Use ImageJ to caluclate the number of cells, nuclei and types of shapes

Continuing the discussion from Use ImageJ to calculate the number of cells, nuclei and types of shapes:

The good news is that I have achieved the desired image.

Now I need to analyse it. I am trying to {Anaylze…} but I need to set a threshold. How would one do this 25 November 2019_STL KO1_ch00 applieed the recomended colours.tif (2.5 MB)

But I don’t know how to overcome this.

For the past week I haved watched the amazing series

Or should I use the blue image only and do apply a threshold from there, and then do analyse particles…

I need to count the total cells and then identify rounded cells vs spindle-shaped ones. Do I train the programme?

This what I have done using your amazing suggestion:

run(“Bio-Formats Importer”, “open=[C:/Users/aminu/Desktop/dataforproject/25 November 2019_STL KO1_ch00.tif] color_mode=Composite display_metadata rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT”);
run(“Enhance Contrast”, “saturated=0.35”);

Apologies for the inconvenience