tissueloc

Localize the tissue regions in whole slide pathology images

Installation

Install OpenSlide.

$ apt-get install openslide-tools

Install tissueloc.

$ pip install tissueloc

Usage

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
    """

Example

Testing slide can be downloaded from Figshare.

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

Procedures

import tissueloc as tl
# Step 1: Select the proper level
slide_path = "../data/SoftTissue/TCGA-B9EB312E82F6.svs"
max_img_size = 2048
s_level, d_factor = tl.select_slide_level(slide_path, max_img_size)
# Step 2: Load Slide image with selected level
slide_img = tl.load_slide_img(slide_path, s_level)
# Step 3: Convert color image to gray
gray_img = tl.rgb2gray(slide_img)
# Step 4: Smooth and Binarize
thresh_val = 0.8
smooth_sigma = 13
bw_img = tl.thresh_slide(gray_img, thresh_val, sigma=smooth_sigma)
# Step 5: Fill tissue holes
bw_fill = tl.fill_tissue_holes(bw_img)
# Step 6: Remove small tissues
min_tissue_size = 10000
bw_remove = tl.remove_small_tissue(bw_fill, min_tissue_size)
# Step 7: Locate tissue regions
cnts = tl.find_tissue_cnts(bw_remove)

Documentation

Hosted in https://tissueloc.readthedocs.io, powered by readthedocs and Sphinx.

License

tissueloc is free software made available under the MIT License. For details see the LICENSE file.

Contributors

See the AUTHORS.md file for a complete list of contributors to the project.

Contributing

Issues and Pull Request are very welcome.

arafatkatze/tissueloc