Z Voxel Scale

Controls the voxel aspect ratio along the z (slice) axis relative to the in-plane x/y pixels, so the generated mesh keeps true physical proportions when your acquisition is anisotropic.

What It Does

Image stacks are often anisotropic: the distance between slices (the z-step) is not the same as the size of a pixel within a slice. By default the mesh generator assumes cubic voxels — that x, y and z are all the same physical size. If that assumption is wrong, the resulting 3D surface looks squashed or stretched along the depth axis even though the segmentation is correct.

The Z Voxel Scale lets you tell the generator how large a voxel is along z compared to x/y, and the mesh is scaled accordingly.

Values

• 1 (default): cubic voxels — x : y : z = 1 : 1 : 1. Use this when slice spacing equals the in-plane pixel size.
• Greater than 1: stretches the stack along z. For example, a value of 2 produces a 1 : 1 : 2 aspect, appropriate when the z-step is twice the in-plane pixel size.
• Less than 1: compresses the stack along z, for finely-sampled z stacks where slices are closer together than the in-plane pixel size.

The accepted range is 0.05 to 20. Invalid or empty entries fall back to 1.

How To Choose

Compute the ratio from your acquisition metadata:

Z Voxel Scale = z-step (slice spacing) / in-plane pixel size

For example, if pixels are 0.2 µm and the spacing between slices is 0.5 µm, set the scale to 0.5 / 0.2 = 2.5.

When the selected file has a recorded physical voxel size with a z value (see the File Info voxel-size row in the file browser), this field is prefilled automatically with z / x. You can still override it.

Where It Applies

The scale is baked into the exported OBJ geometry — and therefore also into any STL, PLY, or glTF file you create from it with the file browser's "Convert to..." action — so meshes opened in external software (Blender, Maya, 3D printing slicers) already have correct z proportions. The built-in 3D Visualization module also reads the recorded aspect and applies it to the Three.js JSON mesh, the slice/capping meshes, and the original-data overlay, so the in-app view matches the exported files.

Tip: If your data is isotropic (cubic voxels), leave this at 1 — the default — and nothing changes.