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Upload your images to the Media Library and record the image IDs, or use Media Tags to tag the images. More options are described at http://ww.wp.xz.cn/plugins/wp-imageflow2/installation/

You can insert any shortcode into a template using the following enclosed in standard PHP tags:

echo do_shortcode('[shortcode option1="value1" option2="value2"]');

For WP Flow Plus with specific image IDs, insert something like this:

echo do_shortcode('[wp-flowplus include="100, 200"]');