Reorganize code

[tlambert03]

This pull request includes the following changes:

• Reorganized the code to improve readability and maintainability.

• Fixed import and formatting issues in multiple files.

These changes aim to enhance the code quality and make it easier to work with.

[codecov]

Codecov Report

Attention: Patch coverage is 82.51121% with 39 lines in your changes are missing coverage. Please review.

Project coverage is 52.93%. Comparing base (7b9d90d) to head (ad14019).
Report is 3 commits behind head on main.

❗ Current head ad14019 differs from pull request most recent head aa9d8f4. Consider uploading reports for the commit aa9d8f4 to get more accurate results

Files	Patch %	Lines
src/microsim/schema/space.py	82.05%	14 Missing ⚠️
src/microsim/util.py	71.42%	14 Missing ⚠️
src/microsim/schema/modality/widefield.py	57.14%	6 Missing ⚠️
src/microsim/schema/simulation.py	90.00%	3 Missing ⚠️
src/microsim/models/_microscope.py	0.00%	1 Missing ⚠️
src/microsim/samples/__init__.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #12      +/-   ##
==========================================
+ Coverage   44.09%   52.93%   +8.84%     
==========================================
  Files          27       37      +10     
  Lines         728      937     +209     
==========================================
+ Hits          321      496     +175     
- Misses        407      441      +34     

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