Jakob Nikolas Kather jnkather
odebeir
/ gist:5038467
Last active
April 1, 2016 23:10
Color deconvolution for python cf : A. C. Ruifrok and D. A. Johnston, “Quantification of histochemical staining by color deconvolution.,” Analytical and quantitative cytology and histology / the International Academy of Cytology [and] American Society of Cytology, vol. 23, no. 4, pp. 291–9, Aug. 2001.
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| def convert_to_optical_densities(rgb,r0,g0,b0): | |
| OD = rgb.astype(float) | |
| OD[:,:,0] /= r0 | |
| OD[:,:,1] /= g0 | |
| OD[:,:,2] /= b0 | |
| return -np.log(OD) | |
| def color_deconvolution(rgb,r0,g0,b0,verbose=False): | |
| stain_OD = np.asarray([[0.18,0.20,0.08],[0.01,0.13,0.0166],[0.10,0.21,0.29]]) #hematoxylin, eosyn, DAB |