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Write tutorial about scientific microscopy image visualization #36

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haesleinhuepf opened this issue Jan 15, 2022 · 1 comment
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@haesleinhuepf
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Related to #35 , we might want to write a tutorial about image visualization.

Back in the days when I wrote this notebook I noticed that it is quite hard to make good visualization of microscopy images with python. Either this is true (and we don't write a blog post about it) or I was wrong and there are amazing resources for doing this properly.

Content could be:

  • Visualize multi-channel images, e.g. for colocalization (magenta, green, mix)
  • Visualize contours on top of images (see example here)
  • How to add scale-bars

I think @guiwitz' microfilm library could be the right starting point.

@guiwitz
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guiwitz commented Jan 19, 2022

First, I really appreciate all your efforts to create these tutorials and teaching materials! Just a comment about microfilm: I wrote microfilm exactly because it seemed odd to me that it was so difficult to create a multi-channel image in Python. I never found and existing library helping for that. And when I released it, people seemed interested and I didn't get any "oh you didn't know that there's already that XYZ awesome package to do that" reaction. If you write a tutorial using microfilm, let me know if you encounter any problem or have suggestions for improvement, it's still very alpha.

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