Stitching images from the Magellan using imageJ

1. Open imageJ and select:

Plugins -> Stitching -> Grid/Collection Stitching

2. Then select:

Filename defined position -> Defined by filename

3. Using the following setting, you can stitch the images without having to rename them. For the filename for tiles, use: Tile_{yyy}-{xxx}-000_0.tif. Make sure to use the appropriate Grid size x, Grid size y and Tile overlap (%) values. For computation paramaters, you can select Save computation time (but use more RAM) if you are using the office PC (since it has 128GB RAM and will be able to hold pretty much any map in memory).