Researchers sometimes inquire whether we have a reference brain volume for juvenile mouse, analogous to the reference framework we have for adult P56 mouse (sometimes referred to as a common coordinate framework, and described in detail in the technical documentation for the Connectivity Atlas). We do not have an ‘average’ reference volume comprised of autofluorescent images, which is how the adult version was created, but we do have 2D reference sets that our gene expression data is registered to - and those are programmatically accessible through the Developing Mouse Brain API.
Example cases for using the reference atlas images and associated data include a Matlab script for download and use of the P4 mouse brain. If you have other examples you’ve developed, feel free to share them here!
I was able to use the example MATLAB code to correctly display the P4 mouse brain, but the data (atlas volumes on the download server: http://download.alleninstitute.org/informatics-archive/current-release/mouse_annotation/) from at least the P14 and P28 timepoints seem to be truncated (set to all zeroes) from a medial-lateral index of 302 to the end of the file. Can anyone else confimr that these data files are complete?
The data files are complete. These are all sections were successfully sectioned and imaged.
At that time, the criteria for data collection was for a set of 2D atlases with coarse z-sampling and serving for a registration template for sagittal data also from one hemisphere and hence it was sufficient to have one hemisphere less intact.