OtsuTissueMasker

tiatoolbox . tools . tissuemask . OtsuTissueMasker

class OtsuTissueMasker

Tissue masker which uses Otsu’s method to determine background.

Otsu’s method.

Examples

>>> from tiatoolbox.tools.tissuemask import OtsuTissueMasker
>>> masker = OtsuTissueMasker()
>>> masker.fit(thumbnail)
>>> masks = masker.transform([thumbnail])

>>> from tiatoolbox.tools.tissuemask import OtsuTissueMasker
>>> masker = OtsuTissueMasker()
>>> masks = masker.fit_transform([thumbnail])

Initialize OtsuTissueMasker.

Methods

fit	Find a binary threshold using Otsu's method.
transform	Create masks using the threshold found during fit().

fit(images, masks=None)

Find a binary threshold using Otsu’s method.

Parameters:

• images (numpy.ndarray) – List of images with a length 4 shape (N, height, width, channels).

• masks (numpy.ndarray) – Unused here, for API consistency.

• self (OtsuTissueMasker)

Return type:

None

transform(images)

Create masks using the threshold found during fit().

Parameters:

• images (numpy.ndarray) – List of images with a length 4 shape (N, height, width, channels).

• self (OtsuTissueMasker)

Returns:

List of images with a length 4 shape (N, height, width, channels).

Return type:

numpy.ndarray