Difference Grids, version 2.0
Allen Institute for Brain Science
October 31, 2007

Requirements

- Brain Explorer, version 1.4.1
-Windows Installer: http://download.alleninstitute.org/sleep/DifferenceGrids/BrainExplorer/InstallBrainExplorer.exe
-Mac Installer: http://download.alleninstitute.org/sleep/DifferenceGrids/BrainExplorer/BrainExplorer.dmg

- In Brain Explorer, difference grids are designed for use with the JET colormap 

Navigation of Difference Grid Files

There are two ways to navigate difference grid files:
- Browse directories. Each folder is labeled with gene names and conditions used for spatial comparison of expression data. Each folder contains 2 files - the forward comparison (condition 1/condition 2) and the reverse comparison (condition 2/condition 1).
- Navigate using the Excel worksheet titled "Index to Difference Grid Files.xls". This file has direct links to difference grid files and original ISH data.

Documentation

A document describing generation of difference grids and recommended use is available in the Difference Grid folder at http://download.alleninstitute.org/sleep/DifferenceGrids/ titled "Visualization of changes in gene expression using Brain Explorer".

Known Issues

Difference Grids are not currently compatible with all features of Brain Explorer. 
- Direct links to ISH image data from the Brain Explorer program are disabled.
- Difference Grids cannot be searched directly from Brain Explorer Search window; difference grids are available only from the download.alleninstitute.org/sleep/ directory or through links in the excel worksheet
- Use data with caution; experimental artifacts may introduce noise in the data