Stitching parameters

Here are the available parameters for the stitching step:

Required

• -i <path to the 1st channel config> -i <path to the 2nd channel config> ...

Optional

• -m restitching-incremental or -m restitching-full - sets the strategy for the rematching iterations:
  • In the incremental mode, only pairs that have not been included in the previous solution are rematched (this mode is used when calling the stitch script)
  • In the full mode, all possible pairs are rematched on every iteration
• -p <xPad,yPad,zPad> - extends the overlapping region by given amount (default is no padding)
• -b <blur sigma> - controls amount of blur applied to the overlapping region to suppress noise (default is 2)
• -w <xTiles,yTiles,zTiles> - sets the size of the search window to look for data points used in the prediction It is given as number of tiles, so that it is converted to pixels automatically based on the tile size (default is 3,3,3)
• -n <number of neighbors for prediction> - sets a minimum number of neighbors in the search window to consider the tile at the predicted location (default is 5)
• --allpairs - uses all pairs for matching instead of only adjacent with large overlap (default is adjacent only)