Improve documention for both contributors and user

[htwangtw]

To-dos

• Add example to use the app on example dataset in user guide (Add examples #166, Unclear inputs required #171)
• Input size vs RAM requirement (memory multiplier of input #186) - run experiment on beluga
• Add atlas set up instructions for contributors and catch up on change log ([BUG] unknown atlas does not give the expected error #173)

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.21%. Comparing base (727d995) to head (685b041).
Report is 7 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #205   +/-   ##
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  Coverage   94.21%   94.21%           
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  Files          18       18           
  Lines         761      761           
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  Hits          717      717           
  Misses         44       44           

Files with missing lines	Coverage Δ
giga_connectome/run.py	95.34% <ø> (ø)