wsinfer.patchlib.segment#
Segment thumbnail of a whole slide image.
Functions#
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Create a binary tissue mask from an image. |
Module Contents#
- wsinfer.patchlib.segment.segment_tissue(im_arr: numpy.typing.NDArray, median_filter_size: int = 7, binary_threshold: int = 7, closing_kernel_size: int = 6, min_object_size_px: int = 512, min_hole_size_px: int = 1024) numpy.typing.NDArray[numpy.bool_][source]#
Create a binary tissue mask from an image.
- Parameters:
im_arr (array-like) – RGB image array (uint8) with shape (rows, cols, 3).
median_filter_size (int) – The kernel size for median filtering. Must be odd and greater than one.
binary_threshold (int) – The pixel threshold for image binarization.
closing_kernel_size (int) – The kernel size for morphological closing (in pixel units).
min_object_size_px (int) – The minimum area of an object in pixels. If an object is smaller than this area, it is removed and is made into background.
min_hole_size_px (int) – The minimum area of a hole in pixels. If a hole is smaller than this area, it is filled and is made into foreground.
- Returns:
Boolean array, where True values indicate presence of tissue.
- Return type:
mask