PDF Viewer & Annotations
Sciorex includes a built-in PDF viewer with a full annotation toolkit. Read papers, highlight key passages, take notes, and export your annotations — all without leaving the IDE.
Annotation Types
Four annotation types are available from the toolbar or via keyboard shortcuts.
| Type | Description | Shortcut |
|---|---|---|
| Highlight | Color overlay on selected text | H after selection |
| Underline | Underline beneath selected text | U after selection |
| Strikeout | Strikethrough across selected text | S after selection |
| Text Note | Floating note pinned to a page location | N after selection |
TIP
Text notes support Markdown formatting. Use them for longer commentary, questions, or links to related sections in your project.
Highlight Colors
Five highlight colors help you categorize annotations visually.
| Color | Suggested Use |
|---|---|
| Yellow | General highlights, key findings |
| Green | Methodology, definitions |
| Blue | Your own ideas, connections to your work |
| Pink | Questions, areas of confusion |
| Red | Critical issues, disagreements, errors |
INFO
Color assignments are suggestions only. You can use any color for any purpose and filter by color during export.
Export
Export your annotations in four formats with flexible filtering options.
| Format | Description |
|---|---|
| Markdown | Formatted as a Markdown document with headers per page |
| JSON | Structured data with full annotation metadata |
| CSV | Tabular format for spreadsheet import |
| Plain Text | Simple text output, one annotation per line |
Export Filters
- By type — Export only highlights, only notes, or any combination
- By color — Filter to specific highlight colors
- By page range — Export annotations from selected pages only
TIP
Use Markdown export to generate a reading summary that you can include in your project notes or share with collaborators.
Navigation
| Feature | Description |
|---|---|
| Page thumbnails | Sidebar with miniature page previews for quick jumping |
| Document outline | Clickable table of contents generated from PDF bookmarks and headings |
| Bookmark navigation | Save and jump to named bookmarks within a document |
| Page input | Jump to a specific page number directly |
Integration
The PDF viewer is tightly connected to other Sciorex features.
- Annotations sync with Reference Library — Annotations made on a PDF linked to a library item are stored with that item and accessible from the library view
- AI text selection — Select any text in the PDF and ask the AI assistant to explain, summarize, or critique the passage
- LaTeX SyncTeX — When viewing a compiled PDF from the LaTeX editor, click-to-source navigation is available
WARNING
Annotation syncing requires the PDF to be associated with a Reference Library item. Standalone PDFs opened from the file explorer store annotations locally in the project.
Search
- Text search — Full-text search within the document with match count and navigation between results
- Match highlighting — All occurrences highlighted in the viewport with the active match emphasized
- Zoom controls — Fit width, fit page, and manual zoom from 50% to 300%
- Page rotation — Rotate individual pages or the entire document in 90-degree increments
AI Integration via MCP
The following MCP tools enable AI agents to interact with the PDF viewer.
| Tool | Description |
|---|---|
pdf_read | Extract text content from a PDF file or specific page range |
pdf_annotate | Add a highlight, underline, strikeout, or text note to a page |
pdf_get_annotations | Retrieve all annotations from a document with metadata and content |
INFO
AI agents can read a paper, extract key sections, and add annotations programmatically. Ask the assistant to "highlight all methodology sections" or "add notes summarizing each figure."
Related
- LaTeX Editor — Write and compile LaTeX with SyncTeX preview
- Reference Library — Organize sources and link annotations
- Split Panels — View PDFs alongside the editor or chat
- MCP Servers — Full list of AI-accessible tools