# Label neighbor filters

## Contents

# Label neighbor filters#

In this notebook, we demonstrate how neighbor-based filters work in the contexts of measurements of cells in tissues. We also determine neighbor of neighbors and extend the radius of such filters.

See also

```
import pyclesperanto_prototype as cle
import numpy as np
import matplotlib
from numpy.random import random
cle.select_device("RTX")
```

```
<Apple M1 Max on Platform: Apple (2 refs)>
```

```
# Generate artificial cells as test data
tissue = cle.artificial_tissue_2d()
touch_matrix = cle.generate_touch_matrix(tissue)
cle.imshow(tissue, labels=True)
```

# Associate artificial measurements to the cells#

```
centroids = cle.label_centroids_to_pointlist(tissue)
coordinates = cle.pull_zyx(centroids)
values = random([coordinates.shape[1]])
for i, y in enumerate(coordinates[1]):
if (y < 128):
values[i] = values[i] * 10 + 45
else:
values[i] = values[i] * 10 + 90
measurements = cle.push_zyx(np.asarray([values]))
# visualize measurments in space
parametric_image = cle.replace_intensities(tissue, measurements)
cle.imshow(parametric_image, min_display_intensity=0, max_display_intensity=100, color_map='jet')
```

# Local averaging smoothes edges#

By averaging measurments locally, we can reduce the noise, but we also introduce a stripe where the region touch

```
local_mean_measurements = cle.mean_of_touching_neighbors(measurements, touch_matrix)
parametric_image = cle.replace_intensities(tissue, local_mean_measurements)
cle.imshow(parametric_image, min_display_intensity=0, max_display_intensity=100, color_map='jet')
```

# Edge preserving filters: median#

By averaging using a median filter, we can also reduce noise while keeping the edge between the regions sharp

```
local_median_measurements = cle.median_of_touching_neighbors(measurements, touch_matrix)
parametric_image = cle.replace_intensities(tissue, local_median_measurements)
cle.imshow(parametric_image, min_display_intensity=0, max_display_intensity=100, color_map='jet')
```

# Increasing filter radius: neighbors of neighbors#

In order to increase the radius of the operation, we need to determin neighbors of touching neighbors

```
neighbor_matrix = cle.neighbors_of_neighbors(touch_matrix)
local_median_measurements = cle.median_of_touching_neighbors(measurements, neighbor_matrix)
parametric_image = cle.replace_intensities(tissue, local_median_measurements)
cle.imshow(parametric_image, min_display_intensity=0, max_display_intensity=100, color_map='jet')
```

## Short-cuts for visualisation only#

If youâ€™re not so much interested in the vectors of measurements, there are shortcuts: For example for visualizing the mean value of neighboring pixels with different radii:

```
# visualize measurments in space
measurement_image = cle.replace_intensities(tissue, measurements)
print('original')
cle.imshow(measurement_image, min_display_intensity=0, max_display_intensity=100, color_map='jet')
for radius in range(0, 5):
print('Radius', radius)
# note: this function takes a parametric image the label map instead of a vector and the touch_matrix used above
parametric_image = cle.mean_of_touching_neighbors_map(measurement_image, tissue, radius=radius)
cle.imshow(parametric_image, min_display_intensity=0, max_display_intensity=100, color_map='jet')
```

```
original
```

```
Radius 0
```

```
Radius 1
```

```
Radius 2
```

```
Radius 3
```

```
Radius 4
```