Cell counting and characterization

Lecture slides

• Lecture - Cell counting and characterization.pptx

FIJI hands-on workshop

• Install and test Fiji
  • Fiji 1.52p is available from the software center for University of Helsinki computers, or from: https://imagej.net/Fiji/Downloads
  • If you already have Fiji installed please make sure it is up to date

  • 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_analysed.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