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.
- Plugins > Stitching > Grid/Collection stitching
- Choose Type: Positions from file
- Choose Order: Defined by image metadata
- Click OK
- 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)
- Select a Fusion method (e.g., Linear Blending looks nice but is slower and obfuscates where tiles are joined)
- Uncheck "Compute overlap" (for Prairie or WiscScan data, the coordinates are already accurate enough)
- Reduce the "Increase overlap" slider to 0
- Uncheck "Subpixel accuracy"
- If your data is too large for computer memory, check the "Use virtual input images" box
- Click OK and wait
For complete instructions on using the Fiji Stitching plugins, see the documentation on the Fiji wiki.