Image Stitching Fiji

Quote from the ImageJ wiki:

The Stitching Plugin (2d-5d) is able to reconstruct big images/stacks from an arbitrary number of tiled input images/stacks, making use of the Fourier Shift Theorem that computes all possible translations (x, y[, z]) between two 2d/3d images at once, yielding the best overlap in terms of the cross correlation measure. If more than two input images/stacks are used the correct placement of all tiles is determined using a global optimization. The stitching is able to align an arbitrary amount of channels and supports timelapse registration. To remove brightness differences at the tile borders, non-linear intensity blending can be applied.

The Image Stitching package comes with 2 different plugins:

• Pairwise Stitching: Stitch two 2d-5d images, rectangular ROIs can be used to limit the area to search in.
• Grid/Collection Stitching: Stitch an arbitrary amount of 2d-5d input images. It supports cases where the approximate alignment is known (grid, stored in file, metadata) as well as completely unguided alignment.