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Alveolus analysis: a web browser-based tool to analyze lung intravital microscopy
BACKGROUND: Acute lung injury and the acute respiratory distress syndrome are characterized by pulmonary inflammation, reduced endothelial barrier integrity and filling of the alveolar space with protein rich edema fluid and infiltrating leukocytes. Animal models are critical to uncovering the patho...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9759058/ https://www.ncbi.nlm.nih.gov/pubmed/36528564 http://dx.doi.org/10.1186/s12890-022-02274-7 |
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author | Politowicz, Alexander L. Burks, Andrew T. Dong, Yushen Htwe, Yu Maw Dudek, Steven M. Elisabeta Marai, G. Belvitch, Patrick |
author_facet | Politowicz, Alexander L. Burks, Andrew T. Dong, Yushen Htwe, Yu Maw Dudek, Steven M. Elisabeta Marai, G. Belvitch, Patrick |
author_sort | Politowicz, Alexander L. |
collection | PubMed |
description | BACKGROUND: Acute lung injury and the acute respiratory distress syndrome are characterized by pulmonary inflammation, reduced endothelial barrier integrity and filling of the alveolar space with protein rich edema fluid and infiltrating leukocytes. Animal models are critical to uncovering the pathologic mechanisms of this devastating syndrome. Intravital imaging of the intact lung via two-photon intravital microscopy has proven a valuable method to investigate lung injury in small rodent models through characterization of inflammatory cells and vascular changes in real time. However, respiratory motion complicates the analysis of these time series images and requires selective data extraction to stabilize the image. Consequently, analysis of individual alveoli may not provide a complete picture of the integrated mechanical, vascular and inflammatory processes occurring simultaneously in the intact lung. To address these challenges, we developed a web browser-based visualization application named Alveolus Analysis to process, analyze and graphically display intravital lung microscopy data. RESULTS: The designed tool takes raw temporal image data as input, performs image preprocessing and feature extraction offline, and visualizes the extracted information in a web browser-based interface. The interface allows users to explore multiple experiments in three panels corresponding to different levels of detail: summary statistics of alveolar/neutrophil behavior, characterization of alveolar dynamics including lung edema and inflammatory cells at specific time points, and cross-experiment analysis. We performed a case study on the utility of the visualization with two members or our research team and they found the tool useful because of its ability to preprocess data consistently and visualize information in a digestible and informative format. CONCLUSIONS: Application of our software tool, Alveolus Analysis, to intravital lung microscopy data has the potential to enhance the information gained from these experiments and provide new insights into the pathologic mechanisms of inflammatory lung injury. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12890-022-02274-7. |
format | Online Article Text |
id | pubmed-9759058 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-97590582022-12-19 Alveolus analysis: a web browser-based tool to analyze lung intravital microscopy Politowicz, Alexander L. Burks, Andrew T. Dong, Yushen Htwe, Yu Maw Dudek, Steven M. Elisabeta Marai, G. Belvitch, Patrick BMC Pulm Med Software BACKGROUND: Acute lung injury and the acute respiratory distress syndrome are characterized by pulmonary inflammation, reduced endothelial barrier integrity and filling of the alveolar space with protein rich edema fluid and infiltrating leukocytes. Animal models are critical to uncovering the pathologic mechanisms of this devastating syndrome. Intravital imaging of the intact lung via two-photon intravital microscopy has proven a valuable method to investigate lung injury in small rodent models through characterization of inflammatory cells and vascular changes in real time. However, respiratory motion complicates the analysis of these time series images and requires selective data extraction to stabilize the image. Consequently, analysis of individual alveoli may not provide a complete picture of the integrated mechanical, vascular and inflammatory processes occurring simultaneously in the intact lung. To address these challenges, we developed a web browser-based visualization application named Alveolus Analysis to process, analyze and graphically display intravital lung microscopy data. RESULTS: The designed tool takes raw temporal image data as input, performs image preprocessing and feature extraction offline, and visualizes the extracted information in a web browser-based interface. The interface allows users to explore multiple experiments in three panels corresponding to different levels of detail: summary statistics of alveolar/neutrophil behavior, characterization of alveolar dynamics including lung edema and inflammatory cells at specific time points, and cross-experiment analysis. We performed a case study on the utility of the visualization with two members or our research team and they found the tool useful because of its ability to preprocess data consistently and visualize information in a digestible and informative format. CONCLUSIONS: Application of our software tool, Alveolus Analysis, to intravital lung microscopy data has the potential to enhance the information gained from these experiments and provide new insights into the pathologic mechanisms of inflammatory lung injury. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12890-022-02274-7. BioMed Central 2022-12-17 /pmc/articles/PMC9759058/ /pubmed/36528564 http://dx.doi.org/10.1186/s12890-022-02274-7 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Software Politowicz, Alexander L. Burks, Andrew T. Dong, Yushen Htwe, Yu Maw Dudek, Steven M. Elisabeta Marai, G. Belvitch, Patrick Alveolus analysis: a web browser-based tool to analyze lung intravital microscopy |
title | Alveolus analysis: a web browser-based tool to analyze lung intravital microscopy |
title_full | Alveolus analysis: a web browser-based tool to analyze lung intravital microscopy |
title_fullStr | Alveolus analysis: a web browser-based tool to analyze lung intravital microscopy |
title_full_unstemmed | Alveolus analysis: a web browser-based tool to analyze lung intravital microscopy |
title_short | Alveolus analysis: a web browser-based tool to analyze lung intravital microscopy |
title_sort | alveolus analysis: a web browser-based tool to analyze lung intravital microscopy |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9759058/ https://www.ncbi.nlm.nih.gov/pubmed/36528564 http://dx.doi.org/10.1186/s12890-022-02274-7 |
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