Misc small cleanup tasks

[x] Clean up the utils folder to leave only scripts that are used in one of the notebooks
[x] In Colab notebook, clarify which correlation is used in step 6.1
[x] In Colab notebook, rename "4.3.1 Save SELECTED compounds" to something more generic than "compounds", "compounds/MOAs" or even just "choices
[x] In Colab notebook, add the "will take about 5 minutes" warning to the header, since by default all the cells are hidden (which I think is the right thing to do, but means an inexperienced user won't see the warning)
[x] In Colab notebook, section 3's first subsection is 3.3 - I assume should be 3.1?
[x] In Colab notebook, since section 5.2 is about just comparing to some compound and it says in the notebook it might not be the neg control, maybe instead of talking about "negative control" in that section talk about "baseline treatment" or "landmark treatment" or something like that?
[x] In Colab notebook section 6, the typing parts confused me; I ran a bunch of cells then waited a long time, because I missed the small text boxes. It would be nice to replace the Y/N things with ipywidgets for a dropdown or radio buttons, and to replace the "number of cells to show" with something like a slider.
[x] In Colab notebook section 6.1 - "Rescale or not image intensity" -> "Should image intensity be rescaled for each image?" ; "User should choose to visualize the images with rescaled intensity or not rescaled." - "Choose whether or not you want the image intensities rescaled".
[x] In Colab notebook, move the image rescaling and cells per image cells to section 6 rather than 6.1; that is how the paper describes where they are (it says the first cell of 6.1 is cell plotting), and I agree that's a better organization.
[x] In Colab notebook, "Imagine if you want to visualize the whole site where your representative cells is. Or you want to have a sense of the cell density/distribution within your sites." -> "Visualize an entire representative field of view"
[x] Current Protocol 2 notebook missing the "Open in Colab" button
[x] Pyarrow needs to be pinned to v9 in the notebook

TINY issues that can be solved after submission
[x] Look through the notebook and do a thoughtful find/replace for where we should replace "compound" with "treatment" or even "sample" to make it more general. We wouldn't want to do 3a5, for example, but probably a few places we could do in section 5
[x] Make whole plate normalization easier to access without a code change

ciminilab / 2023_Garcia-Fossa_Cruz_CurrentProtocols

Misc small cleanup tasks #4

[x] Pyarrow needs to be pinned to v9 in the notebook