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Expanded documentation on MRI registration process, including details on customizing snakebids filters and example CLI calls for selecting images.
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Pull request overview
This PR updates the SPIMquant documentation to improve clarity and accuracy. It removes incomplete documentation sections from the navigation, adds new MRI registration documentation, and updates hardware requirements and FAQ sections with more accurate information and examples.
Changes:
- Removes incomplete/placeholder sections from navigation (Tutorials, How-To Guides entries, Reference entries)
- Adds comprehensive MRI registration documentation with BIDS filtering examples
- Updates hardware requirements with revised memory guidelines and removed outdated warnings
- Revises FAQ with updated information about templates, stains, and workflow options
Reviewed changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 18 comments.
| File | Description |
|---|---|
| mkdocs.yml | Removes incomplete documentation sections from navigation (Tutorials, How-To Guides, some Reference entries) |
| docs/howto/mri_registration.md | New file documenting MRI registration workflow with detailed BIDS filtering examples |
| docs/getting_started/hardware.md | Updates memory requirements, removes outdated warnings, revises storage recommendations and scaling strategies |
| docs/faq.md | Updates template support list, corrects stain names, updates segmentation method descriptions, and refines troubleshooting guidance |
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Contributor
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: akhanf <11492701+akhanf@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Removed multiple how-to guides from mkdocs configuration
Add How-To Guides section to mkdocs.yml navigation
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Various edits to docs for clarity and accuracy