FIJI workshop

Lecture slides

• Cell counting - Image processing workflow.pdf

FIJI hands-on workshop

Get started with Fiji and learn how to handle and process your files, how to count and characterize cells and how to make your analysis faster and more reproducible with macro recording.

• Fiji is available from the software center for University of Helsinki computers, or from: https://imagej.net/Fiji/Downloads
• If you want to get a head start on macro programming, have a look at this video by Anna Klemm:
  

  • https://www.youtube.com/watch?v=o8tfkdcd3DA

Download the following files and store them in an easy-to-find place (e.g. in a folder on your desktop):

All files in one:FIJI practicals 1-3.zip

Practical 1: Basics of FIJI ImageJ

• FIJI practical 1.pdf

Practical 2: Cell counting and characterization 

• FIJI practical 2.pdf
• NucleiDAPIconfocal.png (right-click on image and save)
• Stitched_Corr_PosA.tif
• Results_template.xlsx

Practical 3: Simple macros

• FIJI practical 3.pdf
• Task0_batch_process_example.ijm
• Task0_batch_process_example_with_measure.ijm
• Task1_cell_counting_and_characterization.ijm
• Task2_load_process_and_save.ijm
• batch_process_folders.ijm