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Updating training notebooks - peak_local_max function kwarg deprecated
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 forpeak_local_max
has been deprecated. I have removed it. This also means the returned result is thepeaks
variable, notpeaks_local_max
as before. - Dtypes of
np.bool
are deprecated, and it's advised to replace withbool
instead. I've done that here.