Create documentation to guide architecture of microAPD

[dmitrisvetlov]

In creating the package for automated microscope control that we will use long-term (what I am calling microAPD), we want to utilize already written code existing within several repositories:

• This one
• FISH_Processing
• MicroscopeControlByTatsuya

We also want to utilize existing, validated packages, e.g. Pycromanager, as much as possible. To move forward, we need to understand

1. The architecture and interrelationships of the existing code and
2. How the existing functionality, particularly in terms of its user interface, will be used and understood by experimental biologists.

@Alexandre-David-CSU will handle 2 above by annotating the existing Jupyter notebooks, including asking questions about concepts and code that are not readily comprehensible. @Kyle-Finkel will handle 1 above by creating high-level architecture documents, primarily UML diagrams, to allow all contributors to visualize the interrelationships, particularly between this repository's code and its third-party packages. He will begin by focusing only on the code utilized in the existing Jupyter notebooks.

[dmitrisvetlov]

@Alexandre-David-CSU and @Kyle-Finkel, please add all documentation to the branch I have created for this issue (you will see it linked under the Development category on the right-hand side). @Munsky, please specify a priority ordering for the notebook(s), and whether or not the changes made on this branch should be merged here first.