Convert a research paper to Markdown to read, search, and quote its text in your notes. In MD Factory, add the PDF, choose an output folder, and click Convert. Keep the original PDF beside the result so you can check columns, figures, and equations.
Convert one paper first
- Open MD Factory and add the PDF you want to read.
- Choose a separate output folder for the converted files.
- Click Convert, then open the output folder.
- Open the Markdown in your editor with the PDF beside it.
MD Factory converts the document on your Windows PC and uses local OCR for scanned pages. It saves a Markdown file and exported images without changing the source PDF. Our PDF conversion guide covers scans and general cleanup.
Start with one typical paper. If your collection includes both simple reports and papers with two columns, check one of each before converting the rest.
Read across the column breaks
A PDF can store text in a different order from the page you see, as described in this PDF text extraction guide. A page that looks correct in a PDF viewer can still produce paragraphs in the wrong sequence when converted to text.
Pick a two-column page and follow a paragraph from the bottom of one column to the top of the next. Check that a caption, footnote, or page header has not slipped into the sentence. Move misplaced text only after finding its position in the PDF.
Keep figures and equations in context
Move or copy the whole document folder so its images stay with the Markdown. Check that the figures you need appear and that their captions describe the right image. Keep the PDF open when reading a graph, especially when small axis labels or a legend matter.
Check each equation against the original before using it. Pay attention to subscripts, superscripts, Greek letters, minus signs, and units. If a formula is unclear in Markdown, refer to the PDF page rather than reconstructing it from broken text.
For a result in a table, compare the column heading, row label, value, and unit together. A number copied accurately from the wrong row still changes the meaning.
Check references and quotations
Follow a citation you plan to use from its number in the paragraph to the reference entry. Check the author, title, and DOI or source link.
Compare a quotation with the PDF, including punctuation and any words split across lines. For scanned text, check names and symbols closely. Mark an unreadable passage in your notes instead of guessing what it says.
Add the paper to your research notes
Use a filename you can recognize, such as the lead author's name and a short title. In a note about a finding, record the paper title and the section or PDF page you checked. Keep your own comments separate from quoted text.
If you use an AI agent to compare papers, give it the checked Markdown and ask it to identify the source of each claim. Confirm its quotations and conclusions against the papers yourself. Our guide to preparing documents for AI agents explains how to organize the files.