Biomedical Image Analysis in Python

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

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4 Hours15 Videos54 Exercises12,494 Learners
4400 XP

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Course Description

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.

  1. 1

    Exploration

    Free

    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.

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    Image data
    50 xp
    Load images
    100 xp
    Metadata
    100 xp
    Plot images
    100 xp
    N-dimensional images
    50 xp
    Stack images
    100 xp
    Load volumes
    100 xp
    Field of view
    50 xp
    Advanced plotting
    50 xp
    Generate subplots
    100 xp
    Slice 3D images
    100 xp
    Plot other views
    100 xp
  2. 2

    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.

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  3. 3

    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.

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  4. 4

    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.

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In the following tracks

Image Processing

Collaborators

Lore DirickBecca RobinsSara Snell

Prerequisites

Intermediate Python
Stephen Bailey Headshot

Stephen Bailey

Lead Data Scientist

Stephen Bailey is lead data scientist at Immuta, where he researches and develops best practices in data governance. He is passionate about democratizing science and is an enthusiastic member of the Python community. Stephen has published a number of papers on leveraging medical imaging technology to better understand health and disease, and he is excited to introduce others to this dynamic research field!
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I've used other sites—Coursera, Udacity, things like that—but DataCamp's been the one that I've stuck with.

Devon Edwards Joseph
Lloyds Banking Group

DataCamp is the top resource I recommend for learning data science.

Louis Maiden
Harvard Business School

DataCamp is by far my favorite website to learn from.

Ronald Bowers
Decision Science Analytics, USAA