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

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 conda conda update anaconda conda install git

Setup Clone the repository: git clone https://github.com/SimpleITK/SPIE2019_COURSE.git Create the virtual environment containing all packages required for the course: conda env 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: jupyter nbextension enable --py --sys-prefix widgetsnbextension Go over the setup notebook (requires internet connectivity): jupyter notebook SPIE2019_COURSE/setup.ipynb

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.