Highlight and annotate PDFs in Paperpile

Highlighting and annotating PDFs is now possible in Paperpile! In order to activate the new feature go to “Settings > Browser Integration > PDF Viewer” and choose “Viewer with annotations (beta)” (see screen shot below). We have rolled out this feature just a few days ago and we still consider it to be beta phase. Any kind of feedback and bug reports are very welcome! Feel free to post here or even better - send the PDF that is causing the trouble to andreas@paperpile.com.

For the moment, the new PDF viewer will only work with PDFs in your library and not with PDFs in shared folders. That will require some more changes to Paperpile’s sharing model.

There are a couple of known issues that we are working on right now and that will be fixed with the next update:

  • Text selection sometimes fails to work properly when vertical text is near by
  • The PDF’s table of content is not rendered properly when the ToC is very long and nested


For the moment, the new PDF viewer will only work with PDFs in your library and not with PDFs in shared folders.

If I annotate a PDF and then share it, however, the annotations will be shared? Ideally I would like some way to share a PDF without sharing the annotations as well. Is that going to be possible?


Yes, that’s something we thought about a lot actually. Unlike other products, we deliberately decided to write the annotations right to the file in a standards compliant way so that the can be viewed in other viewers. However, that means we need to get rid of the annotations again when you only want to share the file and not the annotations. That will follow at some later point together with the possibility to collaboratively annotate PDFs in a shared folder.


FYI, today the PDF Annotate highlight in yellow, underlining, highlight and copy, etc isn’t working for SAGE pdfs.
I have previously used it and made no changes in settings since.
I can see the yellow pencil is pressed on, but when I go to highlight nothing actually happens (that I can see).
Is this the appropriate place for a bug report?

Looks good. Although I’m new in Paperpile, so it’s good to know the basics of highlighting and annotating ways of PDF files in Paperpile. Good instructive information, thanks for explaining nicely.

Is it only for the PDFs for this specific publisher? If you reload or re-open the PDF does it work?

Can you send a PDF to andreas@paperpile.com for which you experienced the problems?

I tried using this. Just switched back due to possible bug in keyword searching. After flipping through the first few hits, the viewer stopped highlighting the results, although it still jumped to the (I assume) correct section of the document. It worked in the default viewer, so it’s not a problem with the pdf. Here is the paper: http://www.nature.com/neuro/journal/v12/n8/full/nn.2357.html

Thanks for trying and reporting the issue. Any chance you remember what you searched? A detailed way to reproduce a bug is sometimees the difference between hours of guessing and a one minute fix :slight_smile:

The term was “prior.” And unfortunately, I’m not able to reproduce it. I’m pretty sure I wasn’t imagining things.

One thing that I’ve noticed now fairly consistently, even just from using the new PDF viewer a handful of times, is that after a few page into an article I am no longer able to highlight text beyond that page (i.e., the select-text cursor will not even appear, although it will reappear if I scroll back to the previous pages). This behavior has occasionally been accompanied by some other visual weirdness, such as a page getting (permanently) blacked out or a large chunk of text somehow getting highlighted (without my doing so) which then cannot be undone (i.e., I cannot then bring up the normal menu to remove highlighting).

Has anyone else encountered this behavior?

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Can you reproduce this behaviour or at least make it happen fairly consistent that you could help us debugging?

Can you hit F12 or (alt-cmd-J on Mac) when it happens and send us the content of the “Console” tab that shows up?

I know the forum is a place for problems and bug reports but I wanted to give you some positive feedback as well. After coming back to the metapdf app as it is integrated with paperpile now, I was pleasantly surprised how snappy and fluid the experience has become (fingers crossed this doesn’t change when I keep using it). There are probably lots of things on the agenda, but I appreciate you taking the time to make them work well.


No it’s not, we also love reading posts like yours :wink:

We’re trying hard with the PDF viewer and getting closer to what we think it should feel like. But there is still some work to do and all feedback is welcome.

Another very small thing. I think the reader would be easier on the eyes if the background were a few shades darker.

We try to improve that. Thanks.

We tried now a lot to reproduce this bug but failed. Could it be that you just did not see the green highlight because it was too subtle or over another highlight?

There were no other highlights, and it wasn’t just one instance that I couldn’t find - it was every instance after a certain page (5 I think). I haven’t had the issue since then with this or any other documents. Sorry you’ve spent so much time on this! I will be sure to let you know if I’m able to reproduce.

Hi, newer user here–
is there a way to filter for pdfs that have highlights or annotations in them?
That would be handy for those times when you remember reading something and marking it, but not the author.


That’s not possible at the moment. It will be one of the next steps to include the annotation information from the PDFs in the main user interface. It’s planned but I can’t give an estimate when it will become available.

Just thought I’d say I absolutely love the PDF viewer - its annotation tools are some of the best I’ve used, and the interface is an absolute dream.

I was just wondering if you were planning on adding an ability to save annotations as a separate document (PDF would be good, or perhaps a Google Doc) directly into Google Drive itself from within the PDF viewer?

I tend to write by flicking through an assortment of relevant notes filed in a single folder in Drive, so this would be a really useful feature. At the moment I’m downloading my notes as PDFs then uploading them to Drive, but to be able to save the notes directly to Drive would be a lot simpler and faster.

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