Does anyone have any recommendations for good local PDF readers for Windows? I've been reading a lot of various papers recently, and clicking on a citation in Acrobat reader is very frustrating. The document scrolls to show the citation in view, but doesn't clearly show it in the long list that most papers have, and then I have to scroll up to where I was since it doesn't seem to have a working back feature.
Does anyone have a research paper reading tool they're happy with? Zotero is what meets most of my needs but I wish I could organize the papers faster and I wish the annotation tools were better. AI-assisted reading is a plus too.
I was also unhappy with how reference managers handle annotations. So I rolled my own app (https://getcahier.com), with highlight management integrated in the application. This enables me to extract highlights according to topics, organize them in notes using document elements (like collapsible notes and outlines) and use them to plan more complex arguments. This makes it much easier to read actively.
On the paper organization side, I would also like to find out a better way of doing it. What helps me a lot, from a more methodological perspective, is to categorize books according to time period, school of thoughts, or perspective.
Cahier looks great! Any plans to add backup/sync?
Also, is the data store encrypted at rest even when the app is actively being used?
Thanks! I'm considering that. We might first implement P2P or external services (dropbox, iCloud) sync, but we'll see.
The data is all local, so there's no need for encryption yet. But when we implement sync it'll be end to end encrypted.
Doesn't support Linux though or any of the unixes. Looks good though.
Thank you for your interest! I've received that request more than I thought I would. It's high on the priority list now, and will arrive soon.
Mendeley beat Zotero for me with automatic pdf renaming, organising and its highlight and note taking tools in the reader.
The Elsevier account integration is disgusting though, and I hate the idea of using all Elsevier product.
I use zotfile extension to automatically rename files in Zotero
What do you like about organization in Mendeley?
What does AI assisted reading mean to you?
Those "chat with a PDF" apps get me halfway there, but I'm more imagining something that can explain certain terms in the context of the paper, or automatically dive into the citations and pull explanations from them too.
Readwise Reader has a nice pdf reader with highlighting, notes, and an AI reader tool. I organize sources using tags. It's very new and in active development. Academic research is not it's main focus, though, so it probably won't add mindblowing academic tools. (like citation support/ backlinks. although it does have internet backlinks that tell you want articles link to the one you're reading)
Readwise Reader is a poor PDF reader, unfortunately. Where it shines is making readable text documents out of PDFs, so it depends on the type that you’re reading.
I use Zotero with a bunch of useful Addons. Currently, scite is best available tool for research papers (at least in my field).
pdf-tools [1] + org-ref [2] in Emacs.
Paperpile is fantastic and you can make a shared folder with your lab/team.
I use a combination of Zotero, Locally Linked PDFs/Folder Structure, and SumatraPDFs (Comments etc.):
folders:
- for every literature search, create a folder with date and name
- e.g. 2024-03-21_Quantum_Entanglement
- use CTRL-SHIFT-DRAG to drop files into Zotero as Links, see [#77](https://github.com/zotero/zotero/issues/77)
- You _can_ organize in Zotero, but you don't have to. Files can be linked
to multiple Zotero folders (simply copy library entries in Zotero)
- sync literature folder and zotero database with nextcloud to somewhere, for backup
zotero:
- disable sync
- set “Base directory” (Preferences > Advanced > Files and Folders) to local literature folder
- set PDF View to “System default” (Preferences > General > “Open PDFs using..”)
- Enable recursive quick search in folders: go to Preferences > Advanced > Config Editor, search for `recursiveCollections`, double click (set to True)
- use CTRL-Shift-C to copy bibliography to clipboard
- Dark Theme:
- https://github.com/Rosmaninho/Zotero-Dark-Theme
- Go to `%AppData%\Zotero\Zotero\Profiles\` (`XXXXXXXX.default`)
- Create `chrome` folder
- Place the `userChrome.css`
- Start Zotero
- Add-Ons:
- zotero-pdfkit
- https://github.com/sharpevo/zotero-pdfkit/
- allows to modify/select a “default” PDF attachment to be opened
- ZoteroDuplicatesMerger
- https://github.com/frangoud/ZoteroDuplicatesMerger
- easier merging of duplicates
- zotero-folder-import
- https://github.com/retorquere/zotero-folder-import
- bulk import PDFs from a folder
- zotero-tag
- https://github.com/windingwind/zotero-tag
- allows to add stars to items (Num Key `1`, `2`, `3` etc.)
- PDF Tools:
- qpdf
- removing passwords, unlocking PDFs, conversion
- install in WSL with `apt-get install qpdf`
- remove password with `qpdf --decrypt --password="" input.pdf output.pdf`
- `SumatraPDF`
- _Really_ fast Viewing of PDFs and adding annotations (highlight, comment etc.)
- Highlight Text: `A`, Save to file: `CTRL+SHIFT+S`
- it is much faster than Adobe Acrobat
- [pdfplumber](https://github.com/jsvine/pdfplumber)
- Awesome python package to extract tables from PDFs into data pipelines. Use with Jupyter Lab.
- [PDF X-Change viewer](https://www.tracker-software.com/product/pdf-xchange-editor), `choco install pdfxchangeviewer`
- for manual OCR of pages/PDFsThat's nice and all, but google scholar recently removed all the 'cited by' 'related articles' and other links from the HTML pages of google scholar. It was like this for about two months before they restored the functionality. It likely they will remove it again soon. Google scholar is getting worse, not better. The google devs have no idea what a typical academic's computer is like around the world. They dev for their lived experience and it's just not applicable. A javascript (slow, computationally expensive) pdf reader is just another aspect of this ignorance.
Are you sure this actually happened? I never noticed this. can anyone else collaborate? Maybe you installed some extension that messed with the html
Yes, I confirmed it with 3 other people on IRC a couple months ago. I didn't know google scholar had restored it until I checked right before I wrote the above post. I thought the links were still gone. They had been the last time I'd used google scholar about 3 weeks ago. Back then I also confirmed it myself first using 3 different computers, 4 browsers (with JS disabled), coming from 3 different IP addresses, both logged in to google and logged out. I probably wouldn't have started writing the post at all if I didn't think they were still gone.
I figure in addition to the feedback they received from me (and presumably others) at the time they saw a drop in usage and restored the functional version. But they'll try again.
I think you are wrong - I don't recall seeing this. Screenshots of scholar on twitter from feb, jan, dec all show those links
Check at 2024 Feb 08 09:54:00 (am) CST. I definitely didn't confabulate the memory because the initial conversation about it (with others) is in my IRC logs. Sorry I don't have any screenshots of my own. Perhaps it was A/B testing or something.
I couldn’t agree more, I dont want you displaying the pdf, let me download the file and view it with zathura
Or Sioyek (vim keybindings!), Okular, Xournalpp, Zotero, ...
Alongside this, I have found that Google Scholar's search has become noticeably worse in the last year or so. I can search for an author's name and a few keywords from a paper title and it won't show up, even if the paper has like 5000 citations.
Wow so I am not going mad! I had the same experience and it almost feels like Google is trying to recommend me papers based on my past searches. I hope they revert to their earlier algorithm
Check out https://openalex.org
I'm pretty optimistic that by the time google scholar really goes to shit they'll be good enough to pick up the slack.
What are the base hardware requirements for a JavaScript PDF reader where it isn't "slow"?
A js pdf reader they control has monetization possibilities. Slip in an interstitial page for Naturally Fun Arkansas with an article from Nature. You don't want scholar going the way of reader do you?
Already counting the days until this inevitably gets killed. I've been burned too many times to rely on Google for anything, except tracking me and pushing ads, which they indeed do better every day.
This was promising, but they announced the sunset of this yesterday. The news hasn't propagated yet.
Where did you see the announcement they sunset it?
In an effort to accelerate the development life-cycle, Google will now release sunset announcements before the product release.
I saw that announcement, but I thought they changed their mind about a week before it was announced?
They're sunsetting the sunset?
Scholar is heavily used internally, it’s unlikely to be discontinued even if it has never brought any money to Google.
Google Reader and RSS feeds were also heavily used internally :(
What replaced it - Google Wave ???.
This is about a PDF reader though, not Google Scholar itself.
I wonder if their real intent is to gather training data on which parts of papers are considered important by readers, and which topics are related to each other.
Capturing and visualizing research knowledge is personally an exciting space. I feel that deep reading and absorbing content continues to be challenging, due to the ever-increasing amount of published research, rudimentary reading apps (Google PDF reader finally addressing issue with easily looking up references), and due to somewhat disconnected tools for reading and note-taking. Similar to the readers piggy-backing on the PDFjs library, I've developed an app that helps me capture and organize personal research knowledge [1]. Additionally, visualizations and customizable contexts for notes help to recall and link information.
Zotero does a good job at it, doesn't it?
As a daily Zotero user, not really. The nicest thing I can say about it is, it has plugins and is FOSS. Maybe the new 7.0 release will blow me away, but I've been waiting for it to get out of beta forever.
More fundamentally, we need to stop disseminating scholarly work as PDFs, a format primarily designed for print. Plain HTML would be an improvement. Even better than HTML would be an extended variant with scholarly-specific semantic markup and universal, animated, explorable figures. Embedded notebooks would be cool, too, but disseminating data would still be a major challenge. (And I don't just mean storage/transfer; a lot of researchers are reluctant to share source data to the world.)
So I'm a researcher that almost always uses pdfs... Does HTML have the reproducibility that PDF promises? My feeling is that if I store a PDF, it'll look the same in a decade. But is HTML the same way? It seems like it relies on the web browser and many other things... How would one manage things like images and gifs? Is there a way to keep everything into one HTML file that's easily shareable and feels secure?
I'd like to see PDFs move to Computational Notebooks. One can dream.
The potential to freeze an HTML page in time with minimal changes at render time is already there. [0] Such an ability can even be baked directly into the rendered HTML page so the viewer would be able to download a copy of the page as it is seen at a given time. Other archiving facilities, such as archive.org, take static snapshots of accessible pages if allowed by the publisher of the page and requested by anyone who wants to make that snapshot.
My point is that it is possible to achieve in principle and in practice, albeit that might be practiced as often as one would like to see.
-------
[0] See SingleFile by gildas at https://addons.mozilla.org/en-US/firefox/addon/single-file/: “Save an entire web page—including images and styling—as a single HTML file.”
Machines and humans can both easily use HTML/XML. Extracting information from PDF’s is so much harder that there’s deep learning products dedicated to doing it. They still make mistakes, too.
I’d much rather have something akin to the CHM files where everything I need is in one file, easy to analyze, and has good readers.
I explored tools to export/interchange PDF to HTML in the KnowledgeGarden app, but the results were not optimal, suffering from non-standard layout and poor typesetting of equations. Publishers of scholarly articles generate web pages of papers, but they're not replicas of PDF files.
Re. self-contained HTML (and slightly off-topic), look at TiddlyWiki, which contains data/code/layout all in one interactive, local or hosted HTML. Extensibility, plugins, and community of contributors are some key highlights, among others.
As a daily Zotero user, not really. The nicest thing I can say about it is, it has plugins and is FOSS. Maybe the new 7.0 release will blow me away, but I've been waiting for it to get out of beta forever.
Can you elaborate where you think Zotero drops the ball?
For me, reading papers requires deep focus. I have to have it physically printed out if I'm going to really read the whole thing.
I suggest you try new devices to read papers. Often the perception that paper is a better support is due to a lack of more convenient devices. Paper is better than a 15'' screen for sure, for many reasons including size and posture while reading. But have you tried larger screens (> 27''), large tablets (>= A4) or as large as possible E-Ink readers? Depending on your preferences, you might find that some of these work actually better than paper also for you :-)
There is no way I can perceive reading on an expensive device as more comfortable than paper. Paper is fairly cheap, lightweight and resilient; I can carry it around, fold it, toss it aside, sit on it by accident while thinking, annotate it with scribbles, and pour coffee on it with aplomb and finesse. I can flip it, half-tear it in anger, drool on it when I reach my brain capacity. I can take it hiking with me without fear of breaking or losing it. In other words, paper is a tool that gets out of my way.
I did try all the devices you listed above, even had my department pay serious money, and ended up barely using them for all those reasons. I am a mathematician, I am clumsy and I want to focus on my problem-solving; I want to think, and babysitting devices and tools is not what I want to spend my brainspace on.
"But did you think about the environment? Why don't you by a new device every 2 years with Lithium battery and full of non recyclable plastic in it"
... is what I get told all the time.
With the typical reading volume of an academic and the amount of plastic in my toner cartridges, I'm not sure paper comes out ahead in that comparison.
A high yield toner cartridge can print between 3000 and 8000 pages of text [1]. Average number of pages in a scientific manuscript is 10 [2]. This means that it would take 300 to 800 printed scientific papers to deplete one cartridge. I would have to assume that a single toner cart is not the same amount of waste as a reading device just due to the recyclability of toner carts, but it is up to you how to count them. If I was going to pull a number out of my ass, I would say 10 carts would be equal to one reading device with battery. Let's go low-end and pick 300 papers, which means you would need to print 3000 full scientific manuscripts to equal the waste of one reading device. How many do you read in two years?
[1] https://www.brother-usa.com/supplies/ink-and-toner#sort=rele...
In my experience those people don't even talk about ink, it's all about paper. They must think that you get just a few sheets of paper for a single tree or something like that, when in reality you get like 10 000 sheets of paper for one averagish tree. And those trees are not rare or anything like that, and the process of making paper is nowhere near as bad as electronics industry. Using paper is as ecological as it gets.
Remarkable 2 tablet is very good for reading papers.
Can someone recommend an app for ipad that can read PDFs? I want to be able to bookmark using my browser but read it on my ipad. Sort of like "Save to pocket" extension.
> bookmark using my browser but read it on my ipad
MacOS and iPad: DevonThink paid app with sync via P2P, WebDAV or cloud services.
Optional local mirror/sync of web pages and PDFs, with full text search.
I use Readdle Documents to sync PDF folders with my server PC via FTP. Free version supports PDF highlighting & simple annotations, basic file management, and automatically syncs back everything.
Zotero w/ their first-party storage is the best I've found.
Square icon with up arrow sticking out of it -> Save to books.
It seems to work in MacOS and iOS; an iCloud account is probably required.
Primarily I've been using Zotero and Notability. They each have "save to" on mobile. Zotero has a chrome plugin that requires the desktop app to be running. They both optionally support a dark mode for reading in the dark.
I like the experience of reading in Muse.app on the iPad. It's a nested whiteboarding thing, but also can act as a PDF reader. (It'll let you pull out chunks of the PDF and put it on your canvas with a link back into your document, if that fits your flow.) I often read on my phone, so this is not an option for me.
Apple Notes and Muse slow down with a lot of ink. For taking a page full of notes I'm using Notability.
I've heard good things about GoodReader, but haven't played with it in years.
In theory the built in files app will work for this. However, I like goodnotes, which has good highlighting snd library support. I’ve used it since grad school for reading papers.
I really like PDF Expert for this. It's free. They have a subscription for some editing/advanced features, which I haven't tried.
https://apps.apple.com/us/app/pdf-expert-editor-reader/id743...
Looks great, but can you imagine Google pulling the rug under an academic's document/citation database?
I don't even want to imagine having to migrate all annotations and citations to something else when they inevitably pull the plug on it some years down the road.
Huh? This tool just parses PDFs, it doesn't require academics to actually do anything.
Hm, I got the impression they store notes and annotations to your Google account, but maybe I'm mistaken.
The Chrome Web Store page doesn't say anything about annotations.
I've never seen so many light/dark modes before. There's Device Mode, Light Mode, Dark Mode, and Night Mode. AFAICT Device Mode follows the browser/device's current setting, Dark Mode makes the sidebar dark but doesn't change the PDF, and Night Mode darkens both the sidebar and the PDF. I wonder how they decided to have so many modes?
I’ve seen other apps that have Systen, Light, Dark, and “Very Datk” for OLED devices, so it isn’t out of the question
Did you put "Very Datk" in quotes because it was spelled like that where you saw it? Or is it just "Very Dark" and it's quotes because it doesn't fully imply what you get?
Automatically applying dark mode to documents tends to have poor results, especially when images are involved, but some people are masochists and/or can't be bothered to turn on the light, so they made a separate setting for them. Although I think a toggle would be better instead of dark mode/night mode.
Ha ha lol. Is that really the best they can think of in an age of AI? Instead of turning PDFs into web pages how about some actually useful tools:
* Summarisation
* Succinctly placing the research in context of the broader field
* Highlighting limitations or flaws in research methods, etc.
* An outline view to summarise each paragraph/section and then drill down into the ones you actually want to read in more detail
* Rephrasing into plain English. A lot of academics enjoy sounding clever and usling long words so it'd be nice to be able to switch off "ego mode" and just read stuff in plain English instead of having to wade through their word-soup.
With more effort maybe Google could create a PDF reader that is actually innovative.
The friends I have in academia say that their PhD professors tell them to use "ego mode" or papers won't pass review and be accepted. I'm with you though. And it's not about specific jargon of a field, it's just wankery. Most lawyers do the same thing and you need to get extremely good ones to write good contracts in clear language.
"Sounding smarter through obscurity"
Yeah I'm sure that's true. It'd be nice to be able to opt out though while you're in the first pass research phase.
Does anyone know of a library (or reading material) that can render a pdf (mostly architectural drawings) on to webgl canvas as actual vectors not image?
Not sure if that's what you are looking for but mupdf can render to SVG.
WebGL is inherently a vector-to-raster technology, it’s always backed by a pixel buffer. One might argue that even PDFjs works this way with its calls to the canvas API.
What are you trying to do? Why is webgl the key here?
When can we have a PDF reader where we can hover over a symbol and see its definition?
What kind of symbol?
Hmm, nice to have direct links to references. But the PDF rendering itself seems not as good as the native renderer.
Just tried it and didn't notice any significant differences in PDF rendering myself. Do you have any concrete examples?
I just wish Google Scholar would be a bit more open in terms of debugging why a site isn't picked up by the platform
I would also be interested to know how they decide to pick up a site. I was very surprised to learn that a technical note posted only to my website was picked up somehow. (I am a mathematician and so there are other things on my site, but it’s some custom static site generator thing and I’m still astounded).
Can someone recommend lightweight alternatives to Paperpile or EndNote that have two essential features: 1. Rename a PDF file to a consistent (Author Year Journal) format. 2. Online sync (Mac, iOS and web access) - including via say iCloud or Dropbox.
Maybe this just needs a script? I just paid $100 for EndNote 21 yesterday and don’t think these needs justify that cost.
Maybe try Zotero[1]. There are many addons which can do what you need.
Has anyone tried installing this? It says "PDFs on all sites will have a new look in Chrome."
This makes me nervous. I'm often looking at PDFs that are embedded in a page (either grad school software for commenting on PDFs, or publishers' sites). Is it going to play nicely with those? Is this only for navigating directly to a PDF?
My guess (as someone whose company makes a PDF extension for Chrome) is that it may intercept embedded PDFs as well. Sometimes sites use iframes or the like, and those get intercepted. But if the PDF is displayed through some sort of third party tool then it would be unaffected. Just my 2¢!
Scholar PDF Reader is available as a Chrome browser extension
So it's a closed ecosystem for now ... pass.
Now all they need is a way to grab documents from SciHub..
I use a tool called Scholars
Let you import and read PDF directly, annotate, comment and share with people.
I use an extension called histre, https://histre.com/ for annotation and keeping up with _notes_ / _thoughts_ inline. I found that using tools like Fermat's Library, which provides side bar annotation, histre for inline highlight, annotation and multi-references, and ChatGPT to understand complex terms, all helped with understand recent papers. Even a medical journal paper, https://senthil.learntosolveit.com/posts/2023/10/21/medical-... for me, in one instance.
Zotero is the one I use but found this one useful too: https://synthical.com/
"..have long loved PDFs" not.
It is really nice to see google scholar get some attention. It is essential for a lot of academics and it would be horrible if google "sunset"ed it.
You can focus on absorbing the scholarship – the format is simple and clean.
Unless you need to scroll left and right on your phone instead of absorbing
So I guess this a way for Google to gather (more/fine-grain) data on paper skimming/research interest?
Most important papers can be read with highlighting at https://www.semanticscholar.org/ (PDF Semantic Reader, skimming assist)
This looks great! Since they link it all to one's Gmail account, I wonder if they implement saving annotations to these PDFs and have them live on your Drive or elsewhere.
Edit: Also, Chrome now defaults to this extension for rendering any PDFs you load.
Alt+<- brings you back to where you were after clicking on a reference. You can skip around pretty easily to see the referenced object and this overlay does seem kinda interesting it’s not something crucial.
Zotero's V7 reader is great, built on pdfjs (Mozillas pdf reader) and adds neat things like notations and dark mode.
IIRC, pdfjs is used by Google also, and was based on Foxit? ? Does anyone know?
PDF.js came out of Mozilla, not Foxit.
Yes, but I think Mozilla may have started with code from Foxit.
The PDFium plugin that was part of Chrome was based on C++ code from Foxit.
PDFjs was written in JS from day one, and (as far as I know) was not based on any previous PDF reader.
Maybe that's what I was thinking of. Thanks.
BTW, I didn't mean they necessarily used the actual Foxit code, but it was a starting point maybe reimplemented in JS.
In no sense is PDF.js related to Foxit except that they are both PDF readers.
Where are you accessing Zotero V7? My understanding is that it is currently V6.[1]
[1] https://www.zotero.org/download/
https://www.zotero.org/support/beta_builds
Thanks! I'll try it out
I love zotero. The combination of annotation, highlights, document management and a healthy plug-in ecosystem are just killer for me.
It feels a bit dated sometimes, but I'm yet to find anything that comes close.
It looks a lot nicer after the recent design update!
is it possible to point Zotero to a local dir with papers, or am I forced to import documents into it?
I use Zotero and really like it, especially when working with others. This was the first thing that came into my mind on this thread.
Sioyek is a PDF viewer designed exactly for reading research papers and textbooks: https://github.com/ahrm/sioyek.
Sioyek seems awesome, especially vim inspired features. Too bad u (undo) doesn't work and there doesn't seem to be a way to undo. Am I missing something or is it laking it?
I found this related issue: https://github.com/ahrm/sioyek/issues/633
Improved over that https://github.com/ahrm/sioyek/issues/1011
looks cool
Same question but for MacOS. There don't seem to be many good ones for it.
Try Skim
Unfortunately, Preview has been the best reader in my experience. I say "unfortunately" not because it is inherently bad, but because it is a sad state of affairs when nobody can build something better than the barebones native tool
Just found this one I hadn't seen before, free version may suffice: https://highlightsapp.net/
I am interested in knowing why and how Google Chrome is not enough?
Mostly too slow for a lot of content, not every content is supported, not easy to keep it open at the right page, no comments, not easy to find the right tab, etc.
ive always used SumatraPDF because its super fast and free
Just so you know: normally it scroll down so that the reference is on top of the page.
But most importantly.. ALT+'left arrow' allows you to go back before you clicked on the citation! It doesn't work all the time, but usually it does after some left arrows ;)
Also, in Android: you can click on the 'scrolling sign' on the right of the pdf and specify the page, or see the link to 'jump back' to before you clicked on a link!
I hope that will help
I've been using Sumatra PDF on Windows to read papers (and as my default PDF reader) for more than a decade. Clicking on a citation takes you to the bibliography page and lands the cited paper at the top of the screen. Then Alt-leftarrow brings you back.
What you might consider if finding an ebook reader app and using that. I had a similar issue but on Android (for ebooks not in kindle format). I ended up with Librera but there are several. Turns out it's also equally great at academic or work PDFs.
Jumping back works in SumatraPDF (backspace).
STDU Viewer might also be worth looking into. Default shortcut for jumping back is ctrl+z.
SumatraPDF if you want speed above all else
DrawboardPDF if you want something more full featured and like to annotate, highlight, bookmark and whatnot, particularly if there's any chance you'll also use a stylus
Irrespective of the OS, I recommend Zotero (https://www.zotero.org/).
Okular. You don’t need the rest of KDE. It has a Windows installer and I think it‘s also in the Windows Store.
Mozilla Firefox has put a lot of time into their PDF reader.
https://www.mozilla.org/firefox/browsers/
Zotero!