pyfibre.model.tools.segmentation module¶
PyFibre Image Segmentation Library
Created by: Frank Longford Created on: 18/02/2019
Last Modified: 18/02/2019
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pyfibre.model.tools.segmentation.create_fibre_filter(fibre_networks, shape, area_threshold=200, iterations=5, sigma=0.5)[source]¶ Create binary filter of fibre regions from a list of FibreNetwork instances
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pyfibre.model.tools.segmentation.normalise_stack(image_stack)[source]¶ Normalise intensity values for each image in stack
- Parameters
image_stack (array-like, shape=(I, J, N)) – Stack of N images
- Returns
image_stack – Stack of images, with intensity values normalised across each image
- Return type
array-like, shape=(I, J, N)
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pyfibre.model.tools.segmentation.rgb_segmentation(image_stack, bd_filter, scale=1.0)[source]¶ Return binary filter for cellular identification
- Parameters
image_stack (array-like, shape=(N, I, J)) – Stack of images
bd_filter (BaseBDFilter) – Instance of filtering algorithm to be used
scale (float, optional) – Ratio to rescale size of image to
- Returns
fibre_mask, cell_mask – Binary masks that identify pixels in fibrous and cellular regions
- Return type
array-like, shape=(I, J)