Multispectral tracing in densely labeled mouse brain with nTracer

Bioinformatics. 2019 Sep 15;35(18):3544-3546. doi: 10.1093/bioinformatics/btz084.


Summary: This note describes nTracer, an ImageJ plug-in for user-guided, semi-automated tracing of multispectral fluorescent tissue samples. This approach allows for rapid and accurate reconstruction of whole cell morphology of large neuronal populations in densely labeled brains.

Availability and implementation: nTracer was written as a plug-in for the open source image processing software ImageJ. The software, instructional documentation, tutorial videos, sample image and sample tracing results are available at

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

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

MeSH terms

  • Animals
  • Brain
  • Documentation
  • Image Processing, Computer-Assisted
  • Mice
  • Neurons
  • Software*