I have a WLAN scanner Canon MX922. It has a document feeder on the top that can take multiple pages. The default Windows scanner application revert every other page. Installing the MX920 series MP Drivers and software from Canon solved the issue.

If the pages are scanned as JPEGs, they can be merged into PDF with ImageMagick:

convert "*.jpg" output.pdf

In PowerShell, to convert a set of images whose paths are copied from Explorer ("copy as path", the copied paths are on separate lines), means pressing control-V to paste the copied paths. They are on separate lines but are in the PowerShell array and PowerShell knows to join them by space when invoking convert.exe.

PS> convert @(<CTRL-V>) output.pdf

To avoid naming conflict with Windows builtin filesystem conversion tool (convert.exe), I renamed ImageMagick tool to convertimg.exe.

Note the Canon scan utility is able to output PDF directly. But I like separte images files since I like to feed in several multi-page documents at once, and I don't like to have them mixed into a single PDF.

If the images have their orientations adjusted in Windows File Explorer by setting EXIF info, the above command does not respect the orientation setting. Instead, use the below command:

convert "*.jpg" -auto-orient output.pdf

There is also a PDF utility command line tool called PDFtk, more specificaly PDFtk server. It's open source and seems to be of good quality and have a large user base. I might want to add it to my toolkit in the future, but for this scanning scenario, I don't need it yet.

Rotating every page in a PDF 90° counter-clockwise:

pdftk old.pdf cat 1-endwest output new.pdf

Extracting page(s) from a PDF document:

pdftk original.pdf cat <start_page>-<end_page> output new.pdf

Check out other pdftk examples.