Summary and Schedule

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.

	Setup Instructions	Download files required for the lesson
Duration: 00h 00m	1. Introduction	What sort of scientific questions can we answer with image processing / computer vision? What are morphometric problems?
Duration: 00h 05m	2. Image Basics	How are images represented in digital format?
Duration: 00h 30m	3. Working with scikit-image	How can the scikit-image Python computer vision library be used to work with images?
Duration: 02h 30m	4. Drawing and Bitwise Operations	How can we draw on scikit-image images and use bitwise operations and masks to select certain parts of an image?
Duration: 04h 00m	5. Creating Histograms	How can we create grayscale and colour histograms to understand the distribution of colour values in an image?
Duration: 05h 20m	6. Blurring Images	How can we apply a low-pass blurring filter to an image?
Duration: 06h 20m	7. Thresholding	How can we use thresholding to produce a binary image?
Duration: 08h 10m	8. Connected Component Analysis	How to extract separate objects from an image and describe these objects quantitatively.
Duration: 10h 15m	9. Capstone Challenge	How can we automatically count bacterial colonies with image analysis?
Duration: 11h 05m	10. Multidimensional data	How can we use scikit-image to perform image processing tasks on multidimensional image data? How can we visualise the results using Napari?
Duration: 13h 05m	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.

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

Data

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The example images used in this lesson are available for University of Birmingham staff on SharePoint. Please follow this link, log on if required, and click “Download”. 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

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1. Download and install the Miniforge using AppsAnywhere (preferred and no admin rights required). If you cannot use AppsAnywhere you can manually download and install the Miniforge distribution for your operating system.

2. Use Mamba to make a new environment for this Lesson and install the necessary packages. To do this open a terminal (or Miniforge3 Prompt if using Windows) and run the following commands:

   mamba create -y -n image-env -c conda-forge python=3.9
   mamba activate image-env
   mamba install -y -c conda-forge scikit-image ipympl napari pyqt jupyterlab

   Instructions for Windows

   Launch the Miniforge3 Prompt program and run your commands within this. (Running mamba commands on the standard Command Prompt may return an error: 'mamba' is not recognized as an internal or external command, operable program or batch file.)

3. Open a Jupyter notebook:

   Open a terminal (or Miniforge3 Prompt if using Windows), activate your environment and open Jupyter Lab:

   mamba activate image-env
   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.

4. 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
   import napari
   
   %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)
   
   # open the image in Napari
   viewer = napari.Viewer()
   viewer.add_image(data=image, name="colonies_01", rgb=True)

   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. It will also open a Napari Viewer and display an image within it.

   Running Cells in a Notebook

   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.

   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.

5. A small number of exercises will require you to run commands in a terminal. Windows users should use PowerShell for this. PowerShell is probably installed by default but if not you should download and install it.