Study period: 2022-09-19 - 2022-09-23
Description of the course: The focus of the course is on reaching a broad understanding of computerized image analysis in Life Science (mainly fluorescence and electron microscopy images) and a basic understanding of the theory and algorithms behind the image analysis methods and tools. Hands-on exercises that will teach a broad functionality of these tools and the concepts needed for building suitable workflow for a given application.
This course provides:
- basic concepts of digital images,
- basic computerized image analysis methods and computer exercises
- visualization of multi-dimensional data,
- image processing in preparation for analysis,
- noise and image enhancement,
- binary operations,
- object / particle analysis and intensity and morphometric measurements,
- tracking of particles cells movement
- automatically analyzing large datasets.
We will address the issues of image ethics and proper image acquisition for image analysis. During the course we will use FIJI, an opensource software based on ImageJ2 that bundles a lot of plugins which facilitate scientific image analysis. During the course we will cover:
Module 1 (day 1): Introduction to digital images and ImageJ/FIJI.
Module 2 (day 2): Filters/spatial operations and its use in image processing.
Module 3 (day 3): ImageJ/FIJI macro recorder and macro writing.
Module 4 (day 4): Examples of plugins and bioimage analysis pipelines. Single particle tracking.
Module 5 (day 5): Working with output data tables in python, for basic data analysis and plotting.
Apply here: https://fubasdoc.gu.se/fubasextern/info?kurs=SC00028
Application period: Closed (if you wish to be on the waiting list, please, contact Rafael Camacho <firstname.lastname@example.org>)