipynb
- file: day3.3b_advanced_plotting/03_dataviz_MLsupervised_solution.ipynb
- caption: Information
chapters:
- file: CONDUCT
- file: CONTRIBUTING
- file: LICENSE
- file: imprint