Cell 20 in lesson notebook 02_interactive_analysis.ipynb needs updating to be compatible with the latest versions of scikit-image and numpy. I know this notebook was written several years ago, but it's a great example and I'd like to keep it useable for everyone.
It needs to be:
Now we can try and identify the centers of each of the nuclei by finding peaks of the distance transform
peaks = feature.peak_local_max(
smoothed_distance,
footprint=np.ones((7, 7), dtype=bool),
labels=measure.label(foreground_processed)
)
There are two changes here:
- The
indices keyword argument for peak_local_max has been deprecated. I have removed it. This also means the returned result is the peaks variable, not peaks_local_max as before.
- Dtypes of
np.bool are deprecated, and it's advised to replace with bool instead. I've done that here.
Cell 20 in lesson notebook
02_interactive_analysis.ipynbneeds updating to be compatible with the latest versions of scikit-image and numpy. I know this notebook was written several years ago, but it's a great example and I'd like to keep it useable for everyone.It needs to be:
There are two changes here:
indiceskeyword argument forpeak_local_maxhas been deprecated. I have removed it. This also means the returned result is thepeaksvariable, notpeaks_local_maxas before.np.boolare deprecated, and it's advised to replace withboolinstead. I've done that here.