All video and image files in your collection will be indexed. Note that images and videos from compressed files (like .zip or .tar files) will not be extracted.
A note on S3 prefixes: all images and videos with the S3 prefix you specify when creating your collection will be indexed. Say you have a bucket with the following structure:
s3://my-bucket/videos/
s3://my-bucket/videos-test/
If you create a collection with the S3 URL s3://my-bucket/videos/, only the s3://my-bucket/videos/ will be indexed. If you create a collection with the S3 URL s3://my-bucket/videos, both s3://my-bucket/videos/ and s3://my-bucket/videos-test/ will be indexed, because they both start with s3://my-bucket/videos.