BigStitcher Pairwise shift

The first step in stitching a tiled dataset is determining the pairwise shifts between the views. In the Stitching Mode select the views for the pairwise shift calculation. Then right-click and select Stitching Wizard ▶ Stitch dataset.... The Stitching wizard will guide you through the three steps of pairwise shift determination, link verification and global optimization.

  • If you just want to determine pairwise shifts and skip the other steps, you can use Step-by-step Stitching ▶ Calculate Pairwise Shifts... ▶ Phase Correlation
  • Aside from the default Phase correlation algorithm for shift determination, we also offer alignment via the Lucas-Kanade method or interest point registration, as well as expert view grouping options. For those advanced methods, refer to BigStitcher_Advanced_stitching
BigStitcher stitch 0.png

Pairwise shift calculation

After starting the stitching process, you need to specify how to handle multiple channels (if present) and which downsampling to use.

  • If your dataset has multiple channels, you will be asked which channel to use for the stitching. You can also average the channels for the stitching process.
BigStitcher stitch 1.png
  • Next, choose the the downsampling in x,y,z to be used for the calculation. Select a predefined downsampling factor or choose your own.

BigStitcher stitch 2.png
  • If you ran the Stitching wizard, you will be asked to proceed to Link Preview Mode. Otherwise, you can proceed to this step via the right-click menu.

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