Guide-net maps can be collected either as beam-scans or stage-scans. There shouldn't be any overlaps or gaps between frames, if the maps are collected as stage-scans. However if the frames are collected as beam-scans, there can be misalignments. These misalignments result from improper calibration of the beam-scan parameters. Beam-scans can be calibrated in one of two ways.

1) Using APAP program. If the APAP program is available, go to File >> Get Image >> Beam Calibration,
    and follow the steps outlined in the program.

2) Alternative method. The beam-scan parameters are stored in the file:
    /opt/epma/cali/eos/sgsp.cnd
    The default values should be set to:
          DEF_X 50.000000
          DEF_Y 50.000000
These values define the distance that the beam is deflected at its maximum range. Smaller numbers will produce more overlap and large values will produce more of a gap between the frames. Adjust these values until a good match is produced.