Annotating PDFs with Highlights

Note taking in the era of PDFs has clearly become an issue for most people working with electronic documents on a daily basis. As far as I know most reference managers now implement some form of a note taking/highlighting feature. However, we may not necessarily be happy with those built-in capabilities as they may not be well aligned with our own flavour of note taking. In this constant and incremental “apps vs. user needs” matching exercise it is nice to see new offerings with a slightly different approach.

Just very recently, I came across this light-weight app aptly called Highlights. For those people keen on using Markdown in their writing process, this may be of interest as the distinctive feature of this little program is that it formats notes in Markdown.

When you open a PDF, Highlights asks whether to fetch metadata for the document. In my example below, it successfully grabbed the metadata and automatically added to the notes, which are displayed in the right pane. Highlights also supports integration with Papers (currently only Papers and nothing else) by adding a link (in blue) to the document in the Papers library. (The right pane is in ‘View’ mode, showing  rendered Markdown text.)

Highlights grabs document metadata.

Highlights grabs document metadata.

Highlighted text is extracted on the fly and is automatically added to your notes in Markdown syntax. (One cool feature I noticed during my test run is that hyphenated words are re-joined, unlike in Sente for instance.) The picture below shows the notes pane switched to ‘Edit’ mode revealing the Markdown syntax. Once you are done with note taking, the notes can be exported to HTML, PDF, Markdown, TextBundle formats or passed on to Mail, Evernote, DevonThink or Ulysses.

Highlights adds highlighted text to notes.

Highlights adds highlighted text to notes.

I must admit I have not subjected Highlights to thorough testing (I am reasonably happy with my current apps), I just wanted to raise a little bit of awareness. If you are currently in the market for a PDF reader with note taking capabilities, you might want to give Highlights a try, it has a free trial version:


About Csaba Pusztai

I graduated from CEU with a Ph.D. in Environmental Science and Policy. I taught undergrad and graduate economics and business for 16 years. After spending two years at UNU-IAS in Japan, I am now working in forestry research at Scion in New Zealand. I converted in 2004 purchasing a 12-inch PowerBook which I used until 2012, when it finally gave in. I find pleasure in reading, thinking about and discussing science and technology.
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14 Responses to Annotating PDFs with Highlights

  1. Micah says:

    Thank you for sharing this app with us. Have you had more experiences with the Papers for Mac integration?

    Liked by 1 person

    • Csaba Pusztai says:

      Sorry, I have not made any effort to test out how Highlights shakes hands with Papers. As of now, I am settled with Sente (although I did start out with Papers many years ago and then abandoned it). As I am Markdown-based, Highlights caught my attention because of its support for Markdown rather than Papers. If I find some free time, I may venture into putting them to the test.


  2. YK says:

    I am not sure if this app is worth its cost. Currently I use [Skim](, which is a free app. It allows me to export highlighted texts and my notes in plain text format.


  3. Omolola says:

    Thanks so much for this app. Hope you know so much about the Papers for Mac integration?


  4. omololar says:

    Thanks for this app. Hope you know so much about the Papers for Mac integration?


  5. Michael says:

    Checkout the app TagNotate. Great PDF annotation tools including ability to tag individual annotations within a PDF, such that the tags are quickly searchable across a library of PDFs. Fabulous!


  6. Richard Johnson says:

    I have been using Highlights for a while now. As simple as its functions are, I have yet to find any other annotation app that fits into my academic workflow as well as Highlights. I even contacted a couple of developers whose apps I like for other pdf handling features to see if they would add these simple features. They did not seem to be interested in addressing the needs of the academic market.

    Highlights integrates with Papers or Bookends in some cool ways, but I would really rather it replace the native tools in ether of these apps. It does not. You have to choose to use Highlights with either Papers or Bookends. You cannot readily switch back and forth, at least, not during a single project.

    Highlights does not integrate with Sente proprietary format.

    I chose to use Papers 3. There are other unique features in Papers 3 that I think are essential, though I tried Bookends and Sente. Most of the stability problems with a lot of apps are because of syncing between devices. I have chosen to keep most of my academic work on a single laptop which I transport to various work environments. This has made the recent versions of Papers (3.4.5 currently) really stable, at least for me.

    To use Highlights with Papers, I use the PDF… Open With… feature and choose Highlights. This opens the pdf copy from my Papers database and saves it there too. Highlights lets me highlight or underline text, then write my summaries, paraphrases and notes. I also paste the Papers citekey for the source and any \[tags]\ I want to the end of the note. Highlights exports to a number of formats including markdown language and Ulysses. However, after I am finished with a source, I Select All and use an rtf clipboard called Copy’Em Paste. This preserves fonts and most importantly URLs.

    I paste the information from Highlights onto a source summary page in a notebook/outlining app. I had been using Circus Ponies Notebook (CPN), but with their demise earlier is year, I am exploring the notebook/outlining tools in Scrivener and Outline+. I have yet to make a decision.

    Either way, I make a summary page for each source I am using in the manuscript with a single paste from Highlights. I create a content outline of my manuscript by copying my paraphrases or summaries to the content outline from the summary page. With Scrivener and Outline+, it is easy to create an internal link back to the summary page, easier than with CPN. Highlights automatically included links to the original pdf of the source in Highlights and to the pdf in Papers (or alt Bookends). From the content outline, I write my manuscript. Currently, I use Scrivener, but I plan to explore some other minimalist writing apps soon. I included the Papers citekey with the paraphrase or summary, so it gets pasted into the manuscript as I write ready to create my bibliography.

    One of my favorite mental tricks as I am editing is to “improve” wording and unintentionally change a paraphrase back to a structure and often wording that is very close to the original source, thus inadvertently, but potentially, plagiarizing. However, with this workflow, as I edit, I can open my content outline parallel to my manuscript. I click the internal link to the summary page and read the associated text. If I need to see more, I click one of the external links to either Highlights or Papers to read the context of the passage in the original pdf source.

    A bonus feature with Highlights is that when you mark an entry in the bibliography of a source with a Preference specified color and type, such as gray-underline, it will search for the reference in Papers (or Bookends) and if not found it will search for it online. Currently, I can only do this one entry or two at a time. As I don’t usually go looking for these all at once, it is still a huge timesaver.

    I have some reservations about Highlights. Customer support is minimal to non-existent. Like many apps, Highlights seems to be a one-man show, and on the heels of CPN, a developer taking his toys and going home is a concern. Highlights uses the DOI to look up source metadata. I would prefer it to use the Papers metadata that I have painstakingly made sure is 100% accurate, at least when DOI metadata is unavailable. I would also like to have some control over the formatting and order of the annotation view page. The colors for the highlights are so saturated that you cannot easily read through the highlight, but they work great for underlines. This limits me to about seven colors. I would like to be able to use more sometimes. Page numbers start with 1 rather than actual source page numbers. I have to paste my citekeys in rather than having them be optionally included. There is no tag tool.

    But there are some great features that I have not mentioned like being able to sort the annotations view in several different ways; ability to re-label a highlight color’s name, which be used in many ways; hiding and showing sidebars to maximize the need workspace, copying graphics and their captions with a couple of clicks, etc.

    Despite my reservations and wish list of tweaked features, it is a nice app, and I have not found a viable alternative for my workflow. At least for me, Highlights is poised to become the standard in academic annotation tools.

    Why not use the annotation tool in Papers?
    The annotation tool in Papers completely misses the mark in all but the most rudimentary of features. It highlights, underlines and attaches notes to the text. It creates a file that you can export, but it is in a Papers determined format with preset information little of which I need or use. It is difficult to include citekeys, or URLs linking back to the source. And the deal killer for me is that it does not allow me to associate my notes with the highlighted text in the summary. I have to search for and find the original pdf to read the text that I summarized.

    What about Bookends’ annotation tool?
    Bookends has a nice annotation tool that creates a notecard for each entry, however I am taking my annotations into a content outline. I don’t like the way that Bookends exports its annotations, or perhaps I just prefer what I can do with Highlights. And I am not sure how easy it would be to set up a link back into the source in Bookends from the content outline. Highlights with the Header enables does this automatically.

    What about Sente’s annotation tool?
    The annotation tool in Sente has many of the same functions as Highlights, so you would be duplicating your efforts to use both. Sente is worth considering if you want an integrated annotation tools that works well. However, the process of exporting Sente notes and annotations is a complex and time-consuming one, especially compared to select-copy-point-paste.

    I looked at TagNotate. I love the tags, but my annotations are primarily summaries of long sections and paraphrases of statements in a source. These need to be associated with a particular section of text, so I can refer to them later. As much as I like tags, I need this feature and I can type in my own tags easily enough. I think TagNotate would be a great stand alone tool for anyone not using Papers, Bookends or Sente, which each have their own searching and tagging methods.

    What about Skim?
    Skim is great for many kinds of annotation. It just does not have these specific features. It could if someone coded them in. However, Highlights still has an advantage in that its controls are simple, easy to use and, most important to me, quick to use. Skim tends to be a little complex and fussy, but it does many other things better than Highlights currently does, like contextual page numbers.

    Liked by 1 person

    • msteffens says:

      Hi Richard, many thanks for your detailed feedback and the description of your workflow. This is really helpful!

      I’d like to add one remark about your comments about the Papers annotation tool and its export capabilities. While I agree that its annotations tool doesn’t really compare with what Highlights offers, you could use the scripting support in Papers to fine tune the export of your annotations made in Papers.

      Below are example scripts that show how to export note+highlight annotations in a custom format:

      * export note+highlight annotations to individual files:
      * copy all note+highlight annotations to the clipboard
      * export note+highlight annotations to DEVONthink Pro
      * export note+highlight annotations to Evernote


      • Richard Johnson says:

        Hi msteffens,
        Thanks, it’s a good point. The annotations exporting feature is something that Mekentosj has spent some time addressing. In my experience, anything that the staff at Papers takes time to address works better. In fact, a major reason I returned to Papers after exploring others was that it regularly updates and improves. I have hopes for an improved annotation tool that works for my workflow.

        I think the export feature that I might use most is on the Sidebar > Overview > Cite > Notes, which copies all Papers Notes to a clipboard. Unfortunately, it only pastes in plain text rather than rtf, so I lose all my links.

        I did get Papers to associate my notes with highlighted text. I copied the highlighted or underlined text into the note. I only annotated one journal article in this manner. I found the extra steps a little time consuming and tedious, the two things I try most to eliminate from my workflow. But, it worked and would be adequate for small projects if a user did not want to buy a third-party annotation tool.

        A surprising observation after I finished was that the Note icons placed in the text (one for every highlight) covered so much text it was an obstacle to reading. I moved the icons to the margins, but I began perceiving them as gigantic.

        I think all annotation tool developers could learn some lessons from Highlights. Its main strengths are its simple UI and quick workflow. Select text and a single pop-up menu allows you to select color, annotation style, make notes or delete the annotation. This is also Sente’s best feature, but Highlights’ is easier for me to use. Like the current Papers annotation tool, there is a useful default annotation color and style that is super-quick for first reads.

        I would love to stay in Papers to annotate my pdf sources. In addition to the quicker pop-up menu workflow only two additions would enable that: Association of my notes with the selected text and control over what is included in the output of the annotations.

        In Papers > Preferences > Library there are two fields, “Organize library folders by subdirectory:” and “Rename files in library folder as:”. I envision a tab in Preferences for Output or Annotations with a header/page field and entry field that allow me to specify what is included in the output the highlights and my notes and the order in which it appears. The principal time saver for me would be automatically attaching a citekey to each note, but others might use BibTex and Endnote cite commands. The date and time the notation was created is distracting to me but might be useful to others. There are a few other things that might be included.

        I also include tags with each notation, but my use of tags is not mature nor extensive.

        In the literature review process, Highlights’ ability to search for reference sources used in the journal article and to have nearly instantaneous access to those sources in Papers has begun changing the depth of my research. By daisy chaining back, I have been better able to get to original research and have found that some of the parameters we accept as fact were never actually empirically substantiated. I have started putting those daisy chains as tags in each notation I research.

        Highlights searches for these references with its Underlining Power Tool. In theory, this would create a list of the citations you explored at the bottom of the Annotations page. It actually will only list two entries. Papers might do this by adding an entry to its current pop-up menu similar to “Match with selection,” perhaps “Search for selection” that would search first my library to see if I already have the article and then the Internet to see where the article is available. I have tried to do this with the Search Online feature but this doe not work, additionally I want to search my library before I search online.


    • msteffens says:

      Hi Richard, I’d like to get in contact with you to further discuss your ideas & requirements for an academic note-taking workflow. If you’re interested, you can contact me at “mat at extracts dot de”. Thanks!


  7. dtopps says:

    I have used a lot of these highlighting and annotation tools as well. I very much agree that Highlights is easy to use, has good workflow and most importantly, uses a standard approach to embedding its annotations in a PDF. Unlike Richard Johnson’s comment above, I have found it to be compatible with Sente’s approach.

    The biggest outlier here is Mendeley. I really like Mendeley as a ref manager. I like how easy the highlight/annotation tool is to use. But Mendeley uses a proprietary format. Worse still, it clobbers the standard highlight/annotation marks created by other software such as Highlights or Mendeley. BEWARE!

    I find that the best approach, if I do want to use Mendeley, is to use Highlights on the PDF outside of Mendeley. When the PDF is viewed from within Mendeley, you can still see the annotations. Just don’t edit them.


    • RJohnson says:

      Yes, I think the Sente workflow and a workflow using Highlights are very similar. They just use different apps, so primary preferences are for UI of the apps not the workflow per se. I have not been able to get Sente’s proprietary system to work with Highlights in any meaningful way, but it is meant to be a turnkey system. I am sure that many people have and will love Sente. i just found it tedious and confining. Had I not started with Mendeley then Papers, I might be singing a different tune. There are many ways to create a meaningful workflow. I experiment with new things to create a better workflow whenever it seems helpful.


  8. JohnAtl says:

    I really like Highlights, but it suffers a problem other annotation programs have: in a two-column article, all notes on the right column should follow the notes on the left column. All the programs I have seen just sort by Y position.


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