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ENH: Minor update to documentation to better explain role of experiments#15

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aylward merged 1 commit into
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experiments_readme
Jan 14, 2026
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ENH: Minor update to documentation to better explain role of experiments#15
aylward merged 1 commit into
mainfrom
experiments_readme

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@aylward aylward commented Jan 14, 2026

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Copilot AI review requested due to automatic review settings January 14, 2026 21:24
@aylward aylward merged commit 9f1a90f into main Jan 14, 2026
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@aylward aylward deleted the experiments_readme branch January 14, 2026 21:25
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Pull request overview

This pull request enhances documentation to clarify the role and purpose of the experiments directory, distinguishing it from production-ready code in the scripts directory.

Changes:

  • Significantly expanded experiments/README.md with detailed explanations of each experiment, adaptation strategies, and clear warnings against using experiments as production examples
  • Added consistent notes across all documentation files (quickstart.rst, index.rst, examples.rst, developer/extending.rst, contributing.rst, cli_scripts/overview.rst, architecture.rst) emphasizing that scripts/ contains production code while experiments/ contains research prototypes
  • Established clear guidance for contributors on when to add code to scripts/ vs experiments/ directories

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 2 comments.

Show a summary per file
File Description
experiments/README.md Major expansion with experiment highlights, adaptation strategies, and comprehensive warnings about production usage
docs/quickstart.rst Added important note distinguishing scripts/ from experiments/ directories
docs/index.rst Added tip about code examples and proper resource usage
docs/examples.rst Added note warning against using experiments as usage examples
docs/developer/extending.rst Added important note on using scripts/ and experiments/ as references when extending
docs/contributing.rst Added section on contributing scripts vs experiments with clear guidelines
docs/cli_scripts/overview.rst Added important note emphasizing scripts/ as definitive resource
docs/architecture.rst Added note pointing to implementation references in scripts/ and experiments/

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Comment thread experiments/README.md

**Pipeline stages:**
1. 4D CT reconstruction (using methods from `Reconstruct4DCT`)
2. AI segmentation (TotalSegmentator, Vista3D/Clara Segment Open Model as NIM or local)
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Inconsistent naming: "Vista3D" is used here while "VISTA-3D" is used on line 220. Consider using "VISTA-3D" consistently throughout the document.

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2. AI segmentation (TotalSegmentator, Vista3D/Clara Segment Open Model as NIM or local)
2. AI segmentation (TotalSegmentator, VISTA-3D/Clara Segment Open Model as NIM or local)

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Comment thread experiments/README.md
- Real-time deformable registration for interventional guidance
- Integration with simulation engines (PyAnsys, FEniCS, etc.)

**Output:** Patient-specific USD models ready for physics simulation or AI training.
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Trailing whitespace detected at the end of this line. Consider removing the extra spaces.

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**Output:** Patient-specific USD models ready for physics simulation or AI training.
**Output:** Patient-specific USD models ready for physics simulation or AI training.

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2 participants