Update Documentation #8262
Update Documentation #8262
Conversation
|
Warning Rate limit exceeded@hotzenklotz has exceeded the limit for the number of commits or files that can be reviewed per hour. Please wait 23 minutes and 5 seconds before requesting another review. ⌛ How to resolve this issue?After the wait time has elapsed, a review can be triggered using the We recommend that you space out your commits to avoid hitting the rate limit. 🚦 How do rate limits work?CodeRabbit enforces hourly rate limits for each developer per organization. Our paid plans have higher rate limits than the trial, open-source and free plans. In all cases, we re-allow further reviews after a brief timeout. Please see our FAQ for further information. 📒 Files selected for processing (2)
📝 Walkthrough📝 WalkthroughWalkthroughThis pull request includes updates to the documentation for WEBKNOSSOS, focusing on various tools and features. Key changes involve restructuring and enhancing sections related to the Skeleton Annotation tool, Volume Annotation tools, and team management. Additionally, links have been updated for the AI Quick Select tool, and new sections have been added to guide users on adding users to teams and creating new teams. Overall, these modifications aim to improve clarity and usability in the documentation. Changes
Possibly related PRs
Suggested labels
Poem
Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. CodeRabbit Commands (Invoked using PR comments)
Other keywords and placeholders
CodeRabbit Configuration File (
|
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (12)
docs/volume_annotation/segments_statistics.md (1)
7-7: Simplify phrasingConsider removing "of" in "outside of WEBKNOSSOS" for more concise writing.
-These can be exported as CSV files for further analysis outside of WEBKNOSSOS. +These can be exported as CSV files for further analysis outside WEBKNOSSOS.🧰 Tools
🪛 LanguageTool
[style] ~7-~7: This phrase is redundant. Consider using “outside”.
Context: ...orted as CSV files for further analysis outside of WEBKNOSSOS. In cases, where you only w...(OUTSIDE_OF)
docs/users/teams.md (1)
15-15: Consider adding hyphenationFor consistency with technical writing standards, consider hyphenating "upper-right".
-Click the `Add Team` button in the upper right corner +Click the `Add Team` button in the upper-right corner🧰 Tools
🪛 LanguageTool
[uncategorized] ~15-~15: Consider adding a hyphen.
Context: ...r 2. Click theAdd Teambutton in the upper right corner 3. In the modal that appears: ...(TOP_LEFT_CORNER)
docs/users/new_users.md (2)
8-10: Remove word repetition in section introductionThe word "Teams" appears redundantly at the start of the section.
-## Adding Users to Teams -Teams help organize users into logical groups for better collaboration and access control. By assigning users to specific teams, you can manage dataset permissions, coordinate tasks, and streamline project workflows more efficiently. +## Adding Users to Teams +Organizing users into teams helps create logical groups for better collaboration and access control. By assigning users to specific teams, you can manage dataset permissions, coordinate tasks, and streamline project workflows more efficiently.🧰 Tools
🪛 LanguageTool
[duplication] ~8-~8: Possible typo: you repeated a word
Context: .../users_invite.jpeg) ## Adding Users to Teams Teams help organize users into logical groups...(ENGLISH_WORD_REPEAT_RULE)
18-20: Enhance clarity of team role descriptionsConsider expanding the role descriptions to better highlight the differences between Member and Team Manager roles.
- - **Member** (default): Basic team membership with standard permissions - - **Team Manager**: Extended permissions for team management + - **Member** (default): Basic team membership with standard permissions for viewing and annotating datasets + - **Team Manager**: Extended permissions including managing team members, dataset permissions, and team settingsdocs/skeleton_annotation/tools.md (2)
5-6: Standardize image alignment and sizingFor consistency with other tool icons in the document, consider adjusting the skeleton tool image properties.
-{align=left width="60"} -The **Skeleton tool** enables you to create and edit skeleton annotations: +{align=left width="60"} + +The **Skeleton tool** enables you to create and edit skeleton annotations:
Line range hint
62-77: Enhance keyboard shortcuts section with additional contextConsider adding a brief introduction about the importance of keyboard shortcuts for efficient workflow and grouping them by function type.
## Skeleton Keyboard Shortcuts -The following common keyboard shortcuts are handy for speeding up your annotation workflow: +Keyboard shortcuts significantly speed up your annotation workflow. Here are the most commonly used shortcuts grouped by function: + +### Navigation +| Key Binding | Operation | +| ----------- | -------------------------------------------------- | +| Left Drag | Move around | +| ++s++ | Center Camera on Active Node | + +### Node Operations +| Key Binding | Operation | +| ----------- | -------------------------------------------------- | +| Left Click | Create New Node | +| Left Click | Select Node (Mark as Active Node) under the cursor | +| Left Drag | Move the node under the cursor | +| ++del++ | Delete Active Node | + +### Tree Management +| Key Binding | Operation | +| ----------- | -------------------------------------------------- | +| ++b++ | Create Branch Point | +| ++j++ | Jump to Last Branch Point | +| ++c++ | Create New Tree |🧰 Tools
🪛 LanguageTool
[duplication] ~17-~17: Possible typo: you repeated a word
Context: ...**: Connections between nodes that form trees - Trees: Collections of connected nodes and e...(ENGLISH_WORD_REPEAT_RULE)
docs/ui/toolbar.md (2)
31-33: Fix markdown list indentationThe list indentation is inconsistent with markdown best practices.
-- **Download**: Export your work in standard formats: - - - Skeleton annotations are saved as [NML files](../data/concepts.md#nml-files) - - Volume annotations are exported as [WKW files](../data/wkw.md) - - All associated data and metadata are included in the download +- **Download**: Export your work in standard formats: + - Skeleton annotations are saved as [NML files](../data/concepts.md#nml-files) + - Volume annotations are exported as [WKW files](../data/wkw.md) + - All associated data and metadata are included in the download🧰 Tools
🪛 Markdownlint (0.35.0)
31-31: Expected: 2; Actual: 4
Unordered list indentation(MD007, ul-indent)
32-32: Expected: 2; Actual: 4
Unordered list indentation(MD007, ul-indent)
33-33: Expected: 2; Actual: 4
Unordered list indentation(MD007, ul-indent)
86-86: Add missing commas in tool descriptionsSeveral sentences are missing commas for proper punctuation.
-**Trace Tool**: Create precise boundary definitions by drawing outlines around structures. This tool is particularly useful when accuracy is crucial. For added precision consider using a [pen input device](../pen_tablets.md). +**Trace Tool**: Create precise boundary definitions by drawing outlines around structures. This tool is particularly useful when accuracy is crucial. For added precision, consider using a [pen input device](../pen_tablets.md). -**AI Quick Select**: Annotate a segment automatically with our AI by drawing a rectangular selection over it. Alternatively, single click in the center of a cell to automatically label it. +**AI Quick Select**: Annotate a segment automatically with our AI by drawing a rectangular selection over it. Alternatively, single-click in the center of a cell to automatically label it.Also applies to: 91-92
🧰 Tools
🪛 LanguageTool
[uncategorized] ~86-~86: Possible missing comma found.
Context: ...ful when accuracy is crucial. For added precision consider using a [pen input device](../...(AI_HYDRA_LEO_MISSING_COMMA)
docs/volume_annotation/tools.md (4)
1-3: Maintain consistent heading hierarchy and title case
- The "Proof Reading Tool" section should be an h2 heading (##) instead of h3 (###) to maintain proper hierarchy.
- Ensure consistent title case across all headings.
Apply this diff:
# Volume Annotation Tools -### Proof Reading Tool +## Proof Reading ToolAlso applies to: 35-35
26-26: Fix grammar in Segment Picker descriptionAdd the missing article "an" for better readability.
-**Segment Picker**: Click any segment to use its label ID as the active segment ID and keep annotating with that ID. This is alternative to selecting the segment ID from the [Segments list](./segments_list.md) sidebar or context menu. +**Segment Picker**: Click any segment to use its label ID as the active segment ID and keep annotating with that ID. This is an alternative to selecting the segment ID from the [Segments list](./segments_list.md) sidebar or context menu.🧰 Tools
🪛 LanguageTool
[uncategorized] ~26-~26: You might be missing the article “an” here.
Context: ...d keep annotating with that ID. This is alternative to selecting the segment ID from the [S...(AI_EN_LECTOR_MISSING_DETERMINER_AN)
57-57: Fix typo in brush size descriptionCorrect "suite" to "suit" in the brush size modifier description.
-**Change Brush Size**: Changes the size and radius of the brushing tool. Presets of small, medium and large brush sizes are available which can be modified to suite your workflows. +**Change Brush Size**: Changes the size and radius of the brushing tool. Presets of small, medium and large brush sizes are available which can be modified to suit your workflows.
81-81: Use proper heading syntax instead of emphasisConvert the emphasized text to a proper heading for better document structure.
-**Threshold Mode** +### Threshold Mode🧰 Tools
🪛 Markdownlint (0.35.0)
81-81: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
⛔ Files ignored due to path filters (24)
docs/images/team_overview.jpgis excluded by!**/*.jpgdocs/images/users_team_assignment.jpgis excluded by!**/*.jpgdocs/skeleton_annotation/images/merger-mode-modifier.jpgis excluded by!**/*.jpgdocs/skeleton_annotation/images/new-tree-modifier.jpgis excluded by!**/*.jpgdocs/skeleton_annotation/images/single-node-tree-mode-modifier.jpgis excluded by!**/*.jpgdocs/ui/images/ai-analysis-tools.jpgis excluded by!**/*.jpgdocs/ui/images/boundingbox-tool.jpgis excluded by!**/*.jpgdocs/ui/images/brush-tool.jpgis excluded by!**/*.jpgdocs/ui/images/eraser-tool.jpgis excluded by!**/*.jpgdocs/ui/images/fill-tool.jpgis excluded by!**/*.jpgdocs/ui/images/interpolation-tool.jpgis excluded by!**/*.jpgdocs/ui/images/measure-tool.jpgis excluded by!**/*.jpgdocs/ui/images/move-tool.jpgis excluded by!**/*.jpgdocs/ui/images/proofreading-tool.jpgis excluded by!**/*.jpgdocs/ui/images/quickselect-tool.jpgis excluded by!**/*.jpgdocs/ui/images/segment-picker-tool.jpgis excluded by!**/*.jpgdocs/ui/images/skeleton-tool.jpgis excluded by!**/*.jpgdocs/ui/images/trace-tool.jpgis excluded by!**/*.jpgdocs/volume_annotation/images/2d-modifier.jpgis excluded by!**/*.jpgdocs/volume_annotation/images/3d-modifier.jpgis excluded by!**/*.jpgdocs/volume_annotation/images/brush-size-modifier.jpgis excluded by!**/*.jpgdocs/volume_annotation/images/new-segment-modifier.jpgis excluded by!**/*.jpgdocs/volume_annotation/images/overwrite-empty-modifier.jpgis excluded by!**/*.jpgdocs/volume_annotation/images/overwrite-everything-modifier.jpgis excluded by!**/*.jpg
📒 Files selected for processing (9)
docs/index.md(1 hunks)docs/skeleton_annotation/tools.md(2 hunks)docs/ui/status_bar.md(1 hunks)docs/ui/toolbar.md(1 hunks)docs/users/new_users.md(1 hunks)docs/users/teams.md(1 hunks)docs/volume_annotation/segments_statistics.md(1 hunks)docs/volume_annotation/tools.md(2 hunks)frontend/javascripts/admin/team/edit_team_modal_view.tsx(1 hunks)
✅ Files skipped from review due to trivial changes (2)
- frontend/javascripts/admin/team/edit_team_modal_view.tsx
- docs/index.md
🧰 Additional context used
🪛 LanguageTool
docs/users/new_users.md
[duplication] ~8-~8: Possible typo: you repeated a word
Context: .../users_invite.jpeg) ## Adding Users to Teams Teams help organize users into logical groups...
(ENGLISH_WORD_REPEAT_RULE)
docs/volume_annotation/segments_statistics.md
[style] ~7-~7: This phrase is redundant. Consider using “outside”.
Context: ...orted as CSV files for further analysis outside of WEBKNOSSOS. In cases, where you only w...
(OUTSIDE_OF)
docs/ui/toolbar.md
[uncategorized] ~21-~21: Possible missing preposition found.
Context: ...by clicking on the coordinate display - Adjust camera rotation in flight or oblique mo...
(AI_HYDRA_LEO_MISSING_TO)
[uncategorized] ~39-~39: Possible missing comma found.
Context: ...ns**: Combine multiple annotations into one either by project or by annotation ID. ...
(AI_HYDRA_LEO_MISSING_COMMA)
[style] ~41-~41: As an alternative to the over-used intensifier ‘very’, consider replacing this phrase.
Context: ...andwith and resources when dealing with very large annotation which don't need to be persi...
(EN_WEAK_ADJECTIVE)
[grammar] ~41-~41: There seems to be a noun/verb agreement error. Did you mean “doesn't” or “didn't”?
Context: ...ealing with very large annotation which don't need to be persisted. - **Lock Annotat...
(SINGULAR_NOUN_AGREEMENT_WHO_DONT)
[uncategorized] ~86-~86: Possible missing comma found.
Context: ...ful when accuracy is crucial. For added precision consider using a [pen input device](../...
(AI_HYDRA_LEO_MISSING_COMMA)
docs/skeleton_annotation/tools.md
[duplication] ~17-~17: Possible typo: you repeated a word
Context: ...**: Connections between nodes that form trees - Trees: Collections of connected nodes and e...
(ENGLISH_WORD_REPEAT_RULE)
docs/users/teams.md
[uncategorized] ~15-~15: Consider adding a hyphen.
Context: ...r 2. Click the Add Team button in the upper right corner 3. In the modal that appears: ...
(TOP_LEFT_CORNER)
docs/volume_annotation/tools.md
[uncategorized] ~26-~26: You might be missing the article “an” here.
Context: ...d keep annotating with that ID. This is alternative to selecting the segment ID from the [S...
(AI_EN_LECTOR_MISSING_DETERMINER_AN)
[uncategorized] ~44-~44: Possible missing comma found.
Context: .../ui/status_bar.md) at the bottom of the screen or through the context-sensitive menu w...
(AI_HYDRA_LEO_MISSING_COMMA)
🪛 Markdownlint (0.35.0)
docs/ui/toolbar.md
31-31: Expected: 2; Actual: 4
Unordered list indentation
(MD007, ul-indent)
32-32: Expected: 2; Actual: 4
Unordered list indentation
(MD007, ul-indent)
33-33: Expected: 2; Actual: 4
Unordered list indentation
(MD007, ul-indent)
docs/volume_annotation/tools.md
35-35: Expected: h2; Actual: h3
Heading levels should only increment by one level at a time
(MD001, heading-increment)
81-81: null
Emphasis used instead of a heading
(MD036, no-emphasis-as-heading)
🔇 Additional comments (4)
docs/ui/status_bar.md (1)
5-6: LGTM! Documentation improvements enhance clarity
The changes improve readability through:
- Better formatting of modifier keys using the
++key++syntax - Addition of helpful link to terminology documentation
- Clearer description of mouse position information
docs/volume_annotation/segments_statistics.md (1)
7-7: LGTM! Documentation links are well structured
The changes improve navigation through:
- Clear link to the Segments list documentation
- Specific anchor link to the measurement tool section
Also applies to: 9-9
🧰 Tools
🪛 LanguageTool
[style] ~7-~7: This phrase is redundant. Consider using “outside”.
Context: ...orted as CSV files for further analysis outside of WEBKNOSSOS. In cases, where you only w...
(OUTSIDE_OF)
docs/users/teams.md (1)
11-24: LGTM! Well-structured team creation documentation
The new section provides:
- Clear step-by-step instructions
- Helpful visual aids with relevant images
- Proper cross-referencing to related documentation
🧰 Tools
🪛 LanguageTool
[uncategorized] ~15-~15: Consider adding a hyphen.
Context: ...r 2. Click the Add Team button in the upper right corner 3. In the modal that appears: ...
(TOP_LEFT_CORNER)
docs/volume_annotation/tools.md (1)
Line range hint 1-136: Documentation improvements look great!
The documentation updates effectively achieve the PR objectives:
- Clear tool descriptions with icons
- Well-structured content with appropriate use of admonitions
- Good balance of text, images, and videos
- Helpful tips and warnings where needed
🧰 Tools
🪛 Markdownlint (0.35.0)
35-35: Expected: h2; Actual: h3
Heading levels should only increment by one level at a time
(MD001, heading-increment)
81-81: null
Emphasis used instead of a heading
(MD036, no-emphasis-as-heading)
🪛 LanguageTool
[uncategorized] ~26-~26: You might be missing the article “an” here.
Context: ...d keep annotating with that ID. This is alternative to selecting the segment ID from the [S...
(AI_EN_LECTOR_MISSING_DETERMINER_AN)
[uncategorized] ~44-~44: Possible missing comma found.
Context: .../ui/status_bar.md) at the bottom of the screen or through the context-sensitive menu w...
(AI_HYDRA_LEO_MISSING_COMMA)
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (8)
docs/ui/toolbar.md (4)
6-6: Fix typo in image alt textThere's a typo in the alt text: "und" should be "and".
- +
21-21: Improve clarity in camera rotation descriptionAdd the preposition "in" for better readability.
-- Adjust camera rotation in flight or oblique modes +- Adjust camera rotation in flight or in oblique modes🧰 Tools
🪛 LanguageTool
[uncategorized] ~21-~21: Possible missing preposition found.
Context: ...by clicking on the coordinate display - Adjust camera rotation in flight or oblique mo...(AI_HYDRA_LEO_MISSING_TO)
31-33: Fix list indentation for file formatsAdjust the indentation to follow Markdown standards (2 spaces for nested lists).
-- **Download**: Export your work in standard formats: - - - Skeleton annotations are saved as [NML files](../data/concepts.md#nml-files) - - Volume annotations are exported as [WKW files](../data/wkw.md) - - All associated data and metadata are included in the download +- **Download**: Export your work in standard formats: + + - Skeleton annotations are saved as [NML files](../data/concepts.md#nml-files) + - Volume annotations are exported as [WKW files](../data/wkw.md) + - All associated data and metadata are included in the download🧰 Tools
🪛 Markdownlint (0.35.0)
31-31: Expected: 2; Actual: 4
Unordered list indentation(MD007, ul-indent)
32-32: Expected: 2; Actual: 4
Unordered list indentation(MD007, ul-indent)
33-33: Expected: 2; Actual: 4
Unordered list indentation(MD007, ul-indent)
86-86: Add missing comma for better readabilityAdd a comma after "precision" to improve sentence flow.
-**Trace Tool**: Create precise boundary definitions by drawing outlines around structures. This tool is particularly useful when accuracy is crucial. For added precision consider using a [pen input device](../pen_tablets.md). +**Trace Tool**: Create precise boundary definitions by drawing outlines around structures. This tool is particularly useful when accuracy is crucial. For added precision, consider using a [pen input device](../pen_tablets.md).🧰 Tools
🪛 LanguageTool
[uncategorized] ~86-~86: Possible missing comma found.
Context: ...ful when accuracy is crucial. For added precision consider using a [pen input device](../...(AI_HYDRA_LEO_MISSING_COMMA)
docs/volume_annotation/tools.md (4)
42-42: Add missing comma for better readabilityAdd a comma before "or" in the sentence for better flow.
-The active segment ID under the cursor can be found in the [status bar](../ui/status_bar.md) at the bottom of the screen or through the context-sensitive menu when right-clicking. +The active segment ID under the cursor can be found in the [status bar](../ui/status_bar.md) at the bottom of the screen, or through the context-sensitive menu when right-clicking.🧰 Tools
🪛 LanguageTool
[uncategorized] ~42-~42: Possible missing comma found.
Context: .../ui/status_bar.md) at the bottom of the screen or through the context-sensitive menu w...(AI_HYDRA_LEO_MISSING_COMMA)
48-48: Update heading level for proper hierarchyChange the heading level from h3 to h2 to maintain proper document structure.
-### Tool Modifiers +## Tool Modifiers🧰 Tools
🪛 Markdownlint (0.35.0)
48-48: Expected: h2; Actual: h3
Heading levels should only increment by one level at a time(MD001, heading-increment)
32-34: Adjust list indentation for consistencyFix the indentation of the list items to follow markdown standards.
- - Threshold-based selection mode - - AI-based segmentation (powered by Segment Anything Model 2) +- Threshold-based selection mode +- AI-based segmentation (powered by Segment Anything Model 2)🧰 Tools
🪛 Markdownlint (0.35.0)
32-32: Expected: 0; Actual: 2
Unordered list indentation(MD007, ul-indent)
33-33: Expected: 0; Actual: 2
Unordered list indentation(MD007, ul-indent)
Based on the output, I can now generate the final response since I have gathered the necessary information about the documentation links.
Documentation links need to be updated
Several referenced markdown files in the documentation are missing. Key files that need attention:
./pen_tablets.md- Referenced in volume annotation tools section./segments_list.md- Referenced multiple times for segment management../ui/status_bar.md- Referenced for cursor segment ID display../ui/keyboard_shortcuts.md- Referenced for shortcuts guide../proofreading/tools.md- Referenced for proofreading functionality../proofreading/merger_mode.md- Referenced for merge error fixesPlease ensure these files exist and are properly linked, or update the references to point to the correct documentation locations.
🔗 Analysis chain
Line range hint
1-137: Verify documentation linksLet's ensure all internal documentation links are valid.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that all referenced markdown files exist # Extract and check all internal markdown links echo "Checking internal markdown links..." rg -o '\[.*?\]\((.*?\.md.*?)\)' | cut -d'(' -f2 | cut -d')' -f1 | while read -r link; do # Remove any anchor tags file_path=$(echo "$link" | cut -d'#' -f1) # Remove leading ./ file_path=$(echo "$file_path" | sed 's|^\./||') if ! [ -f "$file_path" ]; then echo "Warning: Missing file: $file_path" fi doneLength of output: 72505
🧰 Tools
🪛 LanguageTool
[uncategorized] ~42-~42: Possible missing comma found.
Context: .../ui/status_bar.md) at the bottom of the screen or through the context-sensitive menu w...(AI_HYDRA_LEO_MISSING_COMMA)
🪛 Markdownlint (0.35.0)
48-48: Expected: h2; Actual: h3
Heading levels should only increment by one level at a time(MD001, heading-increment)
32-32: Expected: 0; Actual: 2
Unordered list indentation(MD007, ul-indent)
33-33: Expected: 0; Actual: 2
Unordered list indentation(MD007, ul-indent)
82-82: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
⛔ Files ignored due to path filters (1)
docs/volume_annotation/images/interpolation-modifier.jpgis excluded by!**/*.jpg
📒 Files selected for processing (2)
docs/ui/toolbar.md(1 hunks)docs/volume_annotation/tools.md(2 hunks)
🧰 Additional context used
🪛 LanguageTool
docs/ui/toolbar.md
[uncategorized] ~21-~21: Possible missing preposition found.
Context: ...by clicking on the coordinate display - Adjust camera rotation in flight or oblique mo...
(AI_HYDRA_LEO_MISSING_TO)
[uncategorized] ~86-~86: Possible missing comma found.
Context: ...ful when accuracy is crucial. For added precision consider using a [pen input device](../...
(AI_HYDRA_LEO_MISSING_COMMA)
docs/volume_annotation/tools.md
[uncategorized] ~42-~42: Possible missing comma found.
Context: .../ui/status_bar.md) at the bottom of the screen or through the context-sensitive menu w...
(AI_HYDRA_LEO_MISSING_COMMA)
🪛 Markdownlint (0.35.0)
docs/ui/toolbar.md
31-31: Expected: 2; Actual: 4
Unordered list indentation
(MD007, ul-indent)
32-32: Expected: 2; Actual: 4
Unordered list indentation
(MD007, ul-indent)
33-33: Expected: 2; Actual: 4
Unordered list indentation
(MD007, ul-indent)
docs/volume_annotation/tools.md
48-48: Expected: h2; Actual: h3
Heading levels should only increment by one level at a time
(MD001, heading-increment)
32-32: Expected: 0; Actual: 2
Unordered list indentation
(MD007, ul-indent)
33-33: Expected: 0; Actual: 2
Unordered list indentation
(MD007, ul-indent)
82-82: null
Emphasis used instead of a heading
(MD036, no-emphasis-as-heading)
🔇 Additional comments (5)
docs/ui/toolbar.md (1)
1-107: Documentation improvements look great!
The documentation is well-structured, comprehensive, and achieves the goal of improving readability. The addition of icons, clear descriptions, and logical organization makes it easier for users to understand the toolbar functionality.
🧰 Tools
🪛 LanguageTool
[uncategorized] ~21-~21: Possible missing preposition found.
Context: ...by clicking on the coordinate display - Adjust camera rotation in flight or oblique mo...
(AI_HYDRA_LEO_MISSING_TO)
[uncategorized] ~86-~86: Possible missing comma found.
Context: ...ful when accuracy is crucial. For added precision consider using a [pen input device](../...
(AI_HYDRA_LEO_MISSING_COMMA)
🪛 Markdownlint (0.35.0)
31-31: Expected: 2; Actual: 4
Unordered list indentation
(MD007, ul-indent)
32-32: Expected: 2; Actual: 4
Unordered list indentation
(MD007, ul-indent)
33-33: Expected: 2; Actual: 4
Unordered list indentation
(MD007, ul-indent)
docs/volume_annotation/tools.md (4)
1-46: Well-structured tool documentation with clear visual aids!
The documentation is well-organized with consistent formatting, clear descriptions, and helpful visual demonstrations for each tool.
🧰 Tools
🪛 LanguageTool
[uncategorized] ~42-~42: Possible missing comma found.
Context: .../ui/status_bar.md) at the bottom of the screen or through the context-sensitive menu w...
(AI_HYDRA_LEO_MISSING_COMMA)
🪛 Markdownlint (0.35.0)
32-32: Expected: 0; Actual: 2
Unordered list indentation
(MD007, ul-indent)
33-33: Expected: 0; Actual: 2
Unordered list indentation
(MD007, ul-indent)
49-68: Clear and comprehensive modifier documentation!
The modifiers section is well-structured with consistent formatting and clear explanations for each tool modifier.
72-96: Excellent documentation of the AI-powered quick-select tool!
The quick-select tool documentation is comprehensive and well-structured, clearly explaining both AI and threshold modes with step-by-step instructions.
🧰 Tools
🪛 Markdownlint (0.35.0)
82-82: null
Emphasis used instead of a heading
(MD036, no-emphasis-as-heading)
Line range hint 102-137: Comprehensive documentation of volume operations!
The volume operations sections are well-documented with:
- Clear step-by-step instructions
- Important usage tips and warnings
- Performance considerations
- Helpful video tutorials
🧰 Tools
🪛 LanguageTool
[uncategorized] ~42-~42: Possible missing comma found.
Context: .../ui/status_bar.md) at the bottom of the screen or through the context-sensitive menu w...
(AI_HYDRA_LEO_MISSING_COMMA)
🪛 Markdownlint (0.35.0)
48-48: Expected: h2; Actual: h3
Heading levels should only increment by one level at a time
(MD001, heading-increment)
32-32: Expected: 0; Actual: 2
Unordered list indentation
(MD007, ul-indent)
33-33: Expected: 0; Actual: 2
Unordered list indentation
(MD007, ul-indent)
82-82: null
Emphasis used instead of a heading
(MD036, no-emphasis-as-heading)
There was a problem hiding this comment.
some of these files are called "modifier" even though they aren't modifiers. icon would always work. or simply button. but maybe it doesnt really matter in the end...
docs/skeleton_annotation/tools.md
Outdated
|
|
||
| ## Controls & Keyboard Shortcuts for Skeleton Annotations | ||
| ### Tool Modifiers |
There was a problem hiding this comment.
hmm, I don't really like the word modifier here. how about "Tool-specific functionality"?
I only use the term modifier in the context of keyboard shortcuts (so, shift, ctrl etc. are modifiers). that's also how we use it in the UI afaik.
I suggest to simply omit modifier in the tool descriptions:
- "New Tree". maybe add "button" or sth similar if you think that's better. but it has nothing to do with a modifier from my understanding.
- "Single Node Tree Mode" and "Merger Mode" <-- there is already the word mode in it. "modifier" doesnt improve it imo.
docs/volume_annotation/tools.md
Outdated
|
|
||
| In the `Segmentation` tab on the right-hand side panel, you can see the segment IDs which are available in your annotation. You can rename segments as needed. | ||
| {align=left width="60"} | ||
| **Overwrite Everything**: When labeling with the brush/trace tool, you can annotate every available voxel without any regard if it was already labeled as a different segment or whether it is unlabelled. This allows you to draw over existing segments. |
There was a problem hiding this comment.
| **Overwrite Everything**: When labeling with the brush/trace tool, you can annotate every available voxel without any regard if it was already labeled as a different segment or whether it is unlabelled. This allows you to draw over existing segments. | |
| **Overwrite Everything**: When labeling with the brush/trace tool, you can annotate every voxel independent of whether it is already an segment id. This allows you to draw over existing segments. |
docs/volume_annotation/tools.md
Outdated
| 1. Select the Quick Select tool from the toolbar | ||
| 2. Choose your preferred mode (AI or threshold) | ||
| 3. Click the settings icon to configure: | ||
| - Number of sections to process |
There was a problem hiding this comment.
I think this is only possible for the AI mode.
|
|
||
| **AI Mode** (Default) | ||
|
|
||
| - Activate the "AI" button in the toolbar |
There was a problem hiding this comment.
probably nitpicky, but it's a bit weird that the headline says that it's enabled by default and then the description contains the imperative "activate it".
maybe move the part about activating/deactivating directly into the intro of "Operating Modes".
| 2. Choose your preferred mode (AI or threshold) | ||
| 3. Click the settings icon to configure: | ||
| - Number of sections to process | ||
| - Preview mode for real-time parameter adjustment |
Co-authored-by: Philipp Otto <[email protected]>
Co-authored-by: Philipp Otto <[email protected]>
Co-authored-by: Philipp Otto <[email protected]>
Co-authored-by: Philipp Otto <[email protected]>
Co-authored-by: Philipp Otto <[email protected]>
There was a problem hiding this comment.
Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (11)
docs/skeleton_annotation/tools.md (2)
1-21: Standardize keyboard shortcut formattingFor consistency with the rest of the documentation, wrap keyboard shortcuts in the
++key++syntax.🧰 Tools
🪛 LanguageTool
[duplication] ~17-~17: Possible typo: you repeated a word
Context: ...**: Connections between nodes that form trees - Trees: Collections of connected nodes and e...(ENGLISH_WORD_REPEAT_RULE)
38-61: Consider revising terminologyBased on previous discussions, the term "modifier" might be confusing. Consider using "Tool-specific functionality" instead, as these are distinct modes or features rather than keyboard modifiers.
docs/ui/toolbar.md (2)
6-6: Fix typo in image captionChange "Saving und Undo/Redo" to "Saving and Undo/Redo".
32-34: Fix list indentationThe nested list items should be indented by 2 spaces instead of 4 for consistency with markdown standards.
🧰 Tools
🪛 Markdownlint (0.37.0)
32-32: Expected: 2; Actual: 4
Unordered list indentation(MD007, ul-indent)
33-33: Expected: 2; Actual: 4
Unordered list indentation(MD007, ul-indent)
34-34: Expected: 2; Actual: 4
Unordered list indentation(MD007, ul-indent)
docs/volume_annotation/tools.md (2)
49-49: Fix heading levelChange the heading level from h3 to h2 to maintain proper document structure:
-### Tool Modifiers +## Tool Modifiers🧰 Tools
🪛 Markdownlint (0.37.0)
49-49: Expected: h2; Actual: h3
Heading levels should only increment by one level at a time(MD001, heading-increment)
73-98: Enhance mode distinction clarityConsider adding a comparison table or note highlighting the key differences between AI and threshold modes to help users choose the appropriate mode for their use case.
🧰 Tools
🪛 Markdownlint (0.37.0)
83-83: null
Emphasis used instead of a heading(MD036, no-emphasis-as-heading)
docs/users/teams.md (1)
14-19: Improve list formatting consistencyThe numbered list items could be formatted more consistently. Consider adding a period after each number and maintaining consistent indentation for sub-bullets.
-1. Navigate to `Admin > Teams` in the navigation bar -2. Click the `Add Team` button in the upper right corner -3. In the dialog that appears: - - Enter a unique team name - - Select users to add to this team (optional) +1. Navigate to `Admin > Teams` in the navigation bar. +2. Click the `Add Team` button in the upper-right corner. +3. In the dialog that appears: + - Enter a unique team name + - Select users to add to this team (optional)🧰 Tools
🪛 LanguageTool
[uncategorized] ~15-~15: Consider adding a hyphen.
Context: ...r 2. Click theAdd Teambutton in the upper right corner 3. In the dialog that appears: ...(TOP_LEFT_CORNER)
docs/users/new_users.md (2)
8-9: Remove word repetitionThe word "Teams" appears twice in succession due to the heading transition.
-## Adding Users to Teams -Teams help organize users into logical groups... +## Adding Users to Teams +User teams help organize members into logical groups...🧰 Tools
🪛 LanguageTool
[duplication] ~8-~8: Possible typo: you repeated a word
Context: .../users_invite.jpeg) ## Adding Users to Teams Teams help organize users into logical groups...(ENGLISH_WORD_REPEAT_RULE)
13-21: Improve list formatting and consistencyThe numbered list formatting could be improved for better readability.
-1. Navigate to `Admin > Users` in the navigation bar -2. Select one or more users from the user list -3. Click on `Edit Teams and Permissions` - - This opens a dialog showing all available teams and user permissions -4. Select or deselect teams as desired for the selected users - - For each team, you can choose the user's role: - - **Member** (default): Basic team membership with standard permissions - - **Team Manager**: Extended permissions for team management -5. Click `Set Teams & Permissions` to confirm your changes +1. Navigate to `Admin > Users` in the navigation bar. +2. Select one or more users from the user list. +3. Click on `Edit Teams and Permissions`. + - This opens a dialog showing all available teams and user permissions. +4. Select or deselect teams as desired for the selected users. + - For each team, you can choose the user's role: + - **Member** (default): Basic team membership with standard permissions + - **Team Manager**: Extended permissions for team management +5. Click `Set Teams & Permissions` to confirm your changes.docs/users/access_rights.md (2)
15-15: Minor style improvements needed.Please address the following style issues:
- Add a period after "etc" for proper American English punctuation
- Fix the list indentation to match other list items
Apply this diff:
- - __Admin:__ Manage a whole organization, including full access to all datasets, teams, and projects. Admins can access all administrative settings - similar to `Team Managers` but for all teams - and have full control over all datasets - similar to `Dataset Managers`. They can promote other users to `Admin` or to `Dataset Manager` by using the `Edit Teams and Permissions` dialog at the top of the user list. Admins can access ALL annotations, datasets, projects, tasks, etc belonging to their respective organization and can modify any setting of an organization. Admins have the most permissions in your organization, and this role should be assigned with care. +- __Admin:__ Manage a whole organization, including full access to all datasets, teams, and projects. Admins can access all administrative settings - similar to `Team Managers` but for all teams - and have full control over all datasets - similar to `Dataset Managers`. They can promote other users to `Admin` or to `Dataset Manager` by using the `Edit Teams and Permissions` dialog at the top of the user list. Admins can access ALL annotations, datasets, projects, tasks, etc. belonging to their respective organization and can modify any setting of an organization. Admins have the most permissions in your organization, and this role should be assigned with care.🧰 Tools
🪛 LanguageTool
[style] ~15-~15: In American English, abbreviations like “etc.” require a period.
Context: ...annotations, datasets, projects, tasks, etc belonging to their respective organizat...(ETC_PERIOD)
🪛 Markdownlint (0.37.0)
15-15: Expected: 0; Actual: 2
Unordered list indentation(MD007, ul-indent)
Fix relative paths in documentation links
The following links need to be updated to point to the correct locations:
../sharing/annotation_sharing.mdexists but needs to be updated to../../sharing/annotation_sharing.md../tasks_projects/tasks.mdis correct and exists../sharing/dataset_sharing.mdexists but needs to be updated to../../sharing/dataset_sharing.md🔗 Analysis chain
Line range hint
1-60: Verify documentation links.Let's ensure all documentation links are valid and up-to-date.
Let me verify if these files exist in different locations by searching the entire repository.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that all linked documentation files exist # Extract and verify relative links from the markdown file # Get all relative links and verify they exist grep -o "\[.*\](\.\./[^)]*)" docs/users/access_rights.md | sed 's/.*(\(.*\))/\1/' | while read -r link; do if [ ! -f "${link}" ]; then echo "❌ Broken link: ${link}" else echo "✅ Valid link: ${link}" fi doneLength of output: 581
Script:
#!/bin/bash # Search for the documentation files across the repository echo "Searching for annotation_sharing.md:" fd "annotation_sharing.md" echo -e "\nSearching for tasks.md:" fd "tasks.md" echo -e "\nSearching for dataset_sharing.md:" fd "dataset_sharing.md"Length of output: 413
🧰 Tools
🪛 LanguageTool
[style] ~15-~15: In American English, abbreviations like “etc.” require a period.
Context: ...annotations, datasets, projects, tasks, etc belonging to their respective organizat...(ETC_PERIOD)
🪛 Markdownlint (0.37.0)
15-15: Expected: 0; Actual: 2
Unordered list indentation(MD007, ul-indent)
17-17: Expected: 0; Actual: 2
Unordered list indentation(MD007, ul-indent)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (10)
docs/automation/ai_segmentation.md(2 hunks)docs/proofreading/merger_mode.md(1 hunks)docs/skeleton_annotation/tools.md(2 hunks)docs/tutorial_automation.md(1 hunks)docs/ui/toolbar.md(1 hunks)docs/users/access_rights.md(1 hunks)docs/users/new_users.md(1 hunks)docs/users/teams.md(1 hunks)docs/volume_annotation/import_export.md(1 hunks)docs/volume_annotation/tools.md(2 hunks)
✅ Files skipped from review due to trivial changes (3)
- docs/automation/ai_segmentation.md
- docs/volume_annotation/import_export.md
- docs/proofreading/merger_mode.md
🧰 Additional context used
🪛 LanguageTool
docs/skeleton_annotation/tools.md
[duplication] ~17-~17: Possible typo: you repeated a word
Context: ...**: Connections between nodes that form trees - Trees: Collections of connected nodes and e...
(ENGLISH_WORD_REPEAT_RULE)
docs/volume_annotation/tools.md
[locale-violation] ~25-~25: In American English, “take a look” is more commonly used.
Context: ...y other underlying (microscopy) layers. Have a look at the [quick-select-tool](./quick_sele...
(HAVE_A_LOOK)
docs/users/access_rights.md
[style] ~15-~15: In American English, abbreviations like “etc.” require a period.
Context: ...annotations, datasets, projects, tasks, etc belonging to their respective organizat...
(ETC_PERIOD)
docs/users/new_users.md
[duplication] ~8-~8: Possible typo: you repeated a word
Context: .../users_invite.jpeg) ## Adding Users to Teams Teams help organize users into logical groups...
(ENGLISH_WORD_REPEAT_RULE)
docs/users/teams.md
[uncategorized] ~15-~15: Consider adding a hyphen.
Context: ...r 2. Click the Add Team button in the upper right corner 3. In the dialog that appears: ...
(TOP_LEFT_CORNER)
🪛 Markdownlint (0.37.0)
docs/volume_annotation/tools.md
49-49: Expected: h2; Actual: h3
Heading levels should only increment by one level at a time
(MD001, heading-increment)
33-33: Expected: 0; Actual: 2
Unordered list indentation
(MD007, ul-indent)
34-34: Expected: 0; Actual: 2
Unordered list indentation
(MD007, ul-indent)
83-83: null
Emphasis used instead of a heading
(MD036, no-emphasis-as-heading)
docs/ui/toolbar.md
32-32: Expected: 2; Actual: 4
Unordered list indentation
(MD007, ul-indent)
33-33: Expected: 2; Actual: 4
Unordered list indentation
(MD007, ul-indent)
34-34: Expected: 2; Actual: 4
Unordered list indentation
(MD007, ul-indent)
docs/users/access_rights.md
15-15: Expected: 0; Actual: 2
Unordered list indentation
(MD007, ul-indent)
🔇 Additional comments (6)
docs/skeleton_annotation/tools.md (2)
26-36: LGTM!
The section provides clear instructions with proper keyboard shortcut formatting.
Line range hint 62-79: LGTM!
The keyboard shortcuts section is well-organized and clearly documented.
🧰 Tools
🪛 LanguageTool
[duplication] ~17-~17: Possible typo: you repeated a word
Context: ...**: Connections between nodes that form trees - Trees: Collections of connected nodes and e...
(ENGLISH_WORD_REPEAT_RULE)
docs/ui/toolbar.md (1)
61-106: LGTM!
The annotation tools section is comprehensive and well-documented.
docs/volume_annotation/tools.md (1)
Line range hint 103-138: LGTM!
The sections on interpolation, extrusion, and flood fills are well-documented with clear explanations and appropriate warnings.
🧰 Tools
🪛 LanguageTool
[locale-violation] ~25-~25: In American English, “take a look” is more commonly used.
Context: ...y other underlying (microscopy) layers. Have a look at the [quick-select-tool](./quick_sele...
(HAVE_A_LOOK)
🪛 Markdownlint (0.37.0)
49-49: Expected: h2; Actual: h3
Heading levels should only increment by one level at a time
(MD001, heading-increment)
33-33: Expected: 0; Actual: 2
Unordered list indentation
(MD007, ul-indent)
34-34: Expected: 0; Actual: 2
Unordered list indentation
(MD007, ul-indent)
83-83: null
Emphasis used instead of a heading
(MD036, no-emphasis-as-heading)
docs/tutorial_automation.md (1)
28-28: LGTM! Terminology update implemented correctly
The change from "modal" to "dialog" aligns with the documentation standards and previous review feedback.
docs/users/access_rights.md (1)
15-15: LGTM! Consistent terminology update.
The change from "modal" to "dialog" aligns with the terminology used across other documentation files, improving consistency.
🧰 Tools
🪛 LanguageTool
[style] ~15-~15: In American English, abbreviations like “etc.” require a period.
Context: ...annotations, datasets, projects, tasks, etc belonging to their respective organizat...
(ETC_PERIOD)
🪛 Markdownlint (0.37.0)
15-15: Expected: 0; Actual: 2
Unordered list indentation
(MD007, ul-indent)
This PR updates the WK documentation:
Impressions:
(Please delete unneeded items, merge only when none are left open)