Multispectral tracing in densely labeled mouse brain with nTracer

Douglas H Roossien; Benjamin V Sadis; Yan Yan; John M Webb; Lia Y Min; Aslan S Dizaji; Luke J Bogart; Cristina Mazuski; Robert S Huth; Johanna S Stecher; Sriakhila Akula; Fred Shen; Ye Li; Tingxin Xiao; Madeleine Vandenbrink; Jeff W Lichtman; Takao K Hensch; Erik D Herzog; Dawen Cai

doi:10.1093/bioinformatics/btz084

Multispectral tracing in densely labeled mouse brain with nTracer

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

Authors

Douglas H Roossien¹, Benjamin V Sadis¹, Yan Yan¹, John M Webb², Lia Y Min^{1

3

4}, Aslan S Dizaji¹, Luke J Bogart⁵, Cristina Mazuski², Robert S Huth¹, Johanna S Stecher¹, Sriakhila Akula¹, Fred Shen¹, Ye Li¹, Tingxin Xiao⁶, Madeleine Vandenbrink¹, Jeff W Lichtman^{7

8}, Takao K Hensch^{5

7

8}, Erik D Herzog², Dawen Cai¹

Affiliations

¹ Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA.
² Department of Biology, Washington University in St. Louis, St. Louis, MO, USA.
³ Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
⁴ School of Art and Design, University of Michigan, Ann Arbor, MI, USA.
⁵ Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
⁶ Department of Biology, University of Toronto, Toronto, ON, Canada.
⁷ Department of Molecular and Cellular Biology Cambridge, MA, USA.
⁸ Center for Brain Science, Harvard University, Cambridge, MA, USA.

Abstract

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 https://www.cai-lab.org/ntracer-tutorial.

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*

Abstract

Publication types

MeSH terms

Grants and funding