Pipeline for collagen pore-size calculation
Reference is the paper Mickel, et al., Robust Pore Size Analysis of Filamentous Networks from Three-Dimensional Confocal Microscopy". Biophysical Journal. V95 Dec 2008.
Minimum resolved fiber spacing is 2 voxels.
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DENOISING: Gaussian smoothing of image, followed by anisotropic smoothing.
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BINARIZATION: Threshold image to binary. All voxels with intensity greater than I_c set to 1 and all others to 0. The 1's are the collagen and the 0's are the fluid.
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ARTIFACT REMOVAL: Morphological Closing -- dilation followed by erosion (width 1).
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EUCLIDEAN DISTANCE MAP OF THE FLUID PHASE
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COVERING RADIUS TRANSFORM (CRT)
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PORE SIZE DISTRIBUTION is the histogram of values of the CRT