Beginner help please! Overlay & capture image issue


I am very new to FIJI and am having difficulties flattening an overlay of numbered points onto a tiff image. When I flatten, the size of my point labels decreases so that you can hardly see them.

I found a similar issue in another post that was solved by scaling their image, however I get an error message (java.lang.ArrayIndexOutOfBoundsException) when I try to do this, even after I have removed the overlay.

I therefore tried Capture Image to generate a WYSIWYG image, however this gave me a zoomed in section of my image, which also included part of my desktop behind the active image.

Please could someone help me to resolve either the screen capture or the overlay size change problem, so that I can generate an image where I can see my overlay clearly?

Many thanks,


Have you updated to the latest daily build of ImageJ? Go to Help > Update ImageJ… and choose “daily build”. Flatten was not working for me until I updated from 1.51n to the daily build.

You can check your version by clicking in the space below the toolbar of the main FIJI/ImageJ window:




1 Like

@J000D97 … just to add to @7rebor’s post… Check out this previous forum post regarding updating Fiji versus ImageJ1.x:

Once you update - let us know if the issue persists.


1 Like

Hi @etadobson and @7rebor,

Thank you so much - that worked! I really appreciate your quick replies, thank you both very much for your help.

Kind regards,


1 Like