Highlights + DEVONthink: Why Did It Take Me So Long!?

Cool Workflows
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As I wrote here, I decided to purchase Highlights after reading the article linked in my post.

I want to share how impressed I am and to encourage anyone who highlights and annotates PDFs and who wants to captue that information for writing, research, etc., to give Highlights a try.

Highlights + DEVONthink just changed my research workflow for the better!

I’ve been using PDF Expert but there is no comparison between PDF Expert and Highlights, for capturing one’s annotatios and processing that information. Highlights wins handsdown.

Highlights is so good at capturing and exporting the highlights/notes that I decided to import, rather than index, my research directly into DEVONthink, I now have DT running all the time in the background (a change for me because I’m a minimalist when it comes to having apps run in the background on my Mac) and I’ll be using Highligts for all PDF reading and annotation.

Below are two screenshots, one showing the highligts extracted from a PDF in Highlights and the other showing the exported markdown file in DT.

For my reading, research, and writing workflow–this is perfect!

Because I’m doing a series on the meaning and implications of personal holiness for my staff next year, my first use of Highlights was on a PDF explaining the etymology of the word holiness in the book of Leviticus (for those who may be interested, the root Hebrew word means Wholeness).

The non-religious can ignore the text if you like, just note how effective the application is and how seamlessly it integrates with DT, Ulysses, Bear…

Highlights App Screenshot of Extracted Highlights

The Way to Wholeness-Holiness Stegman
The Way to Wholeness-Holiness Stegman1920×1082 224 KB

Result in DEVONthink

Screen Shot 2022-04-18 at 12.30.36 PM
Screen Shot 2022-04-18 at 12.30.36 PM1660×1638 242 KB

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Good post - I will check Highlights out.

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This is nice! Out of interest, have you ever tried this on iPad/iOs? For some reason I really dislike annotating PDFs on the Mac, and highlighting without an (e)pencil in hand feels somehow wrong and clunky (pushing a mouse around). So I do all my reading in DT2GO, which still has trouble opening PDFs ‘in place’ in most external PDFs readers, and saving the annotated document straight back (rather I think you need to re-share and then end up with 2 versions of the same file). So I stick religiously to the built-in annotation tools in DT2GO which are pretty good. DT on the Mac of course also has a ‘summarise highlights’ command. What do you reckon Highlights app brings to the table that the native apps don’t?

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I always use my iPad and Apple Pencil to annotate PDFs, I never use the MBP for that purpose. I don’t care for DT2GO—it is clunky so I read and annotate my PDFs in Highlights (formerly used PDF Expert) and then export the annotations to DT—either on the iPad if I don’t have my MBP handy or on the MBP. The nice thing about Highlights is it has the share extension for sharing directly to DT, as shown above, which is nice.

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The problem with highlights for me, unless I’m missing something (very possible) is that you can’t scribble in the margins with your pencil. That is a dealbreaker for me, as I love my scribbly dialogues I initiate quickly via the pencil.

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You’re not missing anything. Highlights does not support handwritten notes sadly, so at least for me, annotating with DTTG and/or PDF Expert is the way to go on the iPad as both will also extract highlights etc. but also support annotating with a pencil.

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this does not relate to DT, but you can insert scribble on pdf using marginnotes or liquidtext on ipad, I believe. I must admit that I have not tried it myself

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Yes — I use either Bookends or PDF expert. I then have a shortcuts action that runs a bunch of scripts to re-format, page bump, and dump into Drafts or Obsidian. It is a bit of a clunky system (particularly compared to the relatively elegant Highlights Devonthink connection) but allows that scribbling in the margins, which I often don’t need ported over, but helps me think/work through my academic texts.

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I just wanted to point out that it is possible to achieve this same thing inside DEVONthink directly. HIghlight any PDF section inside the built-in PDF viewr and then select “Tools > Summarize Highlights”.

Nice touch here is that this mechanism works with PDF highlights and also highlighted RTF and Markdown files. DEVONthink is awesome!

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Does that work with DTTG?

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I dont think so! You could highlight passages in DTTG and then run the “Summarize Highlights” command in the desktop app, though.

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Is there any way to do this in DT3 and also be able to highlight snippets of images or other non-text content - and have those images appear in the eventual Summarize Highlights document?

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It seems more colorful than other PDF apps, but it lacks crucial features such as the PDF table of contents and the ability to click on a note in the right panel and bring out the highlighted section. I also see no reason to justify it being a subscription. The last update it received was over a year ago.

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Thanks for sharing this. I’ve been a DEVONthink user for years, and never realized this feature was there (or I’ve long forgotten it). Your comment led me to try it out in a project I as working on yesterday, and it worked beautifully. It also led me to search for the feature in PDF Expert, which, as it turns out, works much the same way.

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Not that I know of. DT3’s summarize features only pick up on highlights and other text annotations (underline, strikethrough).

Highlights’ image extraction is a great idea, but exporting to markdown had a problem for me. Unfortunately I can’t recall what it was and my subscription has lapsed. Something about controlling where exported images get saved, I think…

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I agree that Highlights is a very good-looking app — and is better than most PDF apps for that purpose. I do worry about it though. It has gone dormant in the past for long periods. The iOS version of the app has been updated in the recent past — but the Mac version has not been updated in a year. I just don’t trust it to be around for a long time.

I use LiquidText now. It is way more feature-rich than Highlights — and much easier to use than MarginNote. You can unlock most features with a one-time purchase of the premium version There is a fairly new syncing feature — which is way over-priced — but you don’t need that for the other pro features. As for syncing, I am paying for the proprietary sync — but I’m pretty sure you can use iCloud to save documents and sync that way.

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There’s really no proper sync besides their cloud. You can manually manage and export each and every documents after every changes and then import them again on another device. I wouldn’t call that a sync…

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My issue too. I like to scribble, circle and note with the pencil. Being restricted to just highlighting text is an issue. (I realise part of the point of the is to export highlights!)

Unfortunately it meant I had to use another app when - as happens sometimes - I was trying to annotate a PDF that had poor OCR. In Highlights I’d end up with the wrong text being highlighted with no fallback so I had to use another app. Zotero’s new PDF annotation has the same issue - no support for inking. The touted academic paper lookup worked only rarely for me: I presume it couldn’t handle some of the theological paper referencing.

Overall, not bad for what it does, but not worth a subscription… especially as others have pointed out it is not getting much love. The stock iOS PDF viewer gave me more functionality for free and can be used alongside the DevonThink or Obsidian highlight extractors.

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LiquidText has built a rather closed system where you depend on their app for syncing to justify a costly subscription, so yet another cloud service where your files are stored, out of your reach essentially for backups etc. When this launched last year, documents could not be exported to iCloud even individually, but I see that it does that now.

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This happens to me quite a bit, downloading academic papers from online repositories. So I find myself getting back to the file on Mac and set right the OCR. DevonTHINK is good with its built-in ABBYY OCR engine, but I also have a copy of stand-alone Fine-reader which has a few features that DT doesn’t offer (mostly, sorting out page-spreads into single-page PDFs; and much finer controls and settings). And then I keep PDF Expert for the invaluable option to add internal Tables of Contents to PDFs (usually for longer PDFs that might be chaptered, or have other meaningful sections). So my PDF suite is more extensive than it ought to be to get the simple work of reading done!

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