Annotations made by HALO for mrxs slide are not read correctly due to limit bounds

[moerlemans]

Describe the bug
A clear and concise description of what the bug is.
When loading an mrxs slide with limit_bounds true and an annotation with the TiledROIDataset.from_standard_tiling. It will not produce the correct annotations, but annotations at an offset equal to the limit bounds as HALO annotations are apperently not taking limit bounds into account in their coordinates.

To Reproduce
A clear and concise description on how to reproduce the problem.
Load slide image and halo annotation using the WsiAnnotations.from_halo_xml and make a dataset using TiledROIsSlideImageDataset.from_standard_tiling with limit_bounds=True. Visualize to check.

Expected behavior
A clear and concise description of what you expected to happen.
Expect the annotations to be returned in the good coordinate system in which the images are as well.

Environment
dlup version: 0.3.25
How installed: pip install -e .
Python version: 3.10
Operating System:

Additional context
Add any other context about the problem here.

[github-actions]

This issue is stale because it has been open 60 days with no activity. Remove stale label or comment or this will be closed in 15 days

[github-actions]

This issue is stale because it has been open 60 days with no activity. Remove stale label or comment or this will be closed in 15 days

[jonasteuwen]

This is probably fixes, depends on upstream changes to pyhaloxml.

[rharkes]

Not in this case. The offsets are in the .mrxs file and need to be used to translate all the annotations. We had the same problem in QuPath, where I tried to fix it for one of our users. It requires some way to get the values out of the .mrxs. This was the class that did the work.

class offset_values {
    @SerializedName("COMPRESSED_STITCHING_ORIG_SLIDE_SCANNED_AREA_IN_PIXELS__LEFT = ")
    private Double left
    @SerializedName("COMPRESSED_STITCHING_ORIG_SLIDE_SCANNED_AREA_IN_PIXELS__TOP = ")
    private Double top

    final Double gettop(){
        return this.top-(this.top%256)
    }
    final Double getleft(){
        return this.left-(this.left%256)
    }
}

Sadly the .annotation files do not contain any option for global offset.

[jonasteuwen]

@rharkes I think this is fixed now by offsetting in the reader

[rharkes]

Good. I remembered it was a pretty annoying problem. When we thought it was fixed, the offset turned out to always be a multiple of 256. Even though the values in the mrxs data were not.

[jonasteuwen]

That’s good to know!