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scverse / squidpy

Spatial Single Cell Analysis in Python
https://squidpy.readthedocs.io/en/stable/
BSD 3-Clause "New" or "Revised" License
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automatic extracton of segmentation features #173

Closed giovp closed 3 years ago

giovp commented 3 years ago

very useful to get features from segmentation labels in pandas dataframe

import pandas as pd

info_table = pd.DataFrame(
    measure.regionprops_table(
        interior_labels,
        intensity_image=nuclei,
        properties=['label', 'slice', 'area', 'mean_intensity', 'solidity'],
    )
).set_index('label')
hspitzer commented 3 years ago

We are now using region props to calculate segmentation features. Closing