Default SWIM Settings:
- Window Width - The full width in pixels of an imaginary, centered grid which SWIM aligns against (default=81.25% of image width).
- Signal Whitening - A SWIM parameter which takes values in the range of -1.00 and 0.00 (default=-0.68).
- Iterations - The number of sequential SWIM refinements. In general, greater iterations results in a more refined alignment up to some limit, except for in cases of local maxima or complete misalignment (default=3).
Multiprocessing Functions – Fully parallelized, chains of calls to iscale2, MIR, and SWIM
- Align All - Align and generate all sections for the current scale.
- Re-Align #_ - Align and generate the current section only.
- Manual Align - Enter/Exit Manual Align Mode (see section on Manual Intervention below).
- Re-Align #_ to #_ - Align and generate the selected range of sections.
- Regenerate All - Regenerate output based on the Null Bias and Bounding Box presets.
Output Settings – Regenerating the alignment--distinct from computing the alignment--refers to the process of generating a new aligned image stack at a particular scale from source images of the same scale using predetermined affine transformations. The resulting images depend on:
- Generate TIFFs - Whether or not to generate TIFF and Zarr output for any alignment, regardless of the alignment method used.
- Bounding Box - When Bounding Box is turned ON, the resulting images will grow an arbitrary amount to ensure that the entire alignment is within frame and no data is cropped out of frame. When Bounding Box is turned OFF (default=OFF) the aligned images will always have the same dimensions as the source images at a particular scale, regardless of drift and the data loss that may result from it.
- Corrective (Polynomial) Bias - An adjustment that can subtract systematic drift of various polynomial orders between 0° and 4° or None (default=None).
Correcting Misalignment - When Default Grid alignment fails, there are several different options to correct with human-intervention.
- Manual Align Mode (Note: It is not possible to enter Manual Align Mode until 'Align All' has been run at least once for a given scale)
- Custom Grid - Similar to Default Grid alignment, but the grid size is customizable and regions (quadrants) can be excluded from the alignment. This works because affine transformation requires at least 3 quadrants, so one can be dropped.
- Region Matching - User provides an alignment hint for SWIM by selecting 3 matching regions. Note: An affine requires at least 3 corresponding regions.
- Point Matching - User forces an alignment based on 3 matching points (SWIM is not used). Note: An affine requires at least 3 corresponding points.
- Include/Exclude - Individual sections may be excluded by deselecting the "Include" toggle switch in the control panel. Sections flagged not to include will not serve as a SWIM reference for any other section (like a dropped frame).