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SimpleITK Setup and Schedule

Learn how to set up SimpleITK and follow the schedule for the SPIE 2019 course, covering topics such as data augmentation, image analysis, and more. Follow step-by-step instructions to configure your environment and access course materials efficiently.

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SimpleITK Setup and Schedule

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  1. SimpleITK Setup and Schedule Ziv Yaniv1,2 , Bradley C. Lowekamp1,2 1National Institutes of Health2Medical Science and Computing LLC

  2. Setup • Download and install the Fiji image viewer into the appropriate directory: • Win: the user directory [C:\Users\your_user_name\] • Linux: ~/bin/ • OS X: /Applications/ • Download and install the most recent version of Anaconda for your operating system. We assume it is installed in a directory named anaconda3. Regardless of the installer, we will be working with Python 3.6 . • On Windows: open the Anaconda Prompt (found under the Anaconda3 start menu).On Linux/Mac: on the command line source path_to_anaconda3/bin/activate base • Update the root anaconda environment and install the git version control system into it: conda update condaconda update anaconda conda install git

  3. Setup • Clone the repository: git clone https://github.com/SimpleITK/SPIE2019_COURSE.git • Create the virtual environment containing all packages required for the course: condaenv create -f SPIE2019_COURSE/environment.yml • Activate the virtual environment (Win: open the Anaconda Prompt, Linux/Mac: commandline):conda activate sitkpySPIE19 • On the command line:jupyternbextension enable --py --sys-prefix widgetsnbextension • Go over the setup notebook (requires internet connectivity):jupyter notebook SPIE2019_COURSE/setup.ipynb

  4. Schedule [1:30PM- 2:00PM] history and overview of SimpleITK. [2:00PM- 2:40PM] spatial transformations, images and resampling. [2:40PM - 3:00PM] data augmentation for deep learning. [3:00PM – 3:30PM] coffee break. [3:30PM – 4:40PM] basic registration, advanced registration. [4:40PM – 5:15PM] segmentation image analysis workflow. [5:15PM - 5:30PM] notebook development and testing, concluding remarks.

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