larvalign: Aligning Gene Expression Patterns from the Larval Brain of Drosophila melanogaster

Neuroinformatics. 2018 Jan;16(1):65-80. doi: 10.1007/s12021-017-9349-6.

Abstract

The larval brain of the fruit fly Drosophila melanogaster is a small, tractable model system for neuroscience. Genes for fluorescent marker proteins can be expressed in defined, spatially restricted neuron populations. Here, we introduce the methods for 1) generating a standard template of the larval central nervous system (CNS), 2) spatial mapping of expression patterns from different larvae into a reference space defined by the standard template. We provide a manually annotated gold standard that serves for evaluation of the registration framework involved in template generation and mapping. A method for registration quality assessment enables the automatic detection of registration errors, and a semi-automatic registration method allows one to correct registrations, which is a prerequisite for a high-quality, curated database of expression patterns. All computational methods are available within the larvalign software package: https://github.com/larvalign/larvalign/releases/tag/v1.0.

Keywords: Drosophila melanogaster; Gene expression patterns; Image registration; Larval brain; Standard brain; elastix.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Brain / anatomy & histology
  • Brain / diagnostic imaging*
  • Brain / physiology*
  • Drosophila melanogaster
  • Gene Expression Regulation, Developmental*
  • Imaging, Three-Dimensional / methods*
  • Larva / anatomy & histology
  • Larva / genetics*