├── .gitignore ├── 00-Index.ipynb ├── 01-Python_bare_minimum.ipynb ├── 02-Numpy_images.ipynb ├── 03-Matplotlib_images.ipynb ├── 04-Image_import.ipynb ├── 05-Filtering_thresholding.ipynb ├── 06-Binary_operations.ipynb ├── 07-Packaging_code.ipynb ├── 08-Time_lapse_tracking.ipynb ├── 09-Pattern_matching.ipynb ├── 10-Watershed.ipynb ├── 11-3D_image_processing.ipynb ├── 12-Registration.ipynb ├── 13-ML_based_segmentation.ipynb ├── 14-PyImageJ.ipynb ├── 15-clijpy.ipynb ├── 16-Experiment_analysis.ipynb ├── LICENSE ├── README.md ├── binder ├── environment.yml └── postBuild ├── course_functions.py ├── illustrations ├── fiji_multiD.png ├── filtering.gif ├── help.png ├── napari.png ├── napari2.png └── watershed.gif ├── installation ├── download_data.py └── environment_minimal.yml └── utils ├── automate_colab_editing.ipynb ├── demo_notebook.ipynb ├── demo_notebook2.ipynb ├── questions.csv └── questions_to_markdown.ipynb /.gitignore: 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