public class StitchOmeTiff
extends Object
implements ij.plugin.PlugIn

A plugin to parse stage position information from the OME-TIFF dataset's metadata block using Bio-Formats, and convert it to a format compatible with Fiji's 2D and 3D Stitching plugins.

One significant difficulty is that stage coordinates are expressed in an arbitrary stage unit, rather than anything convertible such as pixels or microns. Hence, we must use some kind of heuristic to convert from stage units to pixels, which is what the Fiji stitching plugin requires as input.

The current approach requires the user to provide a rough approximation of tile overlap as a percentage, with a default of 20% overlap. We assume image tiles were collected in a roughly rectangular grid; the heuristic will probably fail with most other tile configurations.

The stage unit scaling algorithm (implemented in the computeScale(loci.formats.meta.IMetadata, double, double, boolean) method below) is as follows:

1. Get the list of X stage coordinates for all tiles, and sort it in ascending order.
2. Compute the smallest difference between adjacent X coordinates, above a certain minimum threshold (default 20.0). This accounts for duplicate coordinates, as well as minor jitter or drift between tiles. This smallest difference value represents the X spacing between adjacent tiles in the grid.
3. Compute this same distance in pixels, which is equal to the tile width times the non-overlapping tile fraction; e.g., if the overlap is set to 10%, then the pixel width between adjacent tiles is 90% of tile width.
4. The scale factor to convert from stage units to pixels is then the ratio of these two values: pixelDistance / stageUnitDistance
5. This computation is repeated for the Y and Z dimensions as well.

Once we have the stage unit scale factors, we can write out the stage positions to the tile configuration file in pixels, for use by the Fiji stitching plugin. There is one other minor detail, however: the stage positions may be in a reverse coordinate system from the pixels. Hence, we provide an "Invert stage coordinates" checkbox to indicate this. With this option enabled, the stage unit scale factors will be negative, which will result in the conversion to pixels in the proper direction.