Vectra Polaris tile stitching

Hi,

We would like to assemble individual image tiles from a Vectra Polaris slide scanner into a whole-slide image. The tiles are not overlapping, so stitching is based on coordinates in the file names.

We tried this QuPath script (from Pete Bankhead) - while it works overall, there are zero-value pixels between most of the tiles - see screenshot here:

Just wondering whether anyone else found a way to assemble such files or successfully used the above script?

Many thanks,
Jonny

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Hi John,
for me it seems as if the resolution (stored as TIFFTag) is not precise.
In the script (from Pete Bankhead) you can find two lines of code:

        x = Math.round(xRes * xPos) as int
        y = Math.round(yRes * yPos) as int

Maybe you can try to correct the x and y positions by using a correction factor.
Change the code to

        k = 1.05
        x = Math.round(xRes * xPos * k) as int
        y = Math.round(yRes * yPos * k) as int

and see what happens.
If the width of the gap is changing then it works in principle.
Then find the proper value for k.

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Thanks! It turns out that the underlying problem was a ‘rounding error’ when reading the TIFFTag. I’ve put in a correction factor now as you suggested - seems to work now.
Best wishes,
Jonny

1 Like