Module: Registration 2D-3D ()

Description:

Registers a 2D-slice (SEM) image with 3D tomogram.

Connections:

Data [required]
The data to transform by registration. The input data is directly modified by this tool. Limitation: only 16-bit unsigned data with less than 2 billion voxels are currently supported.

Reference 3D [required]
The reference data for performing the registration. Limitation: only 16-bit unsigned data with less than 2 billion voxels are currently supported.

Ports:

Task

Specifies the orientation of the SEM slice. Possible cases are:

• SEM slice perpendicular to the 3D tomogram Z axis (default),
• QEM slice perpendicular to the 3D tomogram Z axis,
• SEM slice parallel to the 3D tomogram Z axis, no assumption is made about whether the slice is (almost) perpendicular to either the x or y coordinate axis, a full 360 degree search (about z-axis) is performed.
• QEM slice parallel to the 3D tomogram Z axis, no assumption is made about whether the slice is (almost) perpendicular to either the x or y coordinate axis, a full 360 degree search (about z-axis) is performed.
• SEM slice already approximately aligned with 3D, For refinement registering of an approximately aligned SEM image with a tomogram. Uses a significantly reduced search range in exhaustive search stage, assumes plus/minus tilt angle range for all rotational degrees of freedom, and plus/minus translation half range percent (of fixed image size) range for translational degrees of freedom.
• QEM slice already approximately aligned with 3D, For refinement registering of an approximately aligned QEM image with a tomogram. Uses a significantly reduced search range in exhaustive search stage, assumes plus/minus tilt angle range for all rotational degrees of freedom, and plus/minus translation half range percent (of fixed image size) range for translational degrees of freedom.

FFT Correlation Initial Search

Performs FFT correlation for the initial exhaustive search. Provides significant speedup for discovering approximate alignments. Optionally, FFT phase correlation can be used to favour matching of edges within the images.

Max Downsample Factor

Sets the downsampling factor which is used to generate the lowest resolution images for performing the mosaic/stitching registration. Generally, a factor of 16 is good for 2048x2048x2048 tomographic images. For a 1024x768 2D image, a downsample factor of 16 means the lowest resolution registration steps will use images of size 64x48. Allowed values are power of 2, up to 256.

Optimizer Tolerance

Stopping tolerance for the cost function value, when relative difference of cost function is less than this tolerance the optimization iterations are stopped. Typically the registration transformation parameters are at within square root of optimizerT tolerance of the global minimum. The larger the value of this tolerance, the fewer iterations required to achieve convergence, i.e. faster runtime.

Min Overlap

Indicates the volume percentage of overlap of the image pair in the aligned state. It is used in two ways:

• to determine the range of translations in the initial basic search, the higher the min overlap the smaller the translation range and hence a faster runtime for the initial-exhaustive-search.
• to avoid spurious registrations, where a small percentage of overlapping voxels can generate a good/low cost-function value (e.g. a high correlation coefficient). The min overlap is the threshold-percentage of overlapping "voxels" at which a penalty term is added to the cost function and this penalty term discourages selection of alignments/registrations where there is little overlap of non-masked volume. If the percentage of overlapping voxels is greater than min overlap, then a penalty term is not added. The penalty will only be used/effective if the fixed image is masked. When registering stitched/mosaic (40x magnification say) SEM images of a complete core slice with a tomogram, this can be set 85 percent or even higher.

Overlap percent is calculated using the number of non-masked voxels in the transform-image which overlap with non-masked voxels in the fixed-image (divided by the total number of non-masked voxels in the transform-image).

Translation Half Range

The percentage of fixed-image width used as the search range for the translational degrees of freedom. If the image was perfectly aligned then a 0 percent translation range is required. If the SEM image is translated by 20 fixed-image voxels from perfect alignment (with a 2048x2048x2048 fixed image) then a 1% value is enough to find the alignment. Only available for approximately aligned cases.

deg]

The search range for rotation in the "tilt" direction (rotation about the non-z-axes). The range is in the interval [-tilt angle, tilt angle]. Increases runtime by a factor of (tilt angle + 1)*(tilt angle + 1).

In Plane Rotation Correction

If true, prior to registration, an attempt is made to align the straight edges of the SEM image with the coordinate axes. Relevant only for registering thin sections which have been cut parallel to the sample cylinder axis. For example, an SEM image of a rectangular thin-section may have been created with the rectangular-sample-region being at a significant angle (more than 2 degrees) to the image axes. When true, this parameter will lead to an adjustment to the search range (a shift in the range) for the transform parameter corresponding to rotation about the normal to the thin-section image plane.

Point Sample Specify

Check this to set stride below.

Point Sample Specify Stride

Stride used to skip points/voxels in the transform image when calculating metric, value of 1 indicates that no voxels are skipped. Usually reasonable to set (1,8,1) for downsample factor of 16.