Helicon Soft Forum

I am trying to generate a 3D model from a microscopic image stack and export the result as an .obj-file.

The microscope is equipped with a precise motorised Z-stage, so the intervals between to images (Z direction) are known, XY dimensions are also known.

Now I desperately look for a way to scale the Z-dimension but cannot find a way to achieve that. Is there any way to tell helicon the distances between two slices? Or is there any chance to export the height information in a known ratio (e.g. 1 slice = 10 Px)? I have a hard time figuring the relief amplifier out. Is the numeric value in the setting any kind of ratio?

Thanks a lot in advance, Lars

Helicon Focus exports depth map information as a 16 bit grayscale image. Z-value is normalized to efficiently use 16 bit image precision but it is easy to calculate real values.

Here is an example how to do this if you use depth map.


Suppose you made N shots, shot 0 will have z-value 0, shot N will have z-value 65535, shot i will have z value i*65535/(N-1)

z-value in between the layers means that this pixel was computed by mixing two adjacent layers.



And here is example how to set relief amplifier if you are using Helicon 3D Viewer.

Keep in mind that depth (z-value) is calculated as height (y-value)*ReliefAmplifier. So depth = height, if ReliefAmplifier is 100%. You can check this by enabling Draw bounding box and looking at the object from the side.

Example: If vertical size (image height) of field-of-view of your camera is 10 mm, and depth of your stack is 5 mm (6 shots, 1 mm between shots), then you need to set ReliefAmplifier to 50% (5mm/10mm) to correctly display your object.

Dear Stas,
allright, that works fine. Thank you! The next question concerns the smoothing algorithm. It somehow seems to have a similar effect as the relief amplifier. If set to 0, the 3D model develops very spiky peaks. Is there some “close to reality” value that shows the calculated voxels of the model with minimal distortions?
Best regards, Lars

After processing you get noisy (spicky) depth map. It is up to you how much to smooth them out. There is no optimal value because noise level depends on the source stack characteristics.