The course is meant for microscopy users who are new to Image J/FIJI and to image processing in general, as well as for those who have already done their first steps in FIJI and want to gain a better orientation in the environment. We'll start from the very basics, so you don't need to be afraid if even you've never used FIJI before. By the time we are done you will be for example able to write simple macros to automate tedious image processing tasks.

Watch the whole course on YouTube.

The course will be split into a few Zoom sessions of 1.5 hours:

Zoom links

1st session

Date & Time: Monday, August 30th, 2021, 3.30PM
Meeting ID: 848 4872 6268
Passcode: 7Vff8m

Recorded session on YouTube

2nd session

Date & Time: Monday, September 6th, 2021, 3.30PM
Meeting ID: 840 9977 4400
Passcode: WRXB6Z

Recorded session on YouTube

3rd session

Date & Time: Monday, September 20th, 2021, 3.30PM
Meeting ID: 950 7287 7698
Passcode: 568373

Recorded session on YouTube

2D colocalisation histogram macro with ROI selection

4th session

Date & Time: Monday, September 27th, 2021, 3.30PM
Meeting ID: 958 4516 3589
Passcode: 583489

Recorded session on YouTube (with additional material recorded after the live session)

Demo macros from the 4th session with additional explanatory comments:

Before we start

Download FIJI (if you don't have it yet).

FIJI Is Just Image J!


Kota Miura: Bioimage Data Analysis textbook
Old Image J website
New Image J website

FIJI scripting tutorial forum
BioImage Informatics Index
NOBIC macros