Cropping 3d image converts color to grayscale

Hello: first post here, I haven’t used ImageJ in more than a dozen years and it has changed a lot! I can’t seem to solve this issue myself. I am using Crop (3D) in the “Stacks” plugin to remove unnecessary planes from an RGB image. When I do this I get a stack of collated grayscale images representing each color in each plane. How do I turn this back into an RGB stack? Or is there a better way to crop? thank you

Welcome back, @htpetrie! :smile:

I was unable to replicate this problem. I started with this macro:

newImage("HyperStack", "RGB color-mode label", 400, 300, 1, 5, 1);
run("Crop (3D)", "three change");

Then switched to the main HyperStack image window and narrowed the top-left and bottom-right blue grippers to create a smaller selection. Then clicked the Crop button in the Crop Options dialog box. A new image called “cropped HyperStack” appears with the smaller dimensions, still RGB.

Does the status bar of your new image still say “RGB”?

Did you try the plain “Crop” command? Make a selection by dragging with the mouse, with the rectangle tool selected. Then press Ctrl+L for the Command Finder, then type Crop. Or you can press Shift+X.

Good morning: sorry, I didn’t get the notification of a response because it went to spam. Hopefully it will be OK now.

I’m not sure how to run macros. Here is more detail on the problem.

The initial image is a single tile 3 color Z stack generated on a Zeiss scope, opened in Fiji in its original format (czi) and save as a tiff hyperstack for further work. I opened this in Fiji, and have tried the following with and without first converting to a stack (no difference):

plugins > stacks > crop (3D)
use the xz view of the 3 plane view to set crop boundaries to remove planes above/below tissue
click ‘crop’

I now get a black and white image. I have tried converting it to a hyperstack using c=3 z=n t=1, but nothing I do seems to work. thank you for your help! Howard