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residual_artifacts_and_coverage

Creates a binary mask of residual artifacts.

Parameters:

Name Type Description Default
img RGBImage

Image of a tissue.

 required
conversion ColorConversion

Conversion that describes the used staining protocol.

 required
nucleus_area int

Approximate area of a single cell nucleus in pixels.

 required
res_index int

Index of the residual channel in the used staining conversion.

 required
threshold float

Threshold that determines if a given pixel is an artifact. Currently recommended threshold value for H&E stained slides is 0.005. This value was declared emprirically and should provide a strict detection of artifacts. Depending on the match between the tissue and the expected staining protocol, slightly higher values could also provide reasonable results.

 required

Returns:

Type Description
ResidualArtifacts

Dictionary with a binary coverage mask and a coverage number.
Note

The returned dictionary contains the following values:

Key Description
coverage_mask Binary mask of the detected residual artifacts.
coverage A number that states what portion of the image's foreground area is covered by the artifacts.

Examples: 

from skimage.data import immunohistochemistry

from rationai.qc import residual_artifacts_and_coverage
from rationai.staining import ColorConversion


img = immunohistochemistry()

result = residual_artifacts_and_coverage(
    img, ColorConversion.RGB2HDR, nucleus_area=150, res_index=2, threshold=0.013
)

mask = result["coverage_mask"]  # Contains values 0 and 1
print(result["coverage"])

Source code in rationai/qc/residual_artifacts/residual_artifacts_and_coverage.py 
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def residual_artifacts_and_coverage(
    img: RGBImage,
    conversion: ColorConversion,
    nucleus_area: int,
    res_index: int,
    threshold: float,
) -> ResidualArtifacts:
    """Creates a binary mask of residual artifacts.

    Args:
        img: Image of a tissue.
        conversion: Conversion that describes the used staining protocol.
        nucleus_area: Approximate area of a single cell nucleus in pixels.
        res_index: Index of the residual channel in the used staining conversion.
        threshold: Threshold that determines if a given pixel is an artifact.
            Currently recommended threshold value for H&E stained slides is `0.005`.
            This value was declared emprirically and should provide a strict
            detection of artifacts.
            Depending on the match between the tissue and the expected staining protocol,
            slightly higher values could also provide reasonable results.

    Returns:
        Dictionary with a binary coverage mask and a coverage number.

    Note:
        The returned dictionary contains the following values:

        | Key               | Description                                                                                   |
        |-------------------|-----------------------------------------------------------------------------------------------|
        | `coverage_mask`   | Binary mask of the detected residual artifacts.                                               |
        | `coverage`        | A number that states what portion of the image's foreground area is covered by the artifacts. |

    Examples:
    ```python
    from skimage.data import immunohistochemistry

    from rationai.qc import residual_artifacts_and_coverage
    from rationai.staining import ColorConversion


    img = immunohistochemistry()

    result = residual_artifacts_and_coverage(
        img, ColorConversion.RGB2HDR, nucleus_area=150, res_index=2, threshold=0.013
    )

    mask = result["coverage_mask"]  # Contains values 0 and 1
    print(result["coverage"])
    ```
    """
    coverage, cov_heatmap = _get_debris_coverage(
        img=img,
        conv=conversion,
        nucleus_area=nucleus_area,
        res_index=res_index,
        threshold=threshold,
    )

    result: ResidualArtifacts = {
        "coverage_mask": cov_heatmap,
        "coverage": coverage,
    }

    return result