If you wish to execute custom PHP code in your invoice template (ie. have barcode render script added to the invoice) you can do so by adding smarty {php} tag to your invoice template source.

First you need to ensure your smarty have PHP handling enabled (read related article: Integrating templates - tips and tricks)

Then go to Settings → General Setting → Billing → Document Templates → Invoice customization and edit your current invoice template. Click on [HTML] button to edit source. 

Then you can add your php code within {php} {/php} smarty tags, as below:

 {php} echo "Invoice generated at: ".time(); {/php}