Prerequisites:

• a directory with image files, for example in ppm format, one for each page (use “pdfimages file.pdf directory/” if you have one multipage PDF), names sorted in the right order
• tesseract-ocr version 4. It is available in Debian Sid and in stretch-backports. The version 3 is much less accurate
• language packages for tesseract, for example tesseract-ocr-eng (English) and tesseract-ocr-ces (Czech)
• imagemagick, pdftk, poppler-utils, parallel (beware, there is “parallel” program in moreutils package, and this one is different)

First, create individual PDFs out of these images.

for f in *.ppm; do echo "convert -level 25,95% -quality 70 -density 300 -compress jpeg $f ${f%ppm}pdf"; done | parallel

• adjust “level” to match your scanner. The goal is to have black black and white white.
• adjust “density” to your scanner DPI

Next, run OCR engine on the original files and create PDFs with text layer only:

export OMP_THREAD_LIMIT=1
for f in *.ppm; do echo "tesseract -c textonly_pdf=1 --oem 1 --dpi 300 -l eng $f $f pdf"; done | parallel

• adjust “dpi” to your scanner DPI
• “l” is language, e.g. eng, ces or deu
• “pkill -f -USR1 parallel” to get the progress

Now, merge the image layer and the text layer

for f in *.ppm; do echo "pdftk $f.pdf background ${f%.ppm}.pdf output combined-${f%.ppm}.pdf"; done | parallel

And finally merge all the generated pages into one big PDF

pdfunite combined*.pdf output.pdf