Summary and Schedule
This carpentries lesson teaches the basics of image processing catered to biomedical engineers.
After completing this course, you should be able to:
- understand different image formats, and demonstrate associated file operations
- describe a 2D image (as a matrix and colormaps), and demonstrate basic transformations
- extract images from a DICOM database and use as a nifti file
It is desirable that you know:
- fundamentals of programming concepts, e.g. reading and writing files, basic plotting
- no prior knowledge in medical imaging required
| Setup Instructions | Download files required for the lesson | |
| Duration: 00h 00m | 1. Introduction to Image Processing in Biomedical Applications |
Why is image processing an essential learning topic for a biomedical
engineer? Which imaging modalities are used in the biomedical fielsd? How does a researcher/engineer/ clinician know if an image is 2D or 3D? Why is automation in image processing necessary? :::::::::::::::::::::::::::::::::::::::::::::::: |
| Duration: 01h 00m | 2. Two Dimensional (2D) Image basics.md |
What is a 2D image in the context of digital image processing? What parameters would describe a 2D image? How to open and visualise a digital image? |
| Duration: 01h 30m | 3. 2D Image Colourmap |
What is a colourmap? What parameters would describe a 2D image? How to select specific colours? |
| Duration: 01h 45m | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.
FIXME: Setup instructions live in this document. Please specify the tools and the data sets the Learner needs to have installed.
Data Sets
Download the data zip file and unzip it to your Desktop
Software Setup
Details
Setup for different systems can be presented in dropdown menus via a
spoiler tag. They will join to this discussion block, so
you can give a general overview of the software used in this lesson here
and fill out the individual operating systems (and potentially add more,
e.g. online setup) in the solutions blocks.
Use PuTTY
Use Terminal.app
Use Terminal