Annotation & Segmentation

Brainreg-segment

The brainreg-segment tool works alongside the brainreg tool, allowing for manual segmentation of regions/objects within the brain. Brainreg-segment will only work if the user registers their data with brainreg first.

Link to the tool

More information

  • RRID:SCR_023853
  • Software Type:data segmentation, data analysis
  • Modality:brain imaging
  • Allen Resource(s) Utilized:Allen Mouse Brain Atlas, Allen Human Brain Atlas
  • Author(s):Adam Tyson, Charlie Rosseau
  • Year Released:2023

Explore More Resources

Atlas Alignment Meter
Atlas Alignment Meter

The Atlas Alignment Meter is a tool based in Python which can measure the slice-to-slice jaggedness of a volumetric dataset, only in the form of an NRRD file.

Atlas Splitter
Atlas Splitter

The Atlas Splitter contains tools to split brain atlas regions and refine annotations accordingly, applicable to the Allen Mouse Brain Atlas.

SeBRe-Segmenting Brain Regions
SeBRe-Segmenting Brain Regions

SeBRe is a fully automated method for segmenting brain regions of interest. This is a Mask R-CNN-based toolbox created through deep learning.