Identifying labels which touch the background#
In developmental biology it is a common task to differentiate layers of cells, for example in epithelial tissue. Therefore it might be useful to know if a cell is part of an outer layer, if it touches the background. In this notebook we measure and visualize this.
For demonstrating it we simulate a clumb of cells.
import pyclesperanto_prototype as cle
# import a function from a file in the same folder
from simulated_cell_clumb import simulate_data
cells = simulate_data()
cells
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cle._ image
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Determining which cells touch the background#
To determine which cells touch the background, we need to produce a touch matrix which tells us which objects touch which others.
touch_matrix = cle.generate_touch_matrix(cells)
touch_matrix
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cle._ image
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The first row and column in this image represent objects touching the background. We can read out this first row or column like this:
touching_background = touch_matrix[0]
touching_background
cle.array([0. 1. 1. 1. 0. 1. 1. 1. 0. 1. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 1. 0. 0. 1. 0. 0. 1. 0. 1. 1. 0. 0. 1. 1. 0. 0. 1. 1. 1.], dtype=float32)
And we can visualized it in the original image coordinates.
cle.replace_intensities(cells, touching_background)
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cle._ image
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Or we can get a label image representing those objects.
cle.exclude_labels(cle.binary_not([touching_background]), cells)
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cle._ image
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