$ sudo apt-get install openslide-tools

$ pip install scikit-image==0.14.2
$ pip install opencv-python==4.1.2.30
$ pip install openslide-python==1.1.1

$ pip install tissueloc==2.1.0

def locate_tissue_cnts(slide_path,
                       max_img_size=2048,
                       smooth_sigma=13,
                       thresh_val = 0.80,
                       min_tissue_size=10000):
    """ Locate tissue contours of whole slide image
    Parameters
    ----------
    slide_path : valid slide path
        The slide to locate the tissue.
    max_img_size: int
        Max height and width for the size of slide with selected level.
    smooth_sigma: int
        Gaussian smoothing sigma.
    thresh_val: float
        Thresholding value.
    min_tissue_size: int
        Minimum tissue area.
    Returns
    -------
    cnts: list
        List of all contours coordinates of tissues.
    d_factor: int
        Downsampling factor of selected level compared to level 0
    """

import tissueloc as tl
slide_path = "../data/SoftTissue/TCGA-B9EB312E82F6.svs"
# locate tissue contours with default parameters
cnts, d_factor = tl.locate_tissue_cnts(slide_path, max_img_size=2048, smooth_sigma=13,
                                       thresh_val=0.80,min_tissue_size=10000)

@article{chen2019tissueloc,
  author    = {Pingjun Chen and Lin Yang},
  title     = {tissueloc: Whole slide digital pathology image tissue localization},
  journal   = {J. Open Source Software},
  volume    = {4},
  number    = {33},
  pages     = {1148},
  year      = {2019},
  url       = {https://doi.org/10.21105/joss.01148},
  doi       = {10.21105/joss.01148}
}