Documentation: napari-deeplabcut CoTracker integration#3318
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Shorten top-level headings in the napari documentation by removing the redundant "napari-DLC -" prefix for consistency and brevity. Updated docs/gui/napari/basic_usage.md and docs/gui/napari/advanced_usage.md to use simpler headings.
Add a new user guide page for the Tracking Controls widget (docs/gui/napari/tracking/basic_usage.md) describing UI, workflow, requirements, tracking actions, refinement/merge tools, model attribution (CoTracker3), troubleshooting, and limitations. Also add the accompanying controls image (docs/images/napari/tracking/controls.png). These additions document how to run point tracking, refine results, and merge tracked points back into DeepLabCut projects.
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Pull request overview
Adds a new documentation page describing the napari-deeplabcut automated point tracking workflow (CoTracker integration) and wires it into the docs navigation, plus a small cleanup to existing napari page headings.
Changes:
- Added a new napari tracking user guide page covering requirements, UI walkthrough, workflow, troubleshooting, and model attribution/limitations.
- Updated
_toc.ymlto include the new tracking page under the napari section. - Simplified the titles of existing napari “basic” and “advanced” usage pages.
Reviewed changes
Copilot reviewed 4 out of 5 changed files in this pull request and generated 5 comments.
| File | Description |
|---|---|
| docs/gui/napari/tracking/basic_usage.md | New end-to-end tracking workflow documentation and model attribution section. |
| docs/gui/napari/basic_usage.md | Heading/title cleanup for the basic usage page. |
| docs/gui/napari/advanced_usage.md | Heading/title cleanup for the advanced usage page. |
| _toc.yml | Adds the tracking docs page to the napari documentation TOC. |
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Update docs/gui/napari/tracking/basic_usage.md to improve clarity and fix typos: rename "Keypoint Controls layer" to "Keypoint Controls dock widget", correct "Emprical" to "Empirical", and small whitespace/wording tweaks. Restructure the Limitations/Future directions area by adding "Important considerations" and "Future features" headings, move and reword the CoTracker3 note into Future features, consolidate and bullet manual curation and training-set imbalance guidance, and remove duplicate lines. These changes improve readability and provide clearer guidance for users.
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Do we want more images ? |
Clean up docs/gui/napari/tracking/basic_usage.md: add missing blank line in a tip, normalize bullet indentation and spacing, fix inconsistent numbered lists (renumber steps and convert some items to sub-bullets), and improve clarity in workflow instructions. Also add a brief consideration that manual annotation can sometimes be faster than heavy tracking corrections and note preference for continuous frames. These are purely documentation/formatting edits to improve readability and usability.
Revise and clarify the Tracking Controls documentation: wrap third-party model attribution in a note, add a brief reminder that tracking accelerates but does not replace manual review, and split Requirements into “In napari” and “In your Python environment”. Improve UI documentation with a control/description table, a figure placeholder, and a note about available models. Reword and tighten many instructions (frame/reference wording, tracking range, actions, keyboard shortcuts), clarify that tracking runs in a background worker, and explain that tracking-result layers are intermediate and must be merged/saved to update DLC project files. Add a prominent warning that there is currently no undo for deletion/merge operations. Minor formatting and grammar fixes throughout (CoTracker attribution links, troubleshooting bullets, phrasing) to improve readability and consistency.
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Adds documentation for the new automated point tracking feature in the napari plugin.
The main focus is on guiding users through the new tracking workflow, requirements, and troubleshooting, as well as providing proper attribution and empirical limitations for the tracking models.
New documentation for automated point tracking:
docs/gui/napari/tracking/basic_usage.md, with detailed instructions and workflow for using the tracking feature in the napari plugin, including requirements, UI walkthrough, keyboard shortcuts, result interpretation, and troubleshooting._toc.yml) to include the new tracking documentation under the napari section.Related