I’m using 3D Slicer to reconstruct a material volume. The slices of this volume were createt using FIB (Focused Ion Beam) in a SEM. At this point I struggle to set the correct dimensions of my volume. Each image of my stack is 250x250 pixel and 1 pixel is equivalent to 0.025µm. My stack consists of 199 images, where one image reprents one slice created using FIB with a slice thickness of 40nm. How can I implement the slice thickness of 40nm and the correct dimensions to have a correct length bar?
After you import your data, you can edit those fields in the Volumes module. From your description it sounds like spacing should be (0.000025, 0.000025, 0.00004). Default units in slicer is millimeters.
Now, with everything set, the ruler in the 3D view is not correct. I imported the stack via SlicerMorph import tool and set the correct values for image spacing. Then I did the segmentation and export the segmentation to models to use the clipping planes. When I then turn on the ruler, it shows something with meters but the 2D windows show the correct nanometer values. How to fix this?
If you want your ruler and measurement values to display the right units, bring back the default unit to mm, and when you are using the ImageStacks enter the value in form of millimeters, not nanometers. Then both units should display correctly.
Altneratively, use can edit the ruler unit manually after you have taken a screenshot. (the scale will be correct, it appears it is displaying wrong unit).
