Jupyter Notebook

Showing image series

Always start your notebook with:

%matplotlib ipympl

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. When using mouse scrolling, keep shift key pressed to avoid scrolling the window frame.

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()