Re: IHC Image color deconvolution

[Koundinya Desiraju]

Thank you Cedric. That helped a lot.

Regards,
Koundinya

On Fri, Aug 26, 2016 at 9:47 AM Cedric Espenel 
wrote:

> Hi Koundinya,
>
> I'm not sure if that will answer your question but if you try:
>
> from matplotlib.colors import LinearSegmentedColormap
> cmap_Hema = LinearSegmentedColormap.from_list('mycmap', ['white', 'navy'])
> cmap_DAB = LinearSegmentedColormap.from_list('mycmap', ['white',
> 'saddlebrown'])
> cmap_Eosin = LinearSegmentedColormap.from_
>
> list('mycmap', ['darkviolet',
> 'white'])
>
> You won't be able to get back to the original color but it will do a descent 
> job:
>
>
>
> 
>
>
>
> 
>
>
> 
>
> Sincerely,
>
> Cedric
>
>
> On Monday, August 22, 2016 at 10:40:06 PM UTC-7, Koundinya Desiraju wrote:
>
>> In this tutorial,
>> http://scikit-image.org/docs/dev/auto_examples/color_exposure/plot_ihc_color_separation.html#sphx-glr-auto-examples-color-exposure-plot-ihc-color-separation-py
>>
>> After color deconvolution the haematoxylin and DAB channels were plotted
>> in grayscale but I want to show them in respective colors. For example, I
>> want to show DAB channel in brown. Can anyone kindly post How to do that?
>>
>> Thanks,
>> Koundinya
>>
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Re: IHC Image color deconvolution

[Cedric Espenel]

Hi Koundinya,

I'm not sure if that will answer your question but if you try:

from matplotlib.colors import LinearSegmentedColormap
cmap_Hema = LinearSegmentedColormap.from_list('mycmap', ['white', 'navy'])
cmap_DAB = LinearSegmentedColormap.from_list('mycmap', ['white', 
'saddlebrown'])
cmap_Eosin = LinearSegmentedColormap.from_list('mycmap', ['darkviolet', 
'white'])

You won't be able to get back to the original color but it will do a descent 
job: 









Sincerely,

Cedric


On Monday, August 22, 2016 at 10:40:06 PM UTC-7, Koundinya Desiraju wrote:
>
> In this tutorial, 
> http://scikit-image.org/docs/dev/auto_examples/color_exposure/plot_ihc_color_separation.html#sphx-glr-auto-examples-color-exposure-plot-ihc-color-separation-py
>
> After color deconvolution the haematoxylin and DAB channels were plotted 
> in grayscale but I want to show them in respective colors. For example, I 
> want to show DAB channel in brown. Can anyone kindly post How to do that?
>
> Thanks,
> Koundinya
>

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