Write tutorial about scientific microscopy image visualization

BiAPoL / blog

Most of us study and work at the Bio-image Analysis Technology Development group at the DFG Cluster of Excellence “Physics of Life” at the TU Dresden. We blog about image data science, knowledge exchange and research data management in the life sciences.

https://biapol.github.io/blog/

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Write tutorial about scientific microscopy image visualization #36

Open haesleinhuepf opened 2 years ago

haesleinhuepf commented 2 years ago

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 commented 2 years ago

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.