separate-stains

separate_stains

skimage.color.separate_stains(rgb, conv_matrix) [source]

RGB to stain color space conversion.

Parameters:	rgb : array_like The image in RGB format, in a 3-D array of shape (.., .., 3). conv_matrix: ndarray The stain separation matrix as described by G. Landini [R55].
Returns:	out : ndarray The image in stain color space, in a 3-D array of shape (.., .., 3).
Raises:	ValueError If rgb is not a 3-D array of shape (.., .., 3).

Notes

Stain separation matrices available in the color module and their respective colorspace:

• hed_from_rgb: Hematoxylin + Eosin + DAB
• hdx_from_rgb: Hematoxylin + DAB
• fgx_from_rgb: Feulgen + Light Green
• bex_from_rgb: Giemsa stain : Methyl Blue + Eosin
• rbd_from_rgb: FastRed + FastBlue + DAB
• gdx_from_rgb: Methyl Green + DAB
• hax_from_rgb: Hematoxylin + AEC
• bro_from_rgb: Blue matrix Anilline Blue + Red matrix Azocarmine + Orange matrix Orange-G
• bpx_from_rgb: Methyl Blue + Ponceau Fuchsin
• ahx_from_rgb: Alcian Blue + Hematoxylin
• hpx_from_rgb: Hematoxylin + PAS

References

[R55]

(1, 2) http://www.dentistry.bham.ac.uk/landinig/software/cdeconv/cdeconv.html

Examples

>>> from skimage import data
>>> from skimage.color import separate_stains, hdx_from_rgb
>>> ihc = data.immunohistochemistry()
>>> ihc_hdx = separate_stains(ihc, hdx_from_rgb)