Input masks

For some tissue images you may want to restrict analysis to certain parts of the image. For example, the image may have degradation towards the edges, you may wish to exclude non tissue areas, or even perhaps restricting SSAM analysis to previously segmented areas.

SSAM accepts input masks that are defined as polygons.

Example for the VISp smFISH dataset:

from matplotlib.patches import Polygon
from matplotlib.collections import PatchCollection

plt.figure(figsize=[5, 5])
ds.plot_l1norm(cmap="Greys", rotate=1)
ds.plot_localmax(c="Blue", rotate=1, s=0.1)

patch = Polygon(xy, facecolor="black", edgecolor="red", linewidth=10, ls="-")
p = PatchCollection([patch], alpha=0.4)
plt.gca().add_collection(p~)
plt.show()

After the desired region selected, a mask can be created. In this case we define an input_mask and output_mask which restricts all data process anf reported output to the selected region.

from matplotlib.path import Path

x, y = np.meshgrid(np.arange(ds.vf.shape[0]), np.arange(ds.vf.shape[1]))
x, y = x.flatten(), y.flatten()
points = np.vstack((x,y)).T

path = Path(xy)
input_mask = path.contains_points(points)
output_mask = input_mask = input_mask.reshape((ds.vf.shape[1], ds.vf.shape[0], 1)).swapaxes(0, 1)