Stitching

Stitching is the process of combining multiple individual images with overlapping fields of view to produce a segmented larger image. While some microscopes can do this 'on the run', not every microscope comes with software that can parse the data. It should be noted that the quality  of stitching depends heavily on the quality and the nature of the images and if your images have large areas with homogeneous signal or areas with very little signal the results might be lackluster. If you are working with Leica SP8 with motorized stage, the Leica Las X software can perform the stitching rather well. If you are working with Aurox or DeltaVision you will need to perform the stitching with Fiji or Imaris. Imaris stitcher is also good choice if the size of your tile is several gigabytes or bigger.

The instructions on how to stitch and merge images using Fiji can be found below. Do note that the document below assumes that you are at least somewhat familiar with Fiji. In case you are new to Fiji, we recommend you to take a look here.

Stitching images taken with Aurox Clarity 

Using the in-built stitching software in Leica Navigator