Multispectral tracing in densely labeled mouse brain with nTracer

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 I...

Descripción completa

Detalles Bibliográficos
Autores principales: Roossien, Douglas H, Sadis, Benjamin V, Yan, Yan, Webb, John M, Min, Lia Y, Dizaji, Aslan S, Bogart, Luke J, Mazuski, Cristina, Huth, Robert S, Stecher, Johanna S, Akula, Sriakhila, Shen, Fred, Li, Ye, Xiao, Tingxin, Vandenbrink, Madeleine, Lichtman, Jeff W, Hensch, Takao K, Herzog, Erik D, Cai, Dawen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6748755/
https://www.ncbi.nlm.nih.gov/pubmed/30715234
http://dx.doi.org/10.1093/bioinformatics/btz084
_version_ 1783452144264806400
author Roossien, Douglas H
Sadis, Benjamin V
Yan, Yan
Webb, John M
Min, Lia Y
Dizaji, Aslan S
Bogart, Luke J
Mazuski, Cristina
Huth, Robert S
Stecher, Johanna S
Akula, Sriakhila
Shen, Fred
Li, Ye
Xiao, Tingxin
Vandenbrink, Madeleine
Lichtman, Jeff W
Hensch, Takao K
Herzog, Erik D
Cai, Dawen
author_facet Roossien, Douglas H
Sadis, Benjamin V
Yan, Yan
Webb, John M
Min, Lia Y
Dizaji, Aslan S
Bogart, Luke J
Mazuski, Cristina
Huth, Robert S
Stecher, Johanna S
Akula, Sriakhila
Shen, Fred
Li, Ye
Xiao, Tingxin
Vandenbrink, Madeleine
Lichtman, Jeff W
Hensch, Takao K
Herzog, Erik D
Cai, Dawen
author_sort Roossien, Douglas H
collection PubMed
description 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.
format Online
Article
Text
id pubmed-6748755
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-67487552019-09-23 Multispectral tracing in densely labeled mouse brain with nTracer Roossien, Douglas H Sadis, Benjamin V Yan, Yan Webb, John M Min, Lia Y Dizaji, Aslan S Bogart, Luke J Mazuski, Cristina Huth, Robert S Stecher, Johanna S Akula, Sriakhila Shen, Fred Li, Ye Xiao, Tingxin Vandenbrink, Madeleine Lichtman, Jeff W Hensch, Takao K Herzog, Erik D Cai, Dawen Bioinformatics Applications Notes 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. Oxford University Press 2019-09-15 2019-02-04 /pmc/articles/PMC6748755/ /pubmed/30715234 http://dx.doi.org/10.1093/bioinformatics/btz084 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Roossien, Douglas H
Sadis, Benjamin V
Yan, Yan
Webb, John M
Min, Lia Y
Dizaji, Aslan S
Bogart, Luke J
Mazuski, Cristina
Huth, Robert S
Stecher, Johanna S
Akula, Sriakhila
Shen, Fred
Li, Ye
Xiao, Tingxin
Vandenbrink, Madeleine
Lichtman, Jeff W
Hensch, Takao K
Herzog, Erik D
Cai, Dawen
Multispectral tracing in densely labeled mouse brain with nTracer
title Multispectral tracing in densely labeled mouse brain with nTracer
title_full Multispectral tracing in densely labeled mouse brain with nTracer
title_fullStr Multispectral tracing in densely labeled mouse brain with nTracer
title_full_unstemmed Multispectral tracing in densely labeled mouse brain with nTracer
title_short Multispectral tracing in densely labeled mouse brain with nTracer
title_sort multispectral tracing in densely labeled mouse brain with ntracer
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6748755/
https://www.ncbi.nlm.nih.gov/pubmed/30715234
http://dx.doi.org/10.1093/bioinformatics/btz084
work_keys_str_mv AT roossiendouglash multispectraltracingindenselylabeledmousebrainwithntracer
AT sadisbenjaminv multispectraltracingindenselylabeledmousebrainwithntracer
AT yanyan multispectraltracingindenselylabeledmousebrainwithntracer
AT webbjohnm multispectraltracingindenselylabeledmousebrainwithntracer
AT minliay multispectraltracingindenselylabeledmousebrainwithntracer
AT dizajiaslans multispectraltracingindenselylabeledmousebrainwithntracer
AT bogartlukej multispectraltracingindenselylabeledmousebrainwithntracer
AT mazuskicristina multispectraltracingindenselylabeledmousebrainwithntracer
AT huthroberts multispectraltracingindenselylabeledmousebrainwithntracer
AT stecherjohannas multispectraltracingindenselylabeledmousebrainwithntracer
AT akulasriakhila multispectraltracingindenselylabeledmousebrainwithntracer
AT shenfred multispectraltracingindenselylabeledmousebrainwithntracer
AT liye multispectraltracingindenselylabeledmousebrainwithntracer
AT xiaotingxin multispectraltracingindenselylabeledmousebrainwithntracer
AT vandenbrinkmadeleine multispectraltracingindenselylabeledmousebrainwithntracer
AT lichtmanjeffw multispectraltracingindenselylabeledmousebrainwithntracer
AT henschtakaok multispectraltracingindenselylabeledmousebrainwithntracer
AT herzogerikd multispectraltracingindenselylabeledmousebrainwithntracer
AT caidawen multispectraltracingindenselylabeledmousebrainwithntracer

Ejemplares similares