3D Manager: Surf vs. SurfCorr

Hi All,

I’m hoping someone can help me with the following questions:

  1. What is the difference between Surf (unit or pixels) and SurfCorr in the output measurements from the 3D ROI manager? How are these calculated in simple terms? And which one is more accurate?

  2. How is the Surface in pixels converted to unit (in my case microns)? For instance for the volume conversion you just multiply the volume in pixels x the calibrated volume of a voxel. But for surface area I cannot seem to find a conversion system.

Here is an example of my output:


My voxel dimensions are 0.2 x 0.2 x 0.3125 um.

Thanks in advance!

Hi @tal,

The surface in pixels is just the number of voxels belonging to the surface (boundary of the object). To get the surface in unit you multiply the voxels by its area, that can be in XY or XZ, this is why there is no obvious translation from surface in pixel to surface in unit.

The corrected area, that should be a bit more accurate follows the algorithm from Lindblad2005 Surface area estimation of digitized 3D objects using weighted local configurations.

Hope this helps,

Best

Thomas

@ThomasBoudier

Thank you very much for the explanation.

Since there is no obvious conversion system from pixels to unit for the surface, is there a way to convert the corrected surface area to unit?

Hi @tal,

Unfortunately there is no obvious conversion from corrected surface in pixels to a corrected surface in unit, to do that we may need t ogo back to the original article and modify the formula for non square voxels.

However a rough and not accurate answer would be to apply the same ratio from surface to corrected surface to the surface in unit, since this corrected surface will correct for blocks effect and give an idea of a smooth surface.

Best,

Thomas

Hi @ThomasBoudier,

Yes indeed that’s what I was thinking, but I was not sure it was a correct way to do the conversion.
Thank you very much for your inputs!

Perhaps you’re also able to help me on this question Z-stack slice number changes my measurements ? I could not find any previous forums on this and it’s really important.

Best,

Talia