NEUBIAS / training-resources

Resources for teaching/preparing to teach bioimage analysis
https://neubias.github.io/training-resources
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Binarization: wrong concept? #249

Open tischi opened 2 years ago

tischi commented 2 years ago

@manerotoni @stemarcotti

Currently, in the activities, the binarization module teaches how to create a binary image by means of a simple intensity threshold. But the concept map (and example figure) teaches the general concept of converting an intensity image to a binary image by whatever means (could also be a DCNN). So there is some mismatch...

I somehow feel that "binarization" might not be the right concept. I am not sure how to do it better, but some thoughts:

My current feeling is that "Binarization" is not the ideal concept to teach, better would be "Semantic segmentation" and "Intensity threshold" (more ideas for intensity threshold).

Maybe we just add a module "Semantic segmentation" that contains no activities, but just serves to explain the concept (probably including a label mask image as a storage mechanism for the segmentation)? Then a module "Foreground background segmentation by an intensity threshold" or just "Intensity threshold" (?) and there we refer to "Semantic segmentation" and say this is the most simple version for of it?

Maybe something totally different? What do you think?

tischi commented 2 years ago

I think I have an idea 😸

What about we create two new modules:

And the Activities and Exercises in these modules are not about how to create those segmentations, but how such segmentations are typically stored (label mask images) and how to inspect already existing segmentations**; stuff like: how many objects are there, how many semantic classes are there, are they disjoint, what class covers the largest part of the image, ...

I think this could be really good, because it enables the students to understand the output of all the bizillion methods and tools that segment stuff in images.

tischi commented 2 years ago

Maybe better: just one module: "Image segmentation" and there we explain the difference between instance and semantic and that both can be stored as label masks.

tischi commented 2 years ago

=> rename to title: Thresholding tags: Foreground background semantic segmentation