BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes

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Whole-brain fluorescence images require several stages of computational processing to fully reveal the neuron morphology and connectivity information they contain. However, these computational tools are rarely part of an integrated pipeline. Here we present BrainLine, an open-source pipeline that in...

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Detalles Bibliográficos
Autores principales: Athey, Thomas L., Wright, Matthew A., Pavlovic, Marija, Chandrashekhar, Vikram, Deisseroth, Karl, Miller, Michael I., Vogelstein, Joshua T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10002688/
https://www.ncbi.nlm.nih.gov/pubmed/36909631
http://dx.doi.org/10.1101/2023.02.28.530429
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author Athey, Thomas L.
Wright, Matthew A.
Pavlovic, Marija
Chandrashekhar, Vikram
Deisseroth, Karl
Miller, Michael I.
Vogelstein, Joshua T.
author_facet Athey, Thomas L.
Wright, Matthew A.
Pavlovic, Marija
Chandrashekhar, Vikram
Deisseroth, Karl
Miller, Michael I.
Vogelstein, Joshua T.
author_sort Athey, Thomas L.
collection PubMed
description Whole-brain fluorescence images require several stages of computational processing to fully reveal the neuron morphology and connectivity information they contain. However, these computational tools are rarely part of an integrated pipeline. Here we present BrainLine, an open-source pipeline that interfaces with existing software to provide registration, axon segmentation, soma detection, visualization and analysis of results. By implementing a feedback based training paradigm with BrainLine, we were able to use a single learning algorithm to accurately process a diverse set of whole-brain images generated by light-sheet microscopy. BrainLine is available as part of our Python package brainlit: http://brainlit.neurodata.io/.
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spelling pubmed-100026882023-03-11 BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes Athey, Thomas L. Wright, Matthew A. Pavlovic, Marija Chandrashekhar, Vikram Deisseroth, Karl Miller, Michael I. Vogelstein, Joshua T. bioRxiv Article Whole-brain fluorescence images require several stages of computational processing to fully reveal the neuron morphology and connectivity information they contain. However, these computational tools are rarely part of an integrated pipeline. Here we present BrainLine, an open-source pipeline that interfaces with existing software to provide registration, axon segmentation, soma detection, visualization and analysis of results. By implementing a feedback based training paradigm with BrainLine, we were able to use a single learning algorithm to accurately process a diverse set of whole-brain images generated by light-sheet microscopy. BrainLine is available as part of our Python package brainlit: http://brainlit.neurodata.io/. Cold Spring Harbor Laboratory 2023-03-01 /pmc/articles/PMC10002688/ /pubmed/36909631 http://dx.doi.org/10.1101/2023.02.28.530429 Text en https://creativecommons.org/licenses/by-nd/4.0/This work is licensed under a Creative Commons Attribution-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, and only so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Athey, Thomas L.
Wright, Matthew A.
Pavlovic, Marija
Chandrashekhar, Vikram
Deisseroth, Karl
Miller, Michael I.
Vogelstein, Joshua T.
BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes
title BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes
title_full BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes
title_fullStr BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes
title_full_unstemmed BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes
title_short BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes
title_sort brainline: an open pipeline for connectivity analysis of heterogeneous whole-brain fluorescence volumes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10002688/
https://www.ncbi.nlm.nih.gov/pubmed/36909631
http://dx.doi.org/10.1101/2023.02.28.530429
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