Use the Crop tool to select dimensional parameters and cut out a section of the 3D dataset. There are three ways to find the desired cutout:

Cropping Manually

Starting from the leftmost positions of the sliders, a box is cut out to the rightmost positions of the sliders. The numbers NX, NY, and NZ represent the number of voxels in the X-, Y-, and Z-directions, respectively.

Moving the sliders defines a region that appears highlighted in yellow lines forming a rectangle in the 2D preview areas of the three directions. You can also change the size of the yellow rectangles using the left mouse button. Click and drag a line to move it. This is illustrated here for a 3D gray-value image of Berea sandstone. The values of NX, NY, and NZ indicate the size of the domain after cropping. In this case, it is 70 x 70 x 80 voxels.

Cropping Automatically

Checking the Automatic Crop box renders the cropping parameters inactive. Instead, all regions of pure background around the structure are cropped according to the Threshold defined below.

If the Automatic Threshold is enabled, the Otsu method is used to create the threshold. Otherwise, enter a Manual Threshold. Note that this threshold is not used for segmentation; it is only used to determine where the image should be cropped.

Suggesting Cropping Values

Click Suggest to preload the sliders with values that will crop away all pure-background regions according to the Otsu  or manually entered threshold. The cropping values for the three directions can then be changed as needed.

Click Apply to crop the structure using the current settings.