Jupyter Notebook

Showing image series

Always start your notebook with:

%matplotlib widget

Let’s start by creating some random data:

from imagedata import Series
from numpy.random import default_rng
rng = default_rng()
s = Series(rng.standard_normal(4*3*128*128).reshape((4,3,128,128)))

Next, show the image series in the notebook. Notice how you can step through the slices and time points using the arrow keys.

s.show()

Drawing a mask

When drawing a mask using get_roi(), the notebook will go ahead without waiting for the interactive drawing. First draw the mask:

s.get_roi()

When the mask is drawn (possibly in several slices), execute the get_roi_mask() to get the final mask, and show the mask using roi.show():

roi = s.get_roi_mask()
roi.show()