Vectra Polaris tile stitching


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,

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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.


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,

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