The atlas was constructed from the average of eight individual co-registered MR image volumes of C57BL/6J mouse brain collected at postnatal day 0. The atlas space defined by multi animals captured the average geometry of native anatomical space for normal mouse brains at P0, avoiding possible anatomical outliers present in one animal. The label volume based on this average brain is consisted of 13 anatomic structures, which provides a template to facilitate feature-based registration. The probability maps for individual anatomical volumes were defined by the eight -registered MR images used to construct the atlas, which serve as references to map the atlas onto test images and to label the regions of interest of test images. The probability map with a restrictive threshold provides a more accurate mapping, while that with lower threshold labels an image more completely.

The atlas is comprised of:

  1. an image volume of the average brain.
  2. an anatomical label volume ( 13 structures)based on the average brain, and anatomical label volumes ( 13 structures ) retrieved from the probability maps at threshold of 62.5%, 75%, 87.5% and 100% confidences estimated from the population used to construct the atlas ( all structures here are smaller then the sizes of their corresponding average structures ). The names of the structures can be referenced from their intensities of the label volumes with the index table provided.
  3. probability maps for each of the 13 anatomical structures. The probability values in space were encoded with intensities.
  4. sub-volumes for each anatomical structure tessellated from anatomical label volumes described in 2 and as well retrieved from the probability maps with thresholds at 50% confidences. These are volumes with binary values 1 and 0.

There are a number of different applications that can be used to view the atlas. Here is a list of a few of them: