DOC: JNB-RTD consistency for 05-patch-prediction.ipynb

[DavidBAEpstein]

• DOC: Edit metadata to remove hidden cells. Fix one heading
• MAINT: Remove incorrect initial ?>?. Delete incorect double quotes.
• MAINT: Remove incooect double quotes. Improve text. Improve code comment.
• MAINT: Remove incorrect initial ">"
• MAINT: insert empty line before list several times
• MAINT: Insert spaces round backticked words and phrases, where appropriate

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[DavidBAEpstein]

A summary of changes since the develop version of 05-patch-prediction.ipynb

1. All hidden cells unhidden. Hidden cells are visible in jnb rendering, but not in rtd. In rtd, hidden cells incorrectly change sections to subsections with consequent incorrect fontsize. It also messes up readthedocs indexing.
2. "pip install tiatoolbox" was changed to
   "pip install git+https://github/.com/TissueImageAnalytics/tiatoolbox.git@develop" in order to get the legend right ( @Srijay's correction to visualization.py). These commands have substantial output, which I found beneficial, and so I abandoned the use of "tail --lines 1", which, in any case should be changed to "tail -n 1" to avoid the special gnu syntax.
3. Message about restarting the runtime was clarified
4. Made clean-up after run bullet-proof, for example withstanding abnormal termination in the middle of a run. Defined a Python helper function "rmdir", to avoid using bash "rm -rf".
5. Checked that everything ran correctly, including the correct legend, on Colab with GPU, on Colab without GPU, and on Macbook without GPU.
6. Removed the use of greater than signs ">" which are usually rendered literally in rtd
7. Improved some text cells
8. Lists must be preceded and followed by cell boundary or empty line, to give correct rendering in rtd.
9. Ran "make html" on the doc-05 branch, and visually compared the notebook rendering with
   https://tia-toolbox.readthedocs.io/en/doc-05/_notebooks/05-patch-prediction.html

[shaneahmed]

Thanks @DavidBAEpstein
Looks good to me. I have kept hidden cells as the issue with headings is not with hidden cells but to do with nbsphinx rendering. This will be resolved with myst-nb.