LiquidText, Marginnote and similar

I’ve just discovered this forum while searching a way to smartly organize papers and idea for my engineering thesis for master’s degree. Today I use Joplin as general purpose note-taking but it lacks many linking feature for now. I found Liquidtext ( (Marginnote ( is similar but only for Apple ecosystem, not my case) and there are many nice ideas in it. You can create mind map with excerpt of multiple documents and immediately go back to the specific paper. But it lacks bibliographical feature like Zotero.
The major pro is that you can use also image excerpt that is impossible (right?) with Zotero and is important if you want put into the annotation an equation. I also saw that Margin Note support flash cards and it could be very useful for memory.

I’d like to know if you know those programs, what you think about, how you use them, if they are compatible with zettlekasten method and Obsidian. I think you could use Liquidtext and then export to obsidian but I don’t know.

LiquidText recently introduced a Windows version of their product.

I don’t know what “compatible with zettlekasten” means, since Zettlekasten is just a way of taking notes and keeping a running index. I do not recommend either LiquidText or MarginNote as the place where you would maintain a Zettelkasten collection of notes – both apps are designed for annotation and note taking using a PDF as the basis.

Neither app exports directly in markdown format. In both cases you need to do some intermediate step to get notes out of MarginNote or LiquidText and into an Obsidian vault or other destination. Doable, in each case, but moderately cumbersome.


I’ve been using MarginNote for quite a while and I love it!

There’s a very handy Copy note URL under the Edit menu. It will grab a unique URL to the corresponding excerpt, allowing you to create a link into any application (even Obsidian) that will bring you back to that very same excerpt.

I tend to use it whenever I’m quoting from a studied PDF into Obsidian.

That will work with any note in Study Mode (even the document ones).


That sounds nice, but can you actually click the link in obsidian so that the note opens in Margin Note?

Precisely. Just click and MarginNote will open the PDF on the corresponding page and note (it will work even if the note is only in the Document mode and not in a Study mind map).

Oh right that works well.
Now it would be nice to have MarginNote Plugins that would work well for obsidian users.


I’ve copied a link from MN3 into a page in my vault, but I can’t see how to make it live so I can click on it. Am I missing a step? Thanks!

Have you formatted like this:

[your text for the link](marginnote3app://note/588975B1-CA22-4CCC-BA66-BE09740BBA5A)

P.S. Of course this example above has a link to a note of my own and, therefore, will not work on your machine. You should change for the link to your note.

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I have tried a lot and finally found a way round using macro. If you are using Marginnote 3, you could chose to

  • export it into word document,
  • remove all hierarchal numbers or symbols
  • copy all the text from word document to Obsidian
  • Copy all the content again from obsidian
  • then use macro to replace a more readable format. For example, replace ### with - , #### with %Tab%- , etc.

    I wrote a macro with Keyboard Maestro to achieve, couldn’t down upload it, check the settings in the image if you are interested.

    If you don’t want to keep the title, just tweak a little bit in how many# you want to convert to -.



Thank you! I like this solution.

It would be really useful to have a feature in obsidian where you could directly link from a markdown file into a specific point in some media (an annotation or page in a PDF, a time in a video or audio).

@tallguyjenks may have a solution for this using Zotero