select topics for gpt-2024.1.6

.gitignore

@@ -20,3 +20,5 @@ schematics/Jaccard_index_binary.png
 docs/29_algorithm_validation/ideas.ipynb
 docs/29_algorithm_validation/solution for exercise - metrics to investigate segmentation results.ipynb
 docs/22_feature_extraction/blobs_analysis.csv
+
+docs/_build

docs/_toc.yml

@@ -10,98 +10,33 @@ parts:
     - file: 01_introduction/trailer
     - file: 01_introduction/readme
 
-    - file: 02_python_basics/readme
-      sections:
-      - file: 02_python_basics/01_our_first_juptyer_notebook
-      - file: 02_python_basics/02_Math_in_python
-      - file: 02_python_basics/03_Dont_try_this_at_home
-      - file: 02_python_basics/04_Basic_types
-      - file: 02_python_basics/05_lists_tuples
-      - file: 02_python_basics/05a_cropping_lists
-      - file: 02_python_basics/05b_sorting_lists
-      - file: 02_python_basics/06_Dictionaries_and_tables
-      - file: 02_python_basics/07_Conditions
-      - file: 02_python_basics/08_loops
-      - file: 02_python_basics/09_custom_functions
-      - file: 02_python_basics/10_Import_packages
-
-    - file: 04_sustainable_code/readme
-      sections:
-      - file: 04_sustainable_code/readable_code
-      - file: 04_sustainable_code/magic_numbers
-      - file: 04_sustainable_code/divide_and_rule
-      - file: 04_sustainable_code/dont_repeat_yourself
-      - file: 04_sustainable_code/keep_it_short_and_simple.ipynb
-
-    - file: 12_image_analysis_basics/readme
-      sections:
-      - file: 12_image_analysis_basics/01_Images_as_arrays
-      - file: 12_image_analysis_basics/02_Opening_visualizing_images
-      - file: 12_image_analysis_basics/brightness_and_contrast
-      - file: 12_image_analysis_basics/03_Computing_with_images
-      - file: 12_image_analysis_basics/04_Cropping_images
-      - file: 12_image_analysis_basics/05_Masking_images.ipynb
-      - file: 12_image_analysis_basics/06_multi_channel_image_data
-
     - file: 12a_image_file_formats/readme
       sections:
       - file: 12a_image_file_formats/opening_images
       - file: 12a_image_file_formats/opening_images_using_aicsimageio
-      - file: 12a_image_file_formats/opening_czi_files
-      - file: 12a_image_file_formats/opening_lif_files
-      - file: 12a_image_file_formats/opening_tif_folders
       - file: 12a_image_file_formats/tiled_image_file_formats_zarr
-      - file: 12a_image_file_formats/image_file_formats
 
     #  - file: 12_image_analysis_basics/skeletonization
     # todo: https://github.com/jni/skan
     #  - file: 12_image_analysis_basics/analyse_banana_data_set
 
-    - file: 14_machine_learning_basics/readme
-      sections:
-      - file: 14_machine_learning_basics/supervised_machine_learning
-      - file: 14_machine_learning_basics/unsupervised_machine_learning
-      - file: 14_machine_learning_basics/scaling
 
     - file: 16_3d_image_visualization/readme
       sections:
       - file: 16_3d_image_visualization/10_nd_image_data
     # projections
       - file: 16_3d_image_visualization/inspecting_3d_images
-      - file: 16_3d_image_visualization/napari
 
     - file: 18_image_filtering/readme
       sections:
       - file: 18_image_filtering/image_filtering
       #- file: 18_image_filtering/01_Filtering # obsolete
-      - file: 18_image_filtering/convolution
       - file: 18_image_filtering/02_noise_removal
       - file: 18_image_filtering/03_background_removal
       - file: 18_image_filtering/divide_by_gaussian
       - file: 18_image_filtering/edge_detection_and_enhancement
       - file: 18_image_filtering/simpleitk
 
-    - file: 18a_deconvolution/readme
-      sections:
-      - file: 18a_deconvolution/introduction_deconvolution
-      - file: 18a_deconvolution/extract_psf
-      - file: 18a_deconvolution/richardson_lucy_deconvolution
-    #  - file: 18a_deconvolution/deconvolution_pycudadecon
-
-    - file: 19_spatial_transforms/readme
-      sections:
-    # cropping
-    # slicing
-      - file: 19_spatial_transforms/coordinate_systems
-      - file: 19_spatial_transforms/cropping
-      - file: 19_spatial_transforms/scaling
-      - file: 19_spatial_transforms/affine_transforms_scikit_image
-      - file: 19_spatial_transforms/affine_transforms_scipy
-      - file: 19_spatial_transforms/affine_transforms_cupy
-      - file: 19_spatial_transforms/affine_transforms_clesperanto
-      - file: 19_spatial_transforms/scaling_coordinate_lists
-      - file: 19_spatial_transforms/downsampling_with_denoising
-    #  - file: 19_spatial_transforms/transpose
 
   - caption: Image Segmentation
     chapters:
@@ -165,12 +100,6 @@ parts:
       - file: 20h_segmentation_post_processing/label_edges
       - file: 20h_segmentation_post_processing/inner_and_outer_cell_borders
       - file: 20h_segmentation_post_processing/refine_cell_segmentation
-      - file: 20h_segmentation_post_processing/mimicking_imagej_watershed
-
-    - file: 23_blob_detection/readme
-      sections:
-      - file: 23_blob_detection/local_maxima_detection
-      - file: 23_blob_detection/blog_dog_log_doh
 
     - file: 21_surface_processing/readme
       sections:
@@ -235,32 +164,9 @@ parts:
       #- file: 28_colocalization/measure_overlap_between_label_images
 
 
-    - file: 29_algorithm_validation/readme
-      sections:
-      - file: 29_algorithm_validation/segmentation_quality_estimation
-      - file: 29_algorithm_validation/metrics_to_investigate_segmentation_quality
-      - file: 29_algorithm_validation/validate-spot-counting
-      - file: 29_algorithm_validation/scenario_otsu_segmentation
-      - file: 29_algorithm_validation/visual_comparison
-      - file: 29_algorithm_validation/quantiative_comparison
-      - file: 29_algorithm_validation/jaccard_index_versus_accuracy
-
-    - file: 30_simulating_data/readme
-      sections:
-      - file: 30_simulating_data/basic_simulation_noise_background_nuclei
-      - file: 30_simulating_data/counting_cell_neighbors_in_tissues
-
   - caption: Advanced techniques
     chapters:
 
-    - file: 03_advanced_python/readme
-      sections:
-      - file: 03_advanced_python/custom_libraries
-      - file: 03_advanced_python/functional_parameters
-      - file: 03_advanced_python/partial
-      - file: 03_advanced_python/parallelization
-      - file: 03_advanced_python/owncloud
-
     - file: 15_gpu_acceleration/readme
       sections:
       - file: 15_gpu_acceleration/clesperanto
@@ -269,13 +175,6 @@ parts:
       - file: 15_gpu_acceleration/memory_management
       - file: 15_gpu_acceleration/further_reading
 
-    - file: 31_graphical_user_interfaces/readme
-      sections:
-      - file: 31_graphical_user_interfaces/napari
-      - file: 31_graphical_user_interfaces/napari_magicgui
-      - file: 31_graphical_user_interfaces/napari-skimage-regionprops
-      - file: 31_graphical_user_interfaces/napari_dask
-      - file: 31_graphical_user_interfaces/napari_crop
 
     - file: 32_tiled_image_processing/readme
       sections:
@@ -286,61 +185,7 @@ parts:
       - file: 32_tiled_image_processing/tiled_object_measurements
       - file: 32_tiled_image_processing/tiled_area_mapping
       - file: 32_tiled_image_processing/tiled_nuclei_counting
-
-    - file: 33_batch_processing/readme
-      sections: 
-      - file: 33_batch_processing/12_process_folders
-      - file: 33_batch_processing/14_process_timelapse
-    #  - file: 18_image_filtering/run_on_all_hyperslices
-
-    #  - file: 27_cell_classification/cell_classification
-    #  - file: 27_cell_classification/cell_classification_correction.ipynb
-
-    - file: 34_timelapse_analysis/readme
-      sections:
-      - file: 34_timelapse_analysis/intensity_over_time
-      - file: 34_timelapse_analysis/tracking
-
-    - file: 35_parameter_optimization/readme
-      sections:
-      - file: 35_parameter_optimization/optimization_basics
-      - file: 35_parameter_optimization/label_image_optimizer
-      - file: 35_parameter_optimization/membrane_segmentation
-
-    - file: 07_prompt_engineering/readme
-      sections:
-      - file: 07_prompt_engineering/01_prompting
-      - file: 07_prompt_engineering/01_use_cases
-      - file: 07_prompt_engineering/02_generating_images
-      - file: 07_prompt_engineering/02_generating_images_using_huggingface
-      - file: 07_prompt_engineering/02_generating_mri_images.ipynb
-      - file: 07_prompt_engineering/03_generating_code
-      - file: 07_prompt_engineering/04_generating_code_for_processing_images
-      - file: 07_prompt_engineering/05_generating_advanced_image_processing_code
-      - file: 07_prompt_engineering/20_langchain
-      - file: 07_prompt_engineering/30_langchain_bia
-      - file: 07_prompt_engineering/30_langchain_bia_choosing_algorithms
-      - file: 07_prompt_engineering/40_bia_bob
-      - file: 07_prompt_engineering/41_bug_fixing
-      - file: 07_prompt_engineering/42_documenting_code
-      - file: 07_prompt_engineering/45_prompting_pandas
-      - file: 07_prompt_engineering/50_inpainting_darth_d
-      - file: 07_prompt_engineering/50_inpainting_huggingface
-      - file: 07_prompt_engineering/60_image_variations_huggingface
-      - file: 07_prompt_engineering/60_image_variations_pix2pix
-      - file: 07_prompt_engineering/60_image_variations_darth_d
-      - file: 07_prompt_engineering/80_llm_fine_tuning
-      - file: 07_prompt_engineering/99_versions
-
-
-  - caption: Workflow automation
-    chapters:
-    - file: 70_workflows/readme
-      sections:
-      - file: 70_workflows/napari-assistant
-      - file: 70_workflows/notebook_export
-      - file: 70_workflows/napari_workflows
-
+
 
   - caption: Tabular data, plots and statistics
     chapters: