histox.slide.qc

This module contains functions for slide-level quality control, including Otsu’s thresholding and Gaussian blur filtering. Quality control methods are used by passing a list of callables to the qc argument of .extract_tiles(). They can also be directly applied to a slide with histox.WSI.qc().

import slideflow as sf
from histox.slide import qc

# Define custom QC options
qc = [
  qc.Otsu(),
  qc.Gaussian(sigma=2)
]

# Use this QC during tile extraction
P.extract_tiles(qc=qc)

# Alternatively, you can use the same QC directly on a WSI object
wsi = sf.WSI(...)
wsi.qc(qc).show()

class histox.slide.qc.Otsu(slide_level: int | None = None)

class histox.slide.qc.Gaussian(mpp: float | None = None, sigma: int = 3, threshold: float = 0.02)

class histox.slide.qc.Save(dest: str | None = None)

class histox.slide.qc.Load(source: str | None = None)

class histox.slide.qc.StridedDL(model: Callable, pred_idx: int, tile_px: int, tile_um: str | int, *, buffer: int = 8, verbose: bool = False, pred_threshold: float = 0.5, **wsi_kwargs)