Frequently Asked Questions

I want atx-header style Markdown headers, is this possible?

Yes, go to Preferences –> Markdown and turn on “Use # for title/author headers”

Can I have a standard color for each type of annotation?

Yes, go to Preferences –> PDF and set what color you want for each type of annotation.

Is there tagging support in Highlights?

Yes, Highlights supports per file tagging. Select a color for Tags in Preferences –> PDF –> “Underlining power tools”. Underline the words or short sentences in the PDF you want to use as a tag with the selected color. Tags will be embedded as PDF keywords and exported as Finder-tags when saving.

In addition, Highlights supports per annotation tags “Split files” is enabled in Preferences –> Export. To use this feature as add tags as comments to the annotation using the syntax @tagname e.g. @important or @review. The tags will be added as Finder-tags to the file representing that annotation when exporting as split HTML/Markdown files or to DEVONthink.

Does Highlights integrate with any reference managers?

Yes, Highlights integrates with Bookends (tutorial here) and Papers (tutorial here).

Is Highlights scriptable?

No, not yet.

My extracted annotations show up with redundant text, why?

This happens when the PDF is exported from Skim as it saves a backup of the highlighted text in the comment-field of the annotation.

Highlights can not find the correct metadata for my PDF, can I manually lookup a DOI?

Yes, if you select the text containing the DOI-link and selecting “Lookup metadata” in the View-menu (Cmd+Alt+R) Highlights will use the selection for fetching metadata.

Highlights crashed on me, what do I do?

Please email me with as much information as you can provide on when/how/why it crashed (crash reports and screenshots are very helpful).

Is there a trial version?

Yes, you can download it here. The demo has the same features as the full version, but only extracts annotations from every other page of the PDF.

Can Highlights extract annotations made with other apps?

Yes, Highlights uses standard embedded annotations which are supported by most PDF readers on both OS X and iOS.

Some PDF apps (including Skim) and most reference managers use non-standard annotations which are not compatible with Highlights. However, most of these apps allow you to export the PDFs with embedded annotations which will work in Highlights.

How do I customize what is included in each annotation?

Under Customize in Preferences, you can set which information should be included in each annotation (including author, modification date and color category).

How do I use reference lookups?

Check out this tutorial.

How do I use color coding?

Color coding allows for categories of annotations sorted by color. By going to Preferences –> Colors you can see the current order in which the colors will be sorted. You can reorder the sorting and rename the each color to represent a category.

Highlights in the Mac App Store

Quick question or comment? Contact me on Twitter