Stitching Tiles Access

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user-4053
Posts: 54
Joined: Thu Jan 01, 1970 1:00 am

Stitching Tiles Access

Post by user-4053 »

  1. In the Smartzoom SW, the maximum number of tiles is limited to 100 tiles. There is no way at the customer end to modify this. The reason is of course to avoid that the system slows down too much and becomes unresponsive.
  2. There is actually a way to get access to the individual images of a scan. Here it is:
    1. For every stitching run, the SW generates under my pictures\Smartzoom5 a number of *czi files when acquiring data. When running a boxmode stiching, two files are generated:
      • BOXModeStitching.czi : Here the single tilescan is saved, the tiles are already stitched. They are not stitched when stage-based stitching was selected
      • BOXModeStitchingToutPut.czi: Here the further processed tilescan is saved, including shading correction and (if turned on) blending
    2. When another stitching scan is done, the files will be overwritten!
    3. To get access to the single tiles the only way I found (there might be a better on that I don’t know of…) is:
      • Open the czi file in Zen Blue or Zen2Core
      • Use the image export function to *.zvi (Axiovision format)
      • Open Axiovision (I tested it with 4.8.3)
      • Switch to Tile View (By switching to “Edit mode” here you can actually shift the tiles around)
      • Open the “Save As” Dialogue and select “Export"
      • In the export window, select the desired file name(s) and Image file formats
      • This saves the individual images. I don’t know how well the metadata (and scalings) are stored, but as you can see the tile view above, some information is available
      • Alternatively: Open the czi file with ImageJ
Summary written by Tom Calahan. Many thanks!
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