Merge pull request #441 from spotter/color_deconv

ENH: Adding color deconvolution for immunohistochemical images.

doc/examples/plot_ihc_color_separation.py

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+"""
+==============================================
+Immunohistochemical staining colors separation
+==============================================
+
+In this example we separate the immunohistochemical (IHC) staining
+from the hematoxylin counterstaining. The separation is achieved with the
+method described in [1]_, known as "color deconvolution".
+
+The IHC staining expression of the FHL2 protein is here revealed with
+Diaminobenzidine (DAB) which gives a brown color.
+
+
+.. [1] 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.
+"""
+import matplotlib.pyplot as plt
+
+from skimage import data
+from skimage.color import rgb2hed
+
+ihc_rgb = data.immunohistochemistry()
+ihc_hed = rgb2hed(ihc_rgb)
+
+fig, axes = plt.subplots(2, 2, figsize=(7, 6))
+ax0, ax1, ax2, ax3 = axes.ravel()
+
+ax0.imshow(ihc_rgb)
+ax0.set_title("Original image")
+
+ax1.imshow(ihc_hed[:, :, 0], cmap=plt.cm.gray)
+ax1.set_title("Hematoxylin")
+
+ax2.imshow(ihc_hed[:, :, 1], cmap=plt.cm.gray)
+ax2.set_title("Eosin")
+
+ax3.imshow(ihc_hed[:, :, 2], cmap=plt.cm.gray)
+ax3.set_title("DAB")
+
+for ax in axes.ravel():
+    ax.axis('off')
+
+fig.subplots_adjust(hspace=0.3)
+
+
+"""
+.. image:: PLOT2RST.current_figure
+
+Now we can easily manipulate the hematoxylin and DAB "channels":
+"""
+import numpy as np
+
+from skimage.exposure import rescale_intensity
+
+# Rescale hematoxylin and DAB signals and give them a fluorescence look
+h = rescale_intensity(ihc_hed[:, :, 0], out_range=(0, 1))
+d = rescale_intensity(ihc_hed[:, :, 2], out_range=(0, 1))
+zdh = np.dstack((np.zeros_like(h), d, h))
+
+plt.figure()
+plt.imshow(zdh)
+plt.title("Stain separated image (rescaled)")
+plt.axis('off')
+plt.show()
+
+"""
+.. image:: PLOT2RST.current_figure
+"""