I would like to use the node Feature Calculator (beta) to compute the surface area of 3D objects. I only obtain results in pixel units. Most importantly the Z calibration is not taken into account making the computation of the surface impossible.
I use Geometric Features 3D. For the volume it is written that it is in pixel units. Is this the same also for the surface area and other features?
I did a few tests and it seems that the metadata is not considered. I tried to set it manually with “Set Image metadata” node but this had no effect on the computed features.
Please find attached a workbook with the different examples. As example I use a sphere of radius 10 in an image of 100x100x100 (calibration 1,1,1) or an image with less Z-slices 100x100x50 (calibration 1,1,2).
feature_area_demo.knwf (86.0 KB)
These are the 2 test images
resliced_Sphere.tif (496.3 KB) Sphere.tif (988.9 KB)
as I replied myself it may be that my post is ignored. I am shamelessly refer to you. I will have a look into the code to see if the calibration is included at all in the computation of the surface area.
That’s exactly what happened: Sorry about that!
No need to look into the code. The Feature Calculator uses ImageJ Ops for the computations, which in turn doesn’t take calibration into account.
PS: This relates to https://forum.image.sc/t/computing-3d-surface-area-of-binary-object-using-imagej-ops/36807.
could you add a note that for the 3D computations all dimension units are in pixels? It is there for the volume but not the surface. May be a generic warning?
Thank you for you thorough investigation as documented in the linked thread!
Good point! I have opened an issue: https://github.com/knime-ip/knip/issues/524