Help! Wrong note/excerpt order in 2-column documents

Hello.
While working with PDF documents in which text is organized into 2 columns, MarginNote does not seem to recognize that text in the right column is read after text in the left column. As a result, notes (document mode) and excerpts (mind map mode) are not sequenced properly according to how concepts were presented in the source PDF. Rather, they are sequenced according to their distance from the top of the page. As an example, a note/excerpt from the top of the right column will always be positioned ABOVE a note/excerpt from the bottom of the left column even though all text in the right column is read after that in the left column.

Other PDF reading applications correctly recognize that text in the left column precedes that in the right column and can present annotations and highlighted passages in the correct order. Is there a setting/fix for this in MarginNote or will I always have to rearrange excerpts manually in the mind map/outline if I want them to follow the same sequence of ideas as in the source article? There does not seem to be any way of doing this with notes in document mode.

Definitely an unexpected and major limitation, as pretty much every source PDF I need to work with is organized into 2 columns of text

Hello

Hello, I seem to understand what you are saying. But could you please add some screenshots, also you mentioned that there are PDF viewers that can solve this problem, could you provide some comparison screenshots? Thankfully, this allows us to identify specific shortcomings.

Kind Regards,
MarginNote-Edward
Support Team

Sure - see attached images from MarginNote and PDF Expert. The same passages have been highlighted by each app, but the order of the notes in the right-hand outline/pane is different and NOT consecutive in MarginNote despite selecting “page order”. PDF Expert shows the notes in the correct consecutive order.

I have found that notes will be in the correct order as long as each consecutive highlight comes from a later part of the source document - in other words, the notes appear in the order in which the user highlighted/excerpted them. BUT as soon as you need to go back and highlight something from an earlier point of the document, the order falls apart. For example, if the most recent highlight/excerpt in the images below was the passage at the top of the left column (“Electromyography was performed…), MarginNote would put it last in the note order. Other times it seems to order the notes according to how far down the page they are, disregarding the fact that all the text in the left column comes before all the text in the right column. PDF Expert, by contrast, will put it first, where it actually belongs because it appears earlier in the article than any other highlighted passage. Regardless of how and when you highlight any given passage, PDF Expert will always rearrange your notes in the annotations pane to honor their sequence in the original article.

I assume this is some kind of PDF parsing problem. I thought MarginNote would have a command that sorts all notes appropriately, but if so I can’t find it beyond the “page order” command. If you never need to go back and excerpt an earlier passage this may not be a problem for you, but I read a lot of dense and long scientific articles and this is often necessary. I also prefer to work in Outline view, and this behavior of the app means many excerpts are presented in the wrong order relative to the source article, making it difficult to simply refer to the outline for review purposes.

Hello

Thanks for the screenshot, we'll look into it. Because of the lack of previous cases like this, Marginnote defaults to sorting notes in the order in which they were extracted by the user. We'll keep an eye out for similar use cases.

Kind Regards,
MarginNote-Edward
Support Team

Thank you. I would think most users would like the default behavior to be ordering the notes as they are presented in the source article.