Welcome to Basic Image Analysis with scikit-image

This workshop covers the basics of image analysis using scikit-image (skimage), a popular image analysis toolkit written in Python. It is geared toward those with low-to-moderate programming experience, but beginners should be able to follow along with the provided tutorial code. This material will cover image file IO, basic processing such as rescaling and filtering, and basic image segmentation.

Lesson material source code is found in the lessons/ folder. You can access the rendered pages here: https://thejacksonlaboratory.github.io/Basic_skimageJAX/

Setup

Setup Instructions for the Workshop

Lessons

Lesson 1: Images are Arrays

Lesson 2: Filters and convolutions

Lesson 3: Morphology and Segmentation

Additional training material

scikit-image API reference: http://scikit-image.org/docs/stable/api/api.html

“Official” scikit-image tutorial: https://github.com/scikit-image/skimage-tutorials

scikit-image tutorial on YouTube: https://www.youtube.com/watch?v=pZATswy_IsQ