BrainAligner: 3D registration atlases of Drosophila brains

Nat Methods. 2011 Jun;8(6):493-500. doi: 10.1038/nmeth.1602. Epub 2011 May 1.


Analyzing Drosophila melanogaster neural expression patterns in thousands of three-dimensional image stacks of individual brains requires registering them into a canonical framework based on a fiducial reference of neuropil morphology. Given a target brain labeled with predefined landmarks, the BrainAligner program automatically finds the corresponding landmarks in a subject brain and maps it to the coordinate system of the target brain via a deformable warp. Using a neuropil marker (the antibody nc82) as a reference of the brain morphology and a target brain that is itself a statistical average of data for 295 brains, we achieved a registration accuracy of 2 μm on average, permitting assessment of stereotypy, potential connectivity and functional mapping of the adult fruit fly brain. We used BrainAligner to generate an image pattern atlas of 2954 registered brains containing 470 different expression patterns that cover all the major compartments of the fly brain.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Animals
  • Animals, Genetically Modified
  • Brain / anatomy & histology*
  • Brain / metabolism
  • Drosophila Proteins / genetics
  • Drosophila melanogaster / anatomy & histology*
  • Drosophila melanogaster / genetics
  • Gene Expression
  • Green Fluorescent Proteins / genetics
  • Image Processing, Computer-Assisted / statistics & numerical data*
  • Neuropil / cytology
  • Recombinant Proteins / genetics
  • Software
  • Transcription Factors / genetics


  • Drosophila Proteins
  • GAL4 protein, Drosophila
  • Recombinant Proteins
  • Transcription Factors
  • enhanced green fluorescent protein
  • Green Fluorescent Proteins