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josegcpa
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Okay, this looks good to me!
I have just one question - is there any circumstance where non-zero bounds would not need to be applied? The grandqc workflows having an option to apply these makes it seem as though this is optional but I am not sure if that is the case; could you please confirm this whenever you can?
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Good question! Non-zero bounds are effectively required for correct final exported annotation coordinates (GeoJSON/centroids) whenever outputs are intended in viewer/display i.e. QuPath space. The apply_bounds_offset option is present so internal processing in the WSI prediction entrypoint can remain in raw slide coordinates and so zero-bounds slides are handled cleanly afterwards. |
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This PR fixes a coordinate‑offset bug that was causing QuPath‑exported ROIs to be misaligned on slides with non‑zero
openslide.bounds-x/y. The updates read the bounds offsets, shift ROI/tissue/artefact geometries and adjust output GeoJSONs accordingly. The issue and discussion are documented in this Image.sc forum thread.