haesleinhuepf / haesleinhuepf/BioImageAnalysisNotebooks

General questions

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Description

I went a bit through the (great!) material and before trying to improve here and there, I have a few questions:

- Is there anywhere a plan of the entire course (more detailed than what is explained [here](https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/intro.html#structure-of-this-jupyter-book))? Maybe that could help structure the course a bit better. If I take the example of the segmentation chapter, there's a mix of basic notebooks, notebooks going through series of functions and notebooks showing complete workflows. Maybe there could be sub-chapters?
- pyclesperanto: I noticed that in most notebooks introducing new concepts (e.g. thresholding) both scikit-image and pyclesperanto examples are given. I think it's great as it gives people a choice (it also guarantees that people can at least run the non-GPU code in any case). Some more advanced examples e.g. on [nuclei quantification](https://github.com/guiwitz/BioImageAnalysisNotebooks/blob/main/docs/28_colocalization/counting_nuclei_multichannel.ipynb) only exist with pyclesperanto. Would it be accepted (or desired) to have equivalent notebooks using just the classical packages (scikit-image, scipy etc.)?
- the blobs picture is used in lots of places. Is that by design or was it just a first step? I think it makes it in general more interesting to show even simple things like [labelling](https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/20_image_segmentation/09_connected_component_labeling.html#labeling-in-practice) with real images.

A few things I mentioned in other issues, but as they are general questions I put them back here for completeness:
- what's the plan about pyclesperanto's ```imshow```. I just think it's a bit dangerous to depend on pyclesperanto just for image display (even in notebooks where pyclesperanto is not used). Again my (biased) opinion is to use microfilm.
- the numbering both of chapters and of notebooks inside chapters is often strange. Do we avoid fixing this (so that the ```_toc.yml``` doesn't have to change all the time) until things settle down or should fix things bit by bit when we encounter them?
- should the data in general be accessed by url or by paths? url's ensure that it always works, though with internet connection. Paths don't need a connection but only work when cloning the repo (tricky e.g. on Colab).
- should we make the course work on Colab and/or on Binder?

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