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5. Stitch Settings

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Matthew Mueller edited this page Jul 9, 2024 · 11 revisions

1. Stitch Settings Tab

Stitch Settings

  1. Selecting Stitch on the Main tab will let you access this tab from the Next/Previous buttons
  2. Image List Full Paths are the paths to the image list files for each data path that is being processed. 1 image list per data path.
  3. Results Directory Name is the Dir where the stitch results will be placed. Just need a name and not the full path.
  4. Axis order is the axis order for the coordinates. Ex. xyz or -xyz etc.
  5. Blend Method is the method used to handle overlap. Feather recommended
  6. Primary Ch should line up with the primary channel from channel patterns. Ex. CamA_ch0 etc.
  7. XCorr Shift will use cross-correlation based registration stitching.
  8. XCorr Threshold is the threshold used for xcorr, shift is ignored for values below this threshold
  9. XCorr Downsample is the downsample value in Y, X, and Z
  10. XCorr Mode is the reference registration mode: primaryFirst will use the first time point in the primary channel. Primary will use the primary channel. All will use its own xcorr
  11. XY Max Offset is the max offset in the XY axes
  12. Z Max Offset is the max offset in the Z axis
  13. Online Stitch will enable support for online stitching
  14. Generate Image List is the method used for Image List Generation

2. Stitch Advanced Settings

Stitch Advanced Settings

  1. Bound Box Crop is the bounding box to crop the ROI after stitching.
  2. Stitch Info Full Path is the full path to the file that contains the stitch information for secondary channels
  3. FF Correction is flat-field correction
  4. Group File is the file used to define tile groups
  5. FF Image Paths are the full paths of the flag field files
  6. Background Paths are the full paths of the camera dark current images
  7. Tile Offset is the offset added to the tile
  8. Lower Limit is the lower limit for FF correction
  9. Subtract Background from FF will subtract the Background from the FF if true
  10. Shift Method can be local, global, grid, or group
  11. Overlap Type can be none, mean, max, median, or feather
  12. Dist Bounding Boxes are the bounding boxes used for the distance transform
  13. Stitch MIP will generate MIP files based on the axes selected
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