Processing, Registration, Integration

HERBS: Histological E-data Registration in Brain Space

HERBS facilitates the process of brain atlas image registration and image visualization through two and three dimensional visualization of brain atlas volume data, arbitrary slicing, and user defined data.

Link to the tool

More information

  • RRID:SCR_022776
  • Software Type:image registration, image visualization
  • Modality:neuroanatomy, histology
  • Allen Resource(s) Utilized:Allen Mouse Brain Atlas
  • Author(s):Jingyi G. Fuglstad
  • Year Released:2022

Explore More Resources

BREIN (Brain Region Expression Intensity Neuroanalysis)
BREIN (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.

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.