I performed Neutron Computed Tomography on a small component containing a small piston with two O-Rings. Piston diameter and height is about 1/2" each. I completed the reconstruction and have extracted the piston. I imported the .tif slices into Imagej Volume Viewer. This was my first use of this type for Imagej. Previously, I have only made .avi from my imported sequences. I want to visualize the O-Rings only from my slices/volume. Can anyone help this novice? Thank you.
You seem to know your business well but you are posing a very general ImageJ question, maybe because you are not aware of applicable Plugins. Did you already have a look at the possibilities of 3D in ImageJ and/or in Fiji? 3D interactive surface plot, Stack 2D surface plot or Volume Viewer are only three ways to visualise in ImageJ, there might be even more in Fiji.
If you google (Oh, dear!) for “imagej 3d view” you will find links to the plugin and a few movies showcasing its use. Have a look at a few.
After that, you will be able to ask more specific questions about what exactly you want to accomplish, while explaining why a specific situation doesn’t work for you. Thanks!
Thank you Eljonco for your very prompt reply!! I will look toward your suggestions. I was in Volume Viewer and tried surface plot. That is not what I am looking for. I would really like to isolate the O-rings. As though separating them from the piston. That may be segment? I couldn’t really follow that to easily? Some how neutralize surrounding pixels so I only see the O-Rings. I hope that makes more sense? Years ago, my predecessors had done this in Volume Graphics. I am even less experiences in VG than Imagej
Segment, indeed, the O-rings. If the O-rings stand out sufficiently, a Volume Viewer with the LUT (top right hand window) drawn appropriately, might give you a view of the rings that simple.
Otherwise you can try if it is sufficient to do your segmentation on a slice-by-slice basis, ie. not take 3D into account.
If a monochrome stack segments successfully, convert the stack to a colour stack and put the O-ring segmentation in another channel so in the visualisation they stand out better. Like blue piston and yellow O-rings because you put the segmented O-rings in the green channel, is that what you mean?
Thank you so much. Just wanted to tell you Volume Viewer did perfectly. Just a little tweaking, and it was there. I’m sharing this image to show the results. Thanks again. Sorry, the system will not accept my images. They were saved as .tif images directly from imagej?
That’s a well known problem out here. If you zip the image and upload/link the zip file, it works OK… Glad you worked it out!