ABI Expression Data

Script to download expression data from the Allen Mouse Brain data portal ABI. This script will query the database, download available data, convert it from the raw/mhd format to NIfTI, and register it to a standard space (DSURQEC, as seen in the relevant mouse brain preprocessing article).

ABI Expression Data Package Releases

Current recommended release in bold typeface:

• ABI-expression-data-0.2.tar.xz [SHA512 checksum]

Citation Notice

Citation guidelines for use of the Allen mouse brain atlas can be found at: https://alleninstitute.org/legal/citation-policy/

Script mhd_utils_3d.py Author: bjian,Price Jackson Source: https://sites.google.com/site/pjmedphys/scripts (slightly adapted for compatibility with newer Python versions)

Usage

In order to create a new version of the ABI-expression data package, simply navigate to the root directory of this repository and run:

python abi_expression.py -v 0.5

This will create archives with the newest files fetched from upstream and processed according to the instructions standardized in this package. The version suffix will be 0.5 (as per the -v 0.5 parameter).