MarginNote 3.7.x improves working with Pencil, mindmaps, etc

MarginNote recently updated the app to version 3.7.x with a reworking of the mindmap view, improved interaction on iPad with Apple Pencil, and other features. I do most notetaking with MarginNote on longer PDFs and ePUBs, and research libraries. I am glad to see the improvements in 3.7.x as MarginNote is an good choice for working with documents on iPads.

The strongest feature of MarginNote is the ability to create “notebooks” combining multiple PDF/ePUB documents and consolidate notes across all the documents in the notebook.


Thanks for the update and good reminder to back into this app. Previous role needed a lot of research and I was using both MarginNote and LiquidText, ultimately settled for MN. Glad to see MN keeps on adding features and improving.

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A dumb question about MarginNote: are the annotations ever saved down to the PDF file?

I know MarginNote has its own iCloud Drive folder, and any PDF I open in the app appears to get imported to that folder. When I open MarginNote as an app, it shows me those files, and opening them shows synced annotations from other devices as expected. However, if I add annotations in MarginNote, go to the iCloud Drive/MarginNote folder, and open those PDFs in other editors, the annotations are not there…

Not a dumb question at all. MN does not add annotations to the PDF or ePUB. The notes, links, highlights, scribble, etc., are in the database. (Not sure of the format; probably SQLite.) A PDF can be exported (for printing) with the annotations, but it is an image layer and not usable by standard PDF markup apps.

I usually export my notes in .mmap (MindManager) format, open that in MindNode then export the notes to one or more markdown files for use in Obsidian or elsewhere. The notes can optional have marginnote:// backlinks to the relevant page in the document in MN. If you have added images or scribble (images) to the document then MindNode will package the notes and images as .textbundle.


Thanks for the thorough, concise, and swift response!

I’m trying to decide how much it bothers me that I won’t be able to “see” those annotations—as part of the same file—from other apps. Otherwise, MN is quite compelling.

I saw on their forum that they’re aiming to release MarginNote 4 in 2021. That’ll probably make it harder to resist…

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You can export the document and annotations as a PDF, with the underlying document – and I just checked one of those exported documents to confirm that there is an OCR layer on it. The annotations and the document can be searched. So the major limitation of the exported PDF is that the annotations cannot be changed in another PDF program.


@anon41602260: Over time, do you find you keep annotations in MN per-document, in notebooks (of multiple documents), exported out via the MindNode process you mention above, or something else? Or does it depend on the use-case/project/whatever?

Sorry for all the questions! If you’ve described this elsewhere just say so—I can search. :wink: