Tutorial 6: Custom slide filtering

In this brief tutorial, we’ll take a look at how you can implement and preview bespoke slide-level filtering methods.

The slide-level filtering (QC) methods Slideflow currently supports include Otsu’s thresholding and Gaussian blur filtering, which can be applied to a WSI object with WSI.qc(). If you have a custom filtering algorithm you would like to apply to a slide, you can now use WSI.apply_qc_mask() to apply a boolean mask to filter a slide.

For the purposes of this tutorial, we will generate a boolean mask using the already-available Otsu’s thresholding algorithm, but you can replace this with whatever masking algorithm you like.

First, we’ll load a slide:

import numpy as np
import slideflow as sf

wsi = sf.WSI('slide.svs', tile_px=299, tile_um=302)

Next, we’ll apply Otsu’s thresholding to get the boolean mask we’ll use in subsequent steps, then remove the QC once we have the mask:

wsi.qc('otsu')
qc_mask = np.copy(wsi.qc_mask)
wsi.remove_qc()

Our mask should have two dimensions (y, x) and have a dtype of bool:

>>> qc_mask.shape
(1010, 2847)
>>> qc_mask.dtype
dtype('bool')

Our WSI object now has no QC applied. We can manually apply this boolean mask with WSI.apply_qc_mask():

wsi.apply_qc_mask(qc_mask)

And that’s it! We can preview how our mask affects tile filtering by using WSI.preview():

wsi.preview().show()