How to draw arrows pointing to same pixels in different images

Hi,
I am new to Fiji and I cannot find how to draw arrows in exactly the same location in different images (different channels of the same image). I’d like to show the colocalization of different colors in images and put them in the paper.
Thanks! :slight_smile:

Hi @Farnoosh_Saeedinejad,

Welcome to the forum.

The way I would go with is to:

  1. Merge your channels into a composite image Image > Color > Merge Channels
  2. Draw your arrow(s)
  3. Show only one channel at a time with the channels tool Image > Color > Channels Tool ( and select either “Color” or “Grayscale”

John

2 Likes

Hi @Farnoosh_Saeedinejad,

An other solution is that Arrow tool is a Region Of Interest. Every ROI can be restored on another image (Ctrl+Shift+E or Edit>Selection>Restore Selection).

Nico

2 Likes

And, of course, if you have the coordinates in (xStart,yStart) and (xEnd,yEnd), you can do it in a macro with
makeArrow(xStart,yStart,xEnd,yEnd,"notched");

Thank you so much for your reply!

It works! But I have another question of how to save each of the channels (including arrows) in a separate file?

Farnoosh

@Farnoosh_Saeedinejad

Oops, I left that part out.

If you add arrows to the ROI manager (Analyze > Tools > Roi manager).
Then you can do

  • Image > Overlay > From ROI manager
    • this overwrites the pixels in the image with lines / arrows you added
  • Saving the image (as a tif or png or whatever) will have the arrow in it

John

1 Like

Awesome! It worked! thank you so much.

I am still far away from using macro, but thank you so much for your help!