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Scientific articles --> Epub

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Hello,

I have read the sticky discussing conversion from PDF and after a couple of attempts have identified some of these issues. Currently, I am using Briss to cut up the pdf (since it is multi-columned), then acrobat pro to remove hidden text and finally Calibre to convert. After using the tweak feature I am able to generate a epub that I could live with (text wise). However, each article I would like to convert has figures which tend to be a combination of images and text. I have several questions I was hoping could be answered in regard to this conversion.

1) I realize PDF is less than ideal and in many cases I can download a 'complete' web page of the article. Is this a more ideal format to work with than pdf? If so could you put in the right direction to convert it to an epub?

2) Assuming PDF is the better option (seems unlikely), is there a way to generate the epub from a pdf (only the text I am interested in) and then manually insert the images within the text where I would like them to be anchored? Certainly this may not be the best order of operations, but hopefully you get the idea.

Thank you to anyone who offers their help.

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