Image processing with ImageJ

Note: the course of March 2021 is full. Please stay tuned for updates and next courses.

Course content

This course comprises of a basic introduction lecture and 3 optional lecture. Each lecture takes about 2-3 hours and is intended to be hands-on: each participant runs the algorithms using their own laptop. The following topics will be covered:

Course 1: Basics

Example data can be downloaded HERE
The presentation can be downloaded HERE
The video can be opened HERE (MS Teams access needed)

  • Pixels and digital cameras
  • File formats and opening data in ImageJ
  • Histogram
  • Thresholding
  • Overlays, scale bars and annotations in ImageJ
  • Image transformations in ImageJ

Course 1 is mandatory if you want to visit the next courses

Course 2: image processing

Example data can be downloaded HERE
The presentation can be downloaded HERE
The video can be opened HERE (MS Teams access needed)

  • Point operations
  • Fourier transforms
  • Filters
  • Binary operations
  • Fourier transforms / reciprocal space
  • Object size analysis

This is an optional lecture.

Course 3: 3D imaging

Example data can be downloaded HERE
The presentation can be downloaded HERE
The video can be opened HERE (MS Teams access needed)

  • Stacks, Hyperstacks and Virtual stacks
  • Channels, sequences and Z-stacks
  • Visualizing 3D data
  • Surface rendering
  • Volume rendering
  • Imaris and Avizo

This is an optional lecture.

Course 4: Quantification and automation

Example data can be downloaded HERE
The presentation can be downloaded HERE

This course uses R and Rstudio Desktop (free version). Please install R first, then RStudio.

  • Scripting
  • Short introduction in R/R-studio

This is an optional lecture.

Course modality

Flexible choice in lectures

The basics lecture is the prerequisite to enter the optional lectures. You can still decide to sign up for additional optional course after the basic course, but note that the number of participants is limited to 9.

Hands-on

The lectures contain many excercises, which will be carried out by all participants. Prerequisite is the prior installation of FIJI on your laptop. There will be no time to install FIJI during the lectures, make sure you have your laptop prepared.

Do not run this course from a tablet, which has not sufficient calculation power.

BYOD

Bring your own data! Scientific and test datasets will be provided but is is not forbidden,  actually wanted, that you try the excercises on your own scientific images.

Teams and timeline

A Teams link will be made available here to the participants.

The course takes place on Thursday morning from 9 to 11 on:

  • Basics: March 04
  • Image processing: March 11
  • 3D: March 18
  • Quantification and automation: March 25

Sign up

The course is full.