The image stitching plugins, written by Stephan Preibisch, provide a means for reconstructing large mosaics from tiled datasets.


The Image Stitching plugins come standard with the Fiji ImageJ distribution.

Installation and Usage
  1. Plugins > Stitching > Grid/Collection stitching
  2. Choose Type: Positions from file
  3. Choose Order: Defined by image metadata
  4. Click OK
  5. On next dialog, click Browse and select a file from your dataset (for Prairie data it is best to select the XML or CFG file)
  6. Select a Fusion method (e.g., Linear Blending looks nice but is slower and obfuscates where tiles are joined)
  7. Uncheck "Compute overlap" (for Prairie or WiscScan data, the coordinates are already accurate enough)
  8. Reduce the "Increase overlap" slider to 0
  9. Uncheck "Subpixel accuracy"
  10. If your data is too large for computer memory, check the "Use virtual input images" box
  11. Click OK and wait

For complete instructions on using the Fiji Stitching plugins, see the documentation on the Fiji wiki.