Skip to main content
Brain Knowledge Platform
Atlases
Our Research
Support
Search
Search
Brain Knowledge Platform
Atlases
Our Research
Support
Brain-map>Support>Community Tools>BREIN (Brain Region Expression Intensity Neuroanalysis)>BREIN (Brain Region Expression Intensity Neuroanalysis)
Processing, Registration, Integration

BREIN (Brain Region Expression Intensity Neuroanalysis)

Brain region Expression Intensity Neuroanalysis (BREIN) can be used to analyzes RNA in-situ hybridization or immunohistochemical images. It can register images to Allen reference atlas and calculates the signal intensity per brain region, and outputs a spreadsheet of the results.

Link to the tool | Relevant publication

‍More information

  • Software Type:data registration software
  • Modality:gene expression, connectivity, morphology, histology, neuroanatomy
  • Allen Resource(s) Utilized:Allen Mouse Brain Common Coordinate Framework, Allen Mouse Brain Reference Atlas
  • Author(s):Rebecca Refaee, Kif Liakath-Ali, Thomas Sudhof
  • Year Released:2025

Explore More Resources

MENGA: Multimodal Environment for Neuroimaging and Genomic Analysis
MENGA: Multimodal Environment for Neuroimaging and Genomic Analysis

MENGA is a platform for the integration of imaging data and Allen Human Brain Atlas mRNA data. MENGA investigates correlation patterns between various imaging modalities and gene expression profiles based on the Allen Brain Atlas.

Nutil
Nutil

Nutil is a data processing resource which simplifies and streamlines the pre-and-post processing of 2D brain image data from both the mouse and rat. To use Nutil, the user specifies the input and output parameters in the GUI.

Atlas Densities
Atlas Densities

AtlasDenities contains the tools to create the BBP Cell Atlas, using the Allen Mouse Brain Atlas and collected literature density values. It provides a list of volumetric files that provides cell type density estimates for each voxel.