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Run a large-area (stitched) scan

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Learning-oriented, for users. A single camera frame only sees a tiny part of your sample. In this tutorial you'll define a region, let the FRAME image it tile by tile, and view the tiles stitched into one large overview image.

What stitching is (30-second version)​

  • The stage moves the sample under the fixed objective in a grid of positions.
  • One frame is captured at each position; overlapping tiles are stitched together.
  • Link to the concept page: How scanning works.

Before you start​

  • Sample inserted and roughly in focus (first sample).
  • Objective chosen (4x is the easiest first scan — large field, forgiving focus).
  • Illumination set.

Step 1 — Define the scan region​

  • How to set the scan area (corners / centre + size / well selection).
  • How to set tile overlap.

TODO image

Screenshot of the scan/region setup panel. Notion source: FRAME_DOKU_FROM_NOTION/FAT FRAME #0007 Korea - Part 5 ("First Stitching Test").

Step 2 — Choose single-Z (fixed focus) for now​

  • Explain single-Z vs. autofocus vs. focus map (forward-reference the other tutorials).

Step 3 — Run the scan​

  • Start the scan; what the progress display shows; roughly how long 4x takes.

TODO image

Scan-in-progress + resulting stitched overview. Notion source: FAT FRAME #0007 Korea - Part 6 ("Stitching Tests 1-5") and Part 7/Part 8.

Step 4 — View and save the stitched result​

  • Where the stitched image appears; how to save/export it (OME-TIFF).

What "good" looks like vs. artefacts​

  • Seams / brightness steps between tiles → illumination flatness (diffusor), overlap.
  • Notion source for the shadow/diffusor investigation: FAT FRAME #0007 Korea - part 7 ("Imaging test to find bug with shadow", "w/o diffusor").

Try this​

  • Increase tile count / area and compare time and file size.
  • Switch to 20x and notice the smaller field and tighter focus tolerance.