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@nickq -- Welcome to the MR forums! It will really help to have your source PDF, or a enough of a sample of it, posted as an attachment. Then I can try some different parameters with it. If you don't want to post it, send me a private message. It sounds like your source PDF has a complicated and varying layout, and those sometimes need some tweaking. With scans that are not clean, sometimes the -de parameter is useful (sets the defect size).
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