Make the background of 3D viewer transparent


Does anyone know how to change the background of 3d Viewer into transparent? I can only make it white but it hides the other colors in my structure.



Is there anyone knowing how to do it?


I’m not exactly sure what you mean by ‘transparent’… what colors are you missing if the background is white/black? I’m not sure transparency is an option - it follows RGB options for background colors.

It looks like no options for changing the background to transparent in 3d viewer. I just found the colors in the structure are shaded by the white background.

Hi @Charles_hoo ,

are you using the “glasbey” lookup table when showing objects in the ImageJ 3D viewer? If so, did you try to use “glasbey on dark”?

Btw. if you share an example dataset, it’s easier for us to help you. :wink:


Hi Robert:

I don’t know what is glasbey. I just used the morphoLIbj to label the connected components in my structure and give them different colors. Then I want to input them into the 3d viewer to show the 3D distribution. But I found the colors seem to be shaded by either black or white background.

Another thing is about scale bar. You can only adjust the x and y positions? I have no idea to put the scale bar in the right position.

The glasbey lookup table is used to visualise your objects in different colours. You find it in the menu Image > Lookup tables > Glasbey

If you convert your image stack to 8-bit or RGB before sending it to the 3D Viewer, the background becomes transparent:

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Thanks! I just try the glasbey lookup table. Why did it assign the same color to several isolated objects?


I upload three images in this link:

For a scale bar in 3D viewer, it’s true that since it rotates with the object, it’s sometimes hard to see. Provided that your object is correctly calibrated in z, I find it easier to insert a sphere of equivalent diameter (in 3DViewer Add>Sphere, define center as 0,0,0 and radius=scale bar/2).

Concerning your objects “with the same colour”, it may be that the colours have slightly different values but look the same, or you have more than 256 objects.

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