Brainwide Genetic Sparse Cell Labeling to Illuminate the Morphology of Neurons and Glia with Cre-Dependent MORF Mice

Neuron. 2020 Oct 14;108(1):111-127.e6. doi: 10.1016/j.neuron.2020.07.019. Epub 2020 Aug 13.


Cajal recognized that the elaborate shape of neurons is fundamental to their function in the brain. However, there are no simple and generalizable genetic methods to study neuronal or glial cell morphology in the mammalian brain. Here, we describe four mouse lines conferring Cre-dependent sparse cell labeling based on mononucleotide repeat frameshift (MORF) as a stochastic translational switch. Notably, the optimized MORF3 mice, with a membrane-bound multivalent immunoreporter, confer Cre-dependent sparse and bright labeling of thousands of neurons, astrocytes, or microglia in each brain, revealing their intricate morphologies. MORF3 mice are compatible with imaging in tissue-cleared thick brain sections and with immuno-EM. An analysis of 151 MORF3-labeled developing retinal horizontal cells reveals novel morphological cell clusters and axonal maturation patterns. Our study demonstrates a conceptually novel, simple, generalizable, and scalable mouse genetic solution to sparsely label and illuminate the morphology of genetically defined neurons and glia in the mammalian brain.

Keywords: Cre; MORF; astrocyte; imaging; microglia; morphology; neuron; reconstruction; spaghetti monster; sparse labeling.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Video-Audio Media

MeSH terms

  • Animals
  • Astrocytes / metabolism
  • Astrocytes / pathology
  • Astrocytes / ultrastructure*
  • Brain / metabolism
  • Brain / pathology
  • Brain / ultrastructure*
  • Frameshift Mutation / genetics
  • Green Fluorescent Proteins / genetics
  • Integrases
  • Mice
  • Mice, Transgenic
  • Microglia / metabolism
  • Microglia / pathology
  • Microglia / ultrastructure*
  • Microsatellite Repeats / genetics
  • Neurons / metabolism
  • Neurons / pathology
  • Neurons / ultrastructure*
  • Retinal Horizontal Cells / metabolism
  • Retinal Horizontal Cells / pathology
  • Retinal Horizontal Cells / ultrastructure*


  • Green Fluorescent Proteins
  • Cre recombinase
  • Integrases