A highlighted PDF can feel finished even when you haven’t written down why the passage matters. Months later, the color tells you something was interesting. It doesn’t tell you what you intended to do with it.
The useful result is a small chain: passage → source location → interpretation → question or claim. This guide shows how to build that chain in Acres, including what changes when the material is a figure or an image-only scan.
We make Acres. Its reading workflow suits notes you want to arrange alongside other material on a canvas. If you mainly need reference management and manuscript citations, a citation manager may be the better starting point.
Check the PDF before you highlight
Open the PDF and try selecting a sentence. A document can look like text while containing only page images. OCR adds a searchable text layer to a scan; Adobe’s documentation explains this distinction.
For selectable text, use the normal text-highlight path. For a figure, table image or scan, use an area selection. Don’t expect a rectangle around an image to produce readable words.
If you need OCR, use an appropriate tool before this workflow and inspect its output. A misread minus sign, column or author name can make a copied excerpt wrong. Keep the original scan available for checking.
Capture a passage, then make a card
Add the PDF to Acres and open it in the reader. For a text passage:
- Choose the reader’s Text highlight tool, select the passage and choose a highlight color.
- Open Highlights and find the excerpt. Its tile shows the source name and page.
- Open that highlight’s menu. Choose Extract to card to create a note, or Add to whiteboard to create a note on a board you select.
- Open the new card and follow its Source link. Confirm that you return to the intended passage.
The card contains the excerpt as a blockquote followed by a backlink to the PDF page and highlight. A longer passage can produce an unhelpful automatic title; give the note a title that describes what you’ll use it for, while preserving the quotation and source footer.
Choose a short enough passage to review in context. If you need several paragraphs, record which part carries the claim and which part supplies a qualification. Highlighting only the strong sentence can hide a limit in the next one.
Area selections need a different follow-up
Choose Area highlight and mark a rectangle for material such as a diagram. The Highlights gallery shows a crop preview.
In the current gallery, Add to whiteboard creates a source-reference card for that area selection. It supplies the source link and a heading; it does not insert the crop as a board image or turn the image into text. Extract to card is available when a highlight has text, so an empty area selection won’t offer the same text-extraction action.
Write a description in the source-reference card: what the figure shows, which labels matter and what you think it means. Keep observation separate from interpretation.
Example: you’re reading a report with a diagram of a review process. Your note records “The diagram places a second review after revision.” Under that, you write “Possible implication: our handoff checklist needs to say which reviewer returns after an edit.” This is a hypothetical reading note, not a claim about a published study.
For a table, record the row, column, unit and caption you used. An image selection alone doesn’t explain whether a number is a total, percentage or adjusted estimate.
Add your explanation without rewriting the source
Use a repeatable note structure:
| Part | What to write |
|---|---|
| Excerpt or observation | Exact quoted text, or a description labeled as your observation |
| Meaning | What you understand the passage to establish |
| Use | Which question, claim or project it helps answer |
| Limit | What the passage doesn’t establish, or what remains uncertain |
| Source | PDF backlink plus checked bibliographic details |
The blockquote and the interpretation can live in one card. If the interpretation becomes an idea you want to reuse across sources, give it a separate card and link back to the evidence.
Record authors, year, full title and DOI or URL in a source card. Check the printed page number before a formal citation: the reader’s page position can differ from the number printed on a journal article or book page.
Put the note into a comparison
Place the new note beside the question it addresses. Add another source that supports, qualifies or challenges it. Write that relationship down, rather than relying on proximity to explain it.
A reading board might contain one question card, two excerpts and a synthesis card explaining their difference. That is enough to start. Avoid extracting every highlighted sentence into a large board before deciding which ones matter.
For comparisons across papers, continue with the literature review canvas. For ideas you’ll return to across projects, use the visual Zettelkasten workflow.
Keep the source trail when you move or back up
Acres keeps PDF highlight records in annotation files in the vault, separate from the PDF asset. A copied Markdown note preserves the text of its source link, but that link still needs the Acres vault and source asset to resolve.
Back up the complete vault, including assets and annotations. Copying only the notes won’t preserve the full reading workspace. Don’t assume marks will be visible in an external PDF reader simply because you copied the PDF.
Other readers have their own storage rules. Zotero’s PDF documentation, for example, distinguishes database annotations from annotations embedded in an exported PDF. Check the source app’s export behavior when bringing an existing library over. The Heptabase import guide covers that separate migration workflow.
Know when to keep Zotero alongside the canvas
Zotero can add PDF annotations to notes with links back to their source, and its word processor plugins handle manuscript citations and bibliographies. Those are substantial strengths if you’re writing academic work.
You can keep bibliographic records there and manually carry the relevant metadata into Acres for visual synthesis. This is a companion workflow, not a claim of automatic Zotero integration.
An AI agent can compare selected extracted cards, but don’t assume it has read the whole PDF or understands an area selection. Provide the text it needs, ask it to identify supporting notes, and check the originals yourself. The MCP workflow starts with retrieval before drafting. Check the model route too: storing a PDF locally doesn’t make a cloud AI request private.