Highlighting and citing

Creating a highlight

Text highlights — Turn on Text highlight mode, then select text. A popup appears with five colours (yellow, green, blue, pink, purple); pick one and the highlight is written.

Area highlights — Turn on Area highlight mode and drag a rectangle, or hold Alt and drag anywhere without switching modes. Press Escape mid-drag to cancel. Use these for figures, tables, screenshots, and typeset equations — anything whose meaning is not in the text layer.

Clicking an existing highlight reopens the popup, where you can recolour it, copy from it, or delete it. Where two highlights overlap, the click resolves to the topmost one.

Referencing a highlight from your notes

This is the point of the feature: a highlight is not just a mark on a PDF, it is a block you can cite.

1. Click a highlight and choose Copy reference
2. Paste into any markdown file

The pasted text is a block reference — ((highlights/papers/attention#^a1b2c3|Attention is all you need)) — pointing at the companion note, with a short label after the |. It renders inline as a preview of what you highlighted, not as that label:

• A text highlight renders the full quoted sentence, not a truncated label
• An area highlight renders the cropped region of the PDF as an image

Cmd+click a reference to open the PDF at that highlight.

Copy text is also on the popup for text highlights, when you want the raw quoted text and no link. Area highlights do not offer it — there is no text behind a region to copy.

Resizing an area reference

An area reference renders at a percentage of the available width. Drag its right edge to resize it, or write the width by hand:

((highlights/papers/attention#^a1b2c3|Figure 2|w=60))

w= goes last and takes an integer percentage from 10 to 100. The label before it is optional — ((target#^id|w=60)) is equally valid. It is part of the markdown, so the width survives a round-trip and travels with the file — and it is visible in the source, not hidden in a metadata store.