Biomedical Image Analysis in Python

Learn the fundamentals of exploring, manipulating, and measuring biomedical image data.

The field of biomedical imaging has exploded in recent years - but for the uninitiated, even loading data can be a challenge! In this introductory course, you'll learn the fundamentals of image analysis using NumPy, SciPy, and Matplotlib. You'll navigate through a whole-body CT scan, segment a cardiac MRI time series, and determine whether Alzheimer’s disease changes brain structure. Even if you have never worked with images before, you will finish the course with a solid toolkit for entering this dynamic field.

• Exploration
• Prepare to conquer the Nth dimension! To begin the course, you'll learn how to load, build and navigate N-dimensional images using a CT image of the human chest. You'll also leverage the useful ImageIO package and hone your NumPy and matplotlib skills.
• Masks and Filters
• Cut image processing to the bone by transforming x-ray images. You'll learn how to exploit intensity patterns to select sub-regions of an array, and you'll use convolutional filters to detect interesting features. You'll also use SciPy's ndimage module, which contains a treasure trove of image processing tools.
• Measurement
• In this chapter, you'll get to the heart of image analysis: object measurement. Using a 4D cardiac time series, you'll determine if a patient is likely to have heart disease. Along the way, you'll learn the fundamentals of image segmentation, object labeling, and morphological measurement.
• Image Comparison
• For the final chapter, you'll need to use your brain... and hundreds of others! Drawing data from more than 400 open-access MR images, you'll learn the basics of registration, resampling, and image comparison. Then, you'll use the extracted measurements to evaluate the effect of Alzheimer's Disease on brain structure.