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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 >= 0.16
    • scikit-learn >= 0.18
    • napari >= 0.2.6

    Please see "Test your setup" below.

  • Jupyter

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

    $ jupyter --version
4.4.0

Download lecture material

  1. Install Git
  2. Clone the repository at https://github.com/jni/skimage-tutorials
  3. Switch to the monash-df2 branch: git checkout --track origin/monash-df2

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

Test your setup

Please switch into the repository you downloaded in the previous step, and run check_setup.py to validate your installation.

On my computer, I see (but your version numbers may differ):

[✓] scikit-image  0.16.2
[✓] numpy         1.17.0
[✓] scipy         1.3.1
[✓] matplotlib    3.1.1
[✓] notebook      6.0.1
[✓] scikit-learn  0.21.1
[✓] napari        0.2.6

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