Problem with 3D Image Viewer

imagej

#1

Hello there!

I have a set of z-stacks and I am trying to get a 3D-View of the images when stitched together. When I put this into 3d-viewer however, I get a 2d image. When I put a single image into the 3D-Viewer (one of the images from the stitched image) I get a 3D object but I need a 3D view of the whole stitched image.

What should I do to resolve this issue?

Thanks!


#2

@Ary

Can you attach/link the original image file you are working with? How are you opening your z-stack to begin with? We recommend opening images with Bio-Formats - to be sure the metadata is read in correctly.

eta


#3

I just drag it into Image J, and then open it with 3D viewer?


#4

@Ary

Try opening your image using Bio-Formats … and then open it in 3D Viewer. And let us know if that helped solve your issue. :slight_smile: Otherwise… we’ll dig deeper.

eta


#5


Here is an image of the problem I’m having with Simple Neurite Tracer for example, how do I make the width larger so it doesnt appear 2D? Would Bio-Formats help with this?

Thanks


#6

@Ary

Without having your dataset myself… I can’t really tell you definitively what the problem is. You can attach your original image here if you want.

Perhaps?! Again - I’m not positive, but it’s worth you trying.

You can always check the your Image Properties to see if the scaling is correct.

eta