BigStitcher image Fusion problem

Hello ,

I am facing a problem with BigStitcher image fusion. I am stitching 3D(on average 10 Z’s) tiles using BigStitcher. When I am fusing image with " Preserve original data anisotropy" option and downsample=1, its adding 2 empty slices at the beginning and end. In addition, some of the Z slices are missing in stitched volume although there is no overlap in Z’s and I am specifying overlap_z=0% in parameter settings. if I dont select “Preserve original data anisotropy”" its producing lots of z slices. I want exactly same number of Z slice as the input tiles has. Can anyone help or explain the scenario

Thank you

Hi @salam03,

It’s a little tough for me to know what’s happening without seeing images, so if you could post some screenshots, it would help alot.

Some follow up questions:

  1. Are the slices empty, or is there stuff (signal) in them?
  2. Is it really unacceptable that there are extra slices? It might be a good thing (explained below).

I’ll take a guess at why you might be getting the extra slices, but as I said, without seeing the images, it’ll just be a guess.


Why the extra slices?

Stitching translates your tiles so that they’re well-aligned in the overlapping areas. Since you’re doing 3D stitching, the algorithm is allowed to move the tiles in all three dimensions. If it moves in z (the slice dimension), then the fusion might need to add slices in order to make sure that the field of view is big enough to fit both images inside the new image. i.e. If the slices stayed the same - some of the image would get “cut-off”. Maybe the images below explain it better.

Cut off

Extra slices

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