Summary and Setup

This lesson shows how to use Python and scikit-image to do basic image processing.

Prerequisites

This lesson assumes you have a working knowledge of Python and some previous exposure to the Bash shell. These requirements can be fulfilled by: a) completing a Software Carpentry Python workshop or b) completing a Data Carpentry Ecology workshop (with Python) and a Data Carpentry Genomics workshop or c) independent exposure to both Python and the Bash shell.

If you’re unsure whether you have enough experience to participate in this workshop, please read over this detailed list, which gives all of the functions, operators, and other concepts you will need to be familiar with.

Before following the lesson, please make sure you have the software and data required.

Before joining the workshop or following the lesson, please complete the data and software setup described in this page.

Data

The example images used in this lesson are available on Zenodo. To download the data, please visit the dataset page for this workshop and click the “Download all” button. Unzip the downloaded file, and save the contents as a folder called data somewhere you will easily find it again, e.g. your Desktop or a folder you have created for using in this workshop. (The name data is optional but recommended, as this is the name we will use to refer to the folder throughout the lesson.)

Software

  1. Check your conda distribution. On terminal (Mac) or Powershell/WSL (Windows), run:

    conda info
mamba info

    If either command returns information, skip to creating a new environment.

  2. Download and install the latest Miniforge distribution If you wish to use an existing installation, please use a new conda environment to ensure all packages are up to date.

    If running the conda commands on the standard Command Prompt or Powershell returns an error: 'conda' is not recognized as an internal or external command, operable program or batch file.

    Use the Miniforge Prompt in the Start menu instead.

  3. Create a new environment with the necessary packages

    conda create -n imaging-workshop python=3.9 scikit-image ipympl jupyterlab -c conda-forge

    Enabling the ipympl backend in Jupyter notebooks

    This lesson uses Matplotlib features to display images, and some interactive features will be valuable. To enable the interactive tools in JupyterLab, the ipympl package is required.

    The ipympl backend can be enabled with the %matplotlib Jupyter magic. Put the following command in a cell in your notebooks (e.g., at the top) and execute the cell before any plotting commands.

    PYTHON 

    %matplotlib widget

    Older JupyterLab versions

    If you are using an older version of JupyterLab, you may also need to install the labextensions manually, as explained in the README file for the ipympl package.

  4. Start environment

    conda activate imaging-workshop

  5. Open a Jupyter notebook:

    jupyter lab

    After Jupyter Lab has launched, click the “Python 3” button under “Notebook” in the launcher window, or use the “File” menu, to open a new Python 3 notebook.

  6. To test your environment, run the following lines in a cell of the notebook:

    PYTHON 

    import imageio.v3 as iio
import matplotlib.pyplot as plt
import skimage as ski

%matplotlib widget

# load an image
image = iio.imread(uri='data/colonies-01.tif')

# rotate it by 45 degrees
rotated = ski.transform.rotate(image=image, angle=45)

# display the original image and its rotated version side by side
fig, ax = plt.subplots(1, 2)
ax[0].imshow(image)
ax[1].imshow(rotated)

    Upon execution of the cell, a figure with two images should be displayed in an interactive widget. When hovering over the images with the mouse pointer, the pixel coordinates and colour values are displayed below the image.

    Overview of the Jupyter Notebook graphical user interface To run Python code in a Jupyter notebook cell, click on a cell in the notebook (or add a new one by clicking the + button in the toolbar), make sure that the cell type is set to “Code” (check the dropdown in the toolbar), and add the Python code in that cell. After you have added the code, you can run the cell by selecting “Run” -> “Run selected cell” in the top menu, or pressing Shift+Enter.