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Ventana BIF overlap not considered #37

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ap-- opened this issue May 13, 2022 · 0 comments · May be fixed by #40
Open
2 tasks

Ventana BIF overlap not considered #37

ap-- opened this issue May 13, 2022 · 0 comments · May be fixed by #40
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compatibility OpenSlide compatibility related help wanted Extra attention is needed

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ap-- commented May 13, 2022

ts_slide = TiffSlide('OS-2.bif'), os_slide = OpenSlide('OS-2.bif')

    def test_level_dimensions(ts_slide, os_slide):
>       assert ts_slide.level_dimensions == os_slide.level_dimensions
E       AssertionError: assert ((128000, 829...0, 2600), ...) == ((114943, 763...2, 2386), ...)
E         At index 0 diff: (128000, 82960) != (114943, 76349)
E         Full diff:
E           (
E         -  (114943, 76349),
E         -  (57472, 38175),
E         -  (28736, 19088),
E         -  (14368, 9544),...
E         
E         ...Full output truncated (20 lines hidden), use '-vv' to show


Fixing this requires two steps:

  • (1) Generating absolute offset coordinates for each tile from the regular grid in the Ventana file
  • (2) A zarrstore that translates irregular positioned chunks with overlap into a regular grid

Notes:

(1) we get a list of offsets between pairs of tiles with a confidence estimate from the metadata. These would have to be fed into a solver that returns optimal absolute coordinates for each tile.

(2) the same translating store could be used to implement Mirax support. #33

@ap-- ap-- added the compatibility OpenSlide compatibility related label May 13, 2022
@ap-- ap-- linked a pull request Jul 9, 2022 that will close this issue
2 tasks
@ap-- ap-- added the help wanted Extra attention is needed label Oct 11, 2022
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Labels
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