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Freiya’s PDF viewer, called Focus mode, provides a dedicated environment for deep reading and annotation of research papers. Highlight key passages, add comments, categorize your notes, and even ask AI questions about the paper, all in one seamless interface.
Full Focus mode interface showing a PDF paper on the left with colored highlights visible, and the a

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Overview

Focus mode is designed for serious paper reading and analysis. It combines a full-featured PDF viewer with sophisticated highlighting tools and AI integration. Key features:
  • Multi-color highlighting system
  • Comments and notes on highlights
  • Category-based organization
  • Export annotations to markdown
  • AI Q&A about the paper
  • Vector search integration
  • Saved reading sessions
Focus mode is available on all tiers, with advanced features on Pro and above.

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Accessing Focus mode

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Opening papers in Focus

  1. Navigate to a paper in your library
  2. Click View PDF or Focus button
  3. PDF opens in Focus mode
This is the most common way to enter Focus mode.
Paper detail page with the 'View PDF' and 'Focus' buttons prominently displayed in the action bar
PDFs must be available (open access or uploaded) to use Focus mode. Papers without PDFs show a “PDF not available” message.

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PDF viewer controls

Page controls:
  • Next/Previous - Arrow buttons or keyboard arrows
  • Page number - Click to jump to specific page
  • Page thumbnails - Sidebar with preview of all pages
Zoom controls:
  • Zoom in/out - + and - buttons or keyboard
  • Fit to width - Optimizes for screen width
  • Fit to height - Optimizes for screen height
  • Custom zoom - 25% to 400%
PDF viewer top toolbar showing navigation controls (previous, page number/total, next), zoom control

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View modes

Best for: Focused reading, highlighting, detailed studyShows one page at a time with maximum space for content.

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Display options

  • Full-screen mode - Press F or F11 for distraction-free reading
  • Rotate pages - Rotate 90° for landscape papers
  • Dark mode - PDF background adapts to your theme
  • Hide annotations - Toggle highlight visibility with H

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Highlighting system

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Creating highlights

1

Select text

Click and drag to select text in the PDF
2

Choose color

Highlight toolbar appears, select a color
3

Add comment (optional)

Click comment icon to add notes
4

Save

Highlight is saved automatically
Close-up of selected text in PDF with the highlight toolbar visible above it, showing 6 color option

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Highlight colors

Freiya provides six highlight colors, each suited for different purposes:
ColorSuggested UseExample
YellowKey findings, main results”Our method achieves 95% accuracy…”
GreenMethodology, approach”We used a transformer architecture…”
BlueImportant quotes for citation”As Smith et al. demonstrated…”
RedCritical points, limitations”However, this approach has drawbacks…”
PurpleQuestions, future work”Future research should investigate…”
OrangeExamples, case studies”For instance, in the medical domain…”
Develop a consistent color system and stick to it across all papers for easier review and export.

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Highlight categories

In addition to colors, you can assign categories to highlights for better organization: Predefined categories:
  • Methodology
  • Results
  • Discussion
  • Introduction
  • Limitations
  • Future Work
  • Key Concept
  • Definition
  • Citation
  • Custom
Highlight detail in sidebar showing color badge, category dropdown, comment text, and action buttons

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Editing highlights

Modify existing highlights anytime: To edit:
  1. Click the highlight in the PDF or sidebar
  2. Edit comment text
  3. Change color or category
  4. Add or change emoji
  5. Changes save automatically
To delete:
  1. Click the highlight
  2. Click delete button (trash icon)
  3. Confirm deletion
Deleting highlights is permanent and cannot be undone.

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Comments and notes

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Adding comments

Every highlight can have an associated comment:
1

Create highlight

Highlight text as usual
2

Click comment

Click the comment icon in the toolbar
3

Write note

Enter your thoughts, questions, or observations
4

Save

Click outside or press save, comment is linked to highlight
Comment features:
  • Plain text or basic formatting
  • No length limit
  • Edit anytime
  • Searchable
  • Export with highlights
Annotation sidebar showing a highlight with an expanded comment box containing several lines of note

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Emoji reactions

Quick emotional or categorical tagging with emojis: Common emoji uses:
  • 💡 Insight or idea
  • ❓ Question or confusion
  • ⭐ Very important
  • 🔍 Need to investigate further
  • ✅ Understood
  • 🚨 Critical information
To add emoji:
  1. Click highlight
  2. Click emoji picker
  3. Select emoji(s)
  4. Multiple emojis supported

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Annotation sidebar

The sidebar provides a complete overview of all your annotations for the current paper. Main functions:
  • List all highlights chronologically
  • Filter by color
  • Filter by category
  • Search annotations
  • Jump to highlight in PDF
  • Export options
Full annotation sidebar showing list of highlights, each with preview text, color badge, category ta

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Filtering highlights

Filter by color:
  • Click color buttons at top
  • Shows only that color
  • Multiple colors selectable
Filter by category:
  • Dropdown menu
  • Select one or more categories
  • Combine with color filters
Search annotations:
  • Search box at top of sidebar
  • Searches highlighted text and comments
  • Real-time filtering

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Sorting options

  • Page order - From first to last page
  • Chronological - Order highlights were created
  • Color - Group by highlight color
  • Category - Group by assigned category

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Focus sessions

Focus mode automatically saves your reading sessions.

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Session tracking

Each time you open a paper in Focus mode:
  • New session created or existing resumed
  • Reading position saved
  • Scroll position remembered
  • Zoom level preserved
  • Last accessed timestamp updated
Focus sessions list showing recent papers read, with thumbnail, title, last page viewed, and 'Resume'

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Resuming sessions

1

Open Focus menu

Click Focus in the sidebar
2

View sessions

See list of recent reading sessions
3

Click to resume

Click any session to pick up where you left off
Session data includes:
  • Which paper
  • Current page
  • Zoom level
  • Sidebar state
  • Filter settings

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AI-powered Q&A

Ask questions about the paper you’re reading and get AI-powered answers with referenced sections.

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How it works

1

Enable Q&A

Click the AI chat icon in Focus mode
2

Ask a question

Type your question about the paper
3

Get answer

AI responds with relevant passages cited
4

View references

Click citations to jump to that section
Focus mode with AI chat panel open on the right, showing a question about the paper and AI response

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Question examples

Good questions for Focus Q&A: 
What methodology did the authors use for data collection?

Summarize the key findings in the Results section.

What are the main limitations mentioned in the paper?

How does this work compare to the Smith 2020 study?

What future research directions do the authors suggest?
Be specific in your questions. The AI has access to the full paper text and can provide precise answers.

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Vector search integration

Focus mode uses vector search to find relevant passages:
  • Paper automatically indexed when opened
  • Semantic search, not just keyword matching
  • Finds conceptually related sections
  • Understands context and meaning
Database tracking:
  • Papers indexed in Focus mode
  • Chunk count per paper
  • Last indexed timestamp
  • Quick re-indexing when needed

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Exporting annotations

Save your highlights and notes for use in writing and analysis.

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Export formats

Best for: Note-taking apps, writing drafts
# Highlights from "Paper Title"

## Page 3 - Yellow Highlight
> Highlighted text goes here...

**Comment:** My thoughts about this passage
**Category:** Methodology
**Date:** 2025-01-15

---

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Export process

1

Open annotation sidebar

In Focus mode, ensure sidebar is visible
2

Click Export

Find the Export button at top of sidebar
3

Choose format

Select your preferred export format
4

Choose scope

Export all or filtered highlights
5

Download

Save the file to your device
Export dialog showing format options (Markdown, CSV, JSON, Text) with checkboxes for 'Include commen'
Export regularly to keep backups of your annotations, especially for important papers.

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Keyboard shortcuts

Master Focus mode with these shortcuts:
ActionShortcut
Next page→ or Space
Previous page← or Shift + Space
First pageHome
Last pageEnd
Zoom inCtrl/Cmd + +
Zoom outCtrl/Cmd + -
Reset zoomCtrl/Cmd + 0
Full-screenF or F11
Search in PDFCtrl/Cmd + F
Toggle highlightsH
New noteN
Highlight (last color)Ctrl/Cmd + H
Delete highlightDelete (when selected)
See all shortcuts →

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Advanced features

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Highlight toolbar options

Additional features:
  • Copy highlighted text
  • Google Scholar search for selected text
  • Define selected word
  • Translate selection

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Page annotations (coming soon)

Beyond text highlights:
  • Draw shapes and arrows
  • Add sticky notes anywhere
  • Freehand drawing
  • Annotation layers

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Collaborative annotations (coming soon)

Share and collaborate:
  • Share annotated papers
  • Comment threads on highlights
  • Team reading and discussion
  • Permission levels

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Multi-paper comparison (coming soon)

Read multiple papers side-by-side:
  • Split-screen view
  • Compare methodologies
  • Cross-reference findings
  • Synchronized scrolling

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Integration with other features

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With paper management

  • Highlights visible in paper detail
  • Annotation count shown in library
  • Search papers by annotation content
  • Filter by “has annotations”
Learn about paper management →

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With AI chat

  • Start chat about paper from Focus
  • AI has full paper context
  • Reference specific highlights in chat
  • Ask questions about annotated sections
Learn about AI chat →

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With collections

  • Filter collections by annotated papers
  • Export collection annotations
  • Compare annotations across papers
  • Collection-level annotation stats
Learn about collections →

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Best practices

Consistent colors

Use the same color scheme across all papers for consistency

Comment liberally

Add comments to highlights, future you will thank you

Use categories

Categorize highlights for easier filtering and export

Export regularly

Back up annotations periodically in case of data loss

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Effective highlighting

Do:
  • Highlight complete thoughts or sentences
  • Add comments explaining why it’s important
  • Use categories consistently
  • Review and refine highlights
  • Export for your writing
Don’t:
  • Highlight entire paragraphs (be selective)
  • Highlight without reading carefully
  • Use colors randomly
  • Forget to add comments
  • Leave highlights unorganized

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Troubleshooting

Check these issues:
  • PDF URL may be broken or expired
  • File may be too large
  • Network connection problems
  • Try re-adding the paper
Contact support if issue persists.
Possible causes:
  • Network connection lost
  • Browser storage full
  • Account session expired
  • Refresh page and try again
This happens with:
  • Scanned PDFs (image-based, no text layer)
  • Password-protected PDFs
  • Corrupted PDF files
Solution: Try re-uploading or use a different PDF source.
Check if:
  • Viewing the correct paper
  • Highlights filter is active (showing none)
  • Paper was re-uploaded (creates new version)
  • Accidentally deleted
Contact support if highlights are truly lost.
Requirements:
  • Paper must be indexed (automatic on first open)
  • Need active internet connection
  • Must have AI message credits remaining
  • Wait a few seconds for indexing on first use

Paper management

Manage papers and access PDFs for Focus mode

AI chat

Ask questions about papers with AI assistance

Research workflow

Integrate Focus mode into your reading workflow

Tips & best practices

Learn annotation strategies from experienced researchers