Adding colors to the IHC #2279
Adding colors to the IHC #2279
Conversation
|
Thanks, @cespenel! If anyone uses this in their work, please review this PR. |
Current coverage is 90.59% (diff: 100%)@@ master #2279 diff @@
==========================================
Files 304 304
Lines 21425 21425
Methods 0 0
Messages 0 0
Branches 1844 1844
==========================================
Hits 19411 19411
Misses 1661 1661
Partials 353 353
|
| # Create an artificial color close to the orginal one | ||
| cmap_Hema = LinearSegmentedColormap.from_list('mycmap', ['white', 'navy']) | ||
| cmap_DAB = LinearSegmentedColormap.from_list('mycmap', ['white', | ||
| 'saddlebrown']) |
There was a problem hiding this comment.
Please, follow PEP8 for the indentation here and below.
|
One remark from my side. |
soupault
added
📄 type: Documentation
| @@ -35,13 +42,13 @@ | |||
| ax[0].imshow(ihc_rgb) | |||
| ax[0].set_title("Original image") | |||
|
|
|||
| ax[1].imshow(ihc_hed[:, :, 0], cmap=plt.cm.gray) | |||
| ax[1].imshow(ihc_hed[:, :, 0], cmap=cmap_Hema) | |||
|
One remark also mon my side but I'm don't use this feature. |
|
Thank you, I cleaned it. |
|
Hum, on the one hand this PR looks fine to me and I suggest to merge it; on the other hand the example seems very very domain-specific. I wonder if such functions (like What do you think? About this specific example, it was written by @spotter quite a while ago. @cespenel, do you know if a lot of people could be using these functions, or is it very specific to immunohistochemistry? |
|
@emmanuelle, I only used the module for histology and I'm not sure what other application it could have. I do agree that having a Scikit BioImage gallery (or something like that) for confocal images etc. would be very useful, at least in my domain :-) ... |
|
@cespenel thanks for your insights. @scikit-image/core what do you think about projects that would be more domain-specific? |
|
@scikit-image/core this PR looks good and is an improvement so I'm merging it. We can have the discussion about domain-specific projects somewhere else. |
Description
Following google group discussion, I added the colors to the IHC gallery.
Checklist
[It's fine to submit PRs which are a work in progress! But before they are merged, all PRs should provide:]
./doc/examples(new features only)[For detailed information on these and other aspects see scikit-image contribution guidelines]
References
[If this is a bug-fix or enhancement, it closes issue # ]
[If this is a new feature, it implements the following paper: ]