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Consider implementing Phansalkar local thresholding #17

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0x00b1 opened this issue Oct 7, 2015 · 0 comments
Open

Consider implementing Phansalkar local thresholding #17

0x00b1 opened this issue Oct 7, 2015 · 0 comments

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0x00b1 commented Oct 7, 2015

From @LeeKamentsky on September 25, 2015 12:31

See https://github.com/stelfrich/imagej-ops/blob/7ef98f4101700213d49ac11184e4278f26b7a2bd/src/main/java/net/imagej/ops/threshold/localPhansalkar/LocalPhansalkar.java for an implementation in ImageJ and Phansalskar N. et al. Adaptive local thresholding for detection of nuclei in diversity stained cytology images. International Conference on Communications and Signal Processing (ICCSP), 2011, // 218 - 220 for the citation.

A local thresholding method based on a calculation done on the local mean and variance:

# Phansalkar recommends k = 0.25, r = 0.5, p = 2 and q = 10
img_mean = convolve(img, strel_disk(radius))
img_stdev = sqrt(convolve((img - img-mean)**2, strel_disk(radius)))
t = img_mean * (1 + p * exp(-q*img_mean) + k * ((stdev/r) - 1)

Copied from original issue: CellProfiler/CellProfiler#1587

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