├── .circleci └── config.yml ├── .github ├── dependabot.yml └── workflows │ ├── main.yml │ └── scheduled_or_manual.yml ├── .gitignore ├── .readthedocs.yaml ├── CONTRIBUTING.md ├── Data ├── brains_manifest.json ├── characterize_data_user_defaults.json ├── manifest.json └── min_manifest.json ├── LICENSE ├── Python ├── 00_Setup.ipynb ├── 01_Image_Basics.ipynb ├── 02_Pythonic_Image.ipynb ├── 03_Image_Details.ipynb ├── 04_Image_Display.ipynb ├── 05_Results_Visualization.ipynb ├── 10_matplotlibs_imshow.ipynb ├── 11_Progress.ipynb ├── 20_Expand_With_Interpolators.ipynb ├── 21_Transforms_and_Resampling.ipynb ├── 22_Transforms.ipynb ├── 300_Segmentation_Overview.ipynb ├── 30_Segmentation_Region_Growing.ipynb ├── 31_Levelset_Segmentation.ipynb ├── 32_Watersheds_Segmentation.ipynb ├── 33_Segmentation_Thresholding_Edge_Detection.ipynb ├── 34_Segmentation_Evaluation.ipynb ├── 35_Segmentation_Shape_Analysis.ipynb ├── 36_Microscopy_Colocalization_Distance_Analysis.ipynb ├── 51_VH_Segmentation1.ipynb ├── 55_VH_Resample.ipynb ├── 56_VH_Registration1.ipynb ├── 60_Registration_Introduction.ipynb ├── 61_Registration_Introduction_Continued.ipynb ├── 62_Registration_Tuning.ipynb ├── 63_Registration_Initialization.ipynb ├── 64_Registration_Memory_Time_Tradeoff.ipynb ├── 65_Registration_FFD.ipynb ├── 66_Registration_Demons.ipynb ├── 67_Registration_Semiautomatic_Homework.ipynb ├── 68_Registration_Errors.ipynb ├── 69_x-ray-panorama.ipynb ├── 70_Data_Augmentation.ipynb ├── 71_Trust_But_Verify.ipynb ├── ITKv4RegistrationComponentsDiagram.svg ├── ImageOriginAndSpacing.png ├── Output │ └── .gitignore ├── README.md ├── environment.yml ├── fle.svg ├── gui.py ├── hkaAngle.png ├── knobs.jpg ├── myshow.py ├── popi_utilities_setup.py ├── registration_callbacks.py ├── registration_utilities.py ├── requirements.txt ├── resampling.svg ├── scripts │ └── characterize_data.py ├── setup_for_testing.py └── update_path_to_download_script.py ├── R ├── 00_Setup.ipynb ├── 22_Transforms.ipynb ├── 300_Segmentation_Overview.ipynb ├── 33_Segmentation_Thresholding_Edge_Detection.ipynb ├── 34_Segmentation_Evaluation.ipynb ├── 35_Cell_Segmentation.ipynb ├── 60_Registration_Introduction.ipynb ├── 61_Registration_Introduction_Continued.ipynb ├── 65_Registration_FFD.ipynb ├── 66_Registration_Demons.ipynb ├── 70_Data_Augmentation.ipynb ├── ITKv4RegistrationComponentsDiagram.svg ├── Image_Basics.ipynb ├── Output │ └── .gitignore ├── README.md ├── R_style_image.ipynb ├── downloaddata.R ├── registration_utilities.R ├── setup_for_testing.R └── viewing.R ├── README.md ├── SharedImages └── ITKv4RegistrationComponentsDiagram.svg ├── Utilities ├── ClearAllOutputs.py ├── downloaddata.py ├── foldermd5sums.py ├── intro_animation.py └── notes.txt ├── docs ├── Makefile ├── make.bat ├── requirements.txt ├── rtd-requirements.txt └── source │ ├── _static │ ├── orange_itk_icon.svg │ └── organe_itk_banner.svg │ ├── conf.py │ └── index.rst ├── environment.yml ├── registration_visualization.gif ├── 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