Volume Information for Proper Ruler Calibration


I have been trying to use Slicer to take measurements using the ruler tool on JPEG images of a chicken embryo heart. The heart is only about 5 mm across and I have been getting measurements around 300 mm across the heart from the ruler. I tried to manipulate the information in the volume module using the image information. However, the image became extremely zoomed in and I am unsure as to why this occurred. Is there any way that I should be manipulating the volume information so that I can get a proper view of the heart along with correct measurements? The image information is is below and I set the image dimensions to 512 mm x 512 mm x 512 mm and the image spacing to be 16 mm.

VolumeSize 512 512 512

VoxelSize 16

VolumePosition 0 0 0

VolumeScale 0.020 0.020 0.020

Field 0 (Position 0 Size 16 Name “data” Format ui Scale 0.588235 Offset -1294.117676)

I would appreciate any help!

Perhaps you mean 16 micron, not 16mm for image spacing? 512x512x512 at 16mm image spacing would give you a field of view that is 8m across.

So, instead of entering 16, enter 0.016mm as your image spacing. Better yet, use ImageStacks from SlicerMorph to import your JPG sequence and specify the correct spacing at the time of import, so that you don’t have to fiddle with it later on.

I am not sure what the VolumeScale field mean? Where is this data coming from? OPT?
Also you may want to switch to MarkupsLine tool as oppose ruler, since Ruler tool will soon be deprecated.


I really appreciate your help. The image spacing was 16 microns, and I am getting the correct measurements now. The file was opened using Notepad, so that is where the data came from. I will look into using ImageStacks and the MarkupsLine tool for sure.

Thank you!

1 Like