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Include border when generating basin markers for watershed #7362

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merged 6 commits into from Apr 4, 2024

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mkcor
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@mkcor mkcor commented Mar 27, 2024

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Here I'm updating the Segment human cells in mitosis (link to stable):

  • I have removed the very last figure, which I think doesn't add much value;
  • I have added a few words about the watershed segmentation step;
  • I have fixed the way markers are computed, so that basins touching the image border are included. You can see the difference especially if you look at the RHS vertical border of the image (see below).

include_border

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In the gallery example on segmenting human cells (in mitosis),
include the border when generating basin markers for watershed.

@mkcor mkcor added the 📄 type: Documentation Updates, fixes and additions to documentation label Mar 27, 2024
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Thanks @mkcor. Looks already good to me so feel welcome to ignore my other minor suggestions at will. :D

doc/examples/applications/plot_human_mitosis.py Outdated Show resolved Hide resolved
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While we are at it, do you want to switch this over to import skimage as ski? I'd happily review that. 😉

Also, while reviewing this again: is "dichotomy" a well known term? A bit of topic, but rewording that might improve the example also.

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While we are at it, do you want to switch this over to import skimage as ski? I'd happily review that. 😉

Done! facda52

Also, while reviewing this again: is "dichotomy" a well known term? A bit of topic, but rewording that might improve the example also.

I remember learning about this approach in my K-12 education, so I wouldn't consider it hyper-specialized...

doc/examples/applications/plot_human_mitosis.py Outdated Show resolved Hide resolved
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It's a bit weird that the order with which the subplots are created for the over- and underestimation plot is not identical with the with index and plotted order? Maybe reorder?

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Sure: bf81710

@lagru lagru merged commit eab8481 into scikit-image:main Apr 4, 2024
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@stefanv stefanv added this to the 0.23 milestone Apr 4, 2024
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lagru commented Apr 4, 2024

Thanks @mkcor! Merging since this improvement to the gallery probably doesn't need a third maintainer to approve and has been open for some time.

@lagru lagru changed the title Include border when generating basin markers for watershed. Include border when generating basin markers for watershed Apr 4, 2024
@mkcor mkcor deleted the include-border-watershed branch April 4, 2024 11:24
@lagru lagru mentioned this pull request Apr 9, 2024
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3 participants