Example

Below is a simple example demonstrating how to extract all available features.

There are test images provided with this package.

#import libraries
import sys
sys.path.append("../")
import os
from nmco.utils.Run_nuclear_feature_extraction import run_nuclear_chromatin_feat_ext


# initialising paths
labelled_image_path = os.path.join(os.path.dirname(os.getcwd()),'example_data/nuc_labels.tif')
raw_image_path = os.path.join(os.path.dirname(os.getcwd()),'example_data/raw_image.tif')
feature_path = os.path.join(os.path.dirname(os.getcwd()),'example_data/')

# For a quick extraction of all available features for all labelled nuclei given a segmented image with default parameters
features = run_nuclear_chromatin_feat_ext(raw_image_path,labelled_image_path,feature_path)

Alternatively, use the CLI version using default parameters as follows.

::

python measure_nmco_features.py –rawdir <path/to/image> –datadir <path/to/labelled_image> –savedir <path/to/output/folder>

A more detailed implimenataion can be seen in the jupyter notebook “Nuclear_Features.ipynb”