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  1. The Grid/Collection Stitching Plugin is located in Plugins → Stitching → Grid/Collection Stitching.

  2. In the first dialog box, select Type: “Positions from file” and Order: “Defined by image metadata”

  3. In the second dialog box select the first position in your grid for “Multi series file”.

  4. Do you need to invert Coodinatescheck one of the invert Coordinates boxes?

    1. If you're using For data acquired onhighon high-speedspeed microscope, check “Invert Y Coordinates”.

    2. For data acquired on the spinning disk confocal, check “Invert X Coordinates” and “Invert Y Coordinates”.

    3. For data acquired on the CSU-W1 spinning disk confocal, check “Invert Y Coordinates”.

    4. For data acquired on the light sheet microscope, check “Invert X Coordinates”.

    5. For data acquired on the Weill CSU-W1/SoRa, you DO NOT need to invert coordinats
  5. Otherwise, the default options usually work well.

  6. Hit OK, and you should have your stitched image in a few minutes.

  7. This works for single channel and multicolor Z-stack images.