Bioimage Processing in Python Course

This course is not ready yet, but watch this space…

This course contains materials for a 1-day beginner’s python image processing course. These materials have been developed so that students can work through the materials in their own time and at their own rate. Feel free to download the materials and work your way through the course; you can download the whole course from …TBA….

Aim

The overall aim of this course it to:

  1. introduce the handling of multidimensional image data in Python within the comfort of the Jupyter framework
  2. showcase some of the image processing functionality available in Python by demonstrating (and providing take-home resources) numpy, scipy, scikit-image, matplotlib and napari code

This course does not aim to teach image processing concepts - it is a python course. Participants are pointed to useful resources throughout the course but it is assumed that participants already have a basic understanding of the concepts being used.

Philosophy

Our general philosophy for this course is

  1. teach in small chunks starting by introducing python concepts, demonstrating an example, working through a simple case and then setting an exercise. Each exercise is then gone through as a group.
  2. teach through errors, error messages and documentation - so that trainees can debug their own codes after they leave the course
  3. create a safe environment for asking any and all questions.

Contributors

Teaching Yourself Python (12+ hours)

I have designed this course in such a way that it should be easy to follow and work through on your own. Each notebook stands alone and should provide you with all the information needed to complete the tasks (blue boxes) and exercises (yellow boxes).

In order to aid working through the notebooks I have provided short videos for all tasks and exercises (links throughout). These videos provide complete answers for every task and should be viewed after attempting each task or exercise.

In order to work through the notebooks please follow the instructions in setup.pdf for installing Python and Jupyter Lab on your computer, download this repository as a .zip file (using the green button at the top of the landing page), unzip the files and navigate to them from within Jupyter Lab.

I suggest you work through each notebook in turn, attempting at least the tasks on your first run-through. You can then use the exercises to revisit and revise topics when you go through the notebooks again in the future. As with all languages, practice makes perfect.

In-Person Course (1 day)

I have not yet run this course as a standalone 1 day course. If it’s something you’d be interested in organising at your institute, please contact me