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Preparation

Format

The tutorial consists of lecture segments, followed by hands-on exercises. We strongly encourage you to bring a laptop with all the required packages installed in order to participate fully.

Software required

  • Python

If you are new to Python, please install the Anaconda distribution for Python version 3 (available on OSX, Linux, and Windows). Everyone else, feel free to use your favorite distribution, but please ensure the requirements below are met:

  • numpy >= 1.12
  • scipy >= 1.0
  • matplotlib >= 2.1
  • scikit-image >= 0.15
  • scikit-learn >= 0.18
  • itk >= 4.1

Please see "Test your setup" below.

  • ITK

ITK is an open-source toolkit for multidimensional image analysis. If you are using Anaconda, it is easy to install ITK using the conda-forge repository, through the following command:

$ conda install -c conda-forge itk

You can also use the PyPI package:

$ pip3 install --upgrade itk

  • Jupyter

The lecture material includes Jupyter notebooks. Please follow the Jupyter installation instructions, and ensure you have version 4 or later:

  $ jupyter --version
  4.1.0

Download lecture material

  1. Install Git
  2. Clone the repository athttps://github.com/CameraIA/microct_skimage

We may make editorial corrections to the material until the day before the workshop, so please execute git pull to update.

Test your setup

Please switch into the repository you downloaded in the previous step, and run python check_setup.py to validate your installation. Click [check_setup.py] to locate the file.

On my computer, the previous command results in:

[✓] scikit-image  0.16.dev0
[✓] numpy         1.16.4
[✓] scipy         1.3.0
[✓] matplotlib    3.1.0
[✓] notebook      6.0.0
[✓] scikit-learn  0.21.2

Please note your version numbers may differ.

If you do not have a working setup, please contact the instructors.