The new iPad (3rd generation and above) has a Retina display of 2048 x 1536, giving a total of 3,145,728 pixels. If you wish to take full advantage of this display in your books there are a few things to consider:
Firstly, Apple require each image in an iBook to be no more than 2 million pixels and books with larger images have been rejected by the iBookstore. To meet this requirement Book Creator will ensure that images are never larger than 2 million pixels.
If you definitely want to use every pixel a workaround is to chop your 3.1 million pixel image into smaller images with each no larger than 2 million pixels. Then just line them up on the page.
We would recommend checking that the size of your final book is still acceptable with the larger images, and also bear in mind that the page turning of your book may not be as smooth due to iBooks having to load several large images from the iPad’s memory.
For more information also check out Liz Castro’s article: Retina Images in iBooks on iPad.