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Any suggestions on the best way to keep file size small but with high-resolution print quality? I am saving from Illustrator, some of the images are embedded instead of linked. I am not familiar with all of the compression settings. Also if images are linked, and I save as high-quality PDF, will I still need to include them when sending file to the printer?
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In a PDF images are always embedded even if they are linked inside the AI file.
If you want High resolution for print, file sizes will be large.
First of all, you need to stick to the printer's file specifications, presumably PDF/X. Ask them for the specifications.
Make sure your images are not of higher resolution than necessary for the print. Also use Photoshop to crop the images. Clipping masks will not do that.
If you are not saving as PDF/X for whatever reason, do not check the option that preserves Illustrator editability.
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Save as PDF/X. JPG compression, maximum image quality. Sampling down to 300ppi or as much as you need.
You'll receive a lightweight PDF, good for printing but not editable.