Fix and organize README documentation

[phonchi]

• Fixed grammar and spelling errors (Deomnstrate → Demonstrates, "focus on" → "focused on")
• Updated table of contents to include all sections and subsections with proper hierarchy
• Renamed "Resources" subsection to "Learning Resources" to avoid naming confusion
• Removed duplicate entries (TomoTwin in Particle picking, Ctfplotter in CTF estimation)
• Standardized formatting throughout:
  • Consistent use of backticks for software names
  • Standardized list numbering format
  • Fixed spacing issues around dashes and parentheses
  • Consistent hyphenation (Fiducial-based, Fiducial-less)
• Fixed PolNet paper link to point to actual publication instead of GitHub repo
• Removed trailing whitespace from entries

[gemini-code-assist]

Summary of Changes

Hello @phonchi, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request significantly improves the quality and organization of the project's README documentation. The changes aim to make the information more accessible, accurate, and consistent for anyone consulting the guide. By refining the structure, correcting textual errors, and standardizing presentation, the README now serves as a more reliable and user-friendly resource.

Highlights

• Documentation Organization: The README's table of contents has been comprehensively updated and expanded to include all sections and subsections with a proper hierarchical structure, improving navigation and clarity.
• Grammar and Spelling Corrections: Numerous grammar and spelling errors, such as 'Deomnstrate' to 'Demonstrates' and 'focus on' to 'focused on', have been fixed to enhance readability and professionalism.
• Content Refinement: Duplicate entries for tools like TomoTwin and Ctfplotter have been removed, and the 'Resources' subsection was renamed to 'Learning Resources' to avoid confusion. A PolNet paper link was also corrected to point to the actual publication.
• Formatting Standardization: Consistent formatting has been applied throughout the document, including the standardized use of backticks for software names, uniform list numbering, consistent hyphenation (e.g., 'Fiducial-based'), and corrected spacing around dashes and parentheses.

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[gemini-code-assist]

Code Review

This pull request significantly improves the README file by fixing grammatical errors, updating the table of contents, standardizing formatting, and removing duplicate entries. The changes enhance readability and organization. I have one minor suggestion to ensure consistency in formatting.