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AutoScanJ: A Suite of ImageJ Scripts for Intelligent Microscopy
We developed AutoscanJ, a suite of ImageJ scripts enabling to image targets of interest by automatically driving a motorized microscope at the corresponding locations. For live samples, our software can sequentially detect biological events from their onset and further image them at high resolution,...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9581036/ https://www.ncbi.nlm.nih.gov/pubmed/36303768 http://dx.doi.org/10.3389/fbinf.2021.627626 |
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author | Tosi, Sébastien Lladó, Anna Bardia, Lídia Rebollo, Elena Godo, Anna Stockinger, Petra Colombelli, Julien |
author_facet | Tosi, Sébastien Lladó, Anna Bardia, Lídia Rebollo, Elena Godo, Anna Stockinger, Petra Colombelli, Julien |
author_sort | Tosi, Sébastien |
collection | PubMed |
description | We developed AutoscanJ, a suite of ImageJ scripts enabling to image targets of interest by automatically driving a motorized microscope at the corresponding locations. For live samples, our software can sequentially detect biological events from their onset and further image them at high resolution, an action that would be impractical by user operation. For fixed samples, the software can dramatically reduce the amount of data acquired and the acquisition duration in situations where statistically few targets of interest are observed per field of view. AutoScanJ is compatible with motorized fluorescence microscopes controlled by Leica LAS AF/X or Micro-Manager. The software is straightforward to set up and new custom image analysis workflows to detect targets of interest can be simply implemented and shared with minimal efforts as independent ImageJ macro functions. We illustrate five different application scenarios with the system ranging from samples fixed on micropatterned surfaces to live cells undergoing several rounds of division. The target detection functions for these applications are provided and can be used as a starting point and a source of inspiration for new applications. Overall, AutoScanJ helps to optimize microscope usage by autonomous operation, and it opens up new experimental avenues by enabling the real-time detection and selective imaging of transient events in live microscopy. |
format | Online Article Text |
id | pubmed-9581036 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-95810362022-10-26 AutoScanJ: A Suite of ImageJ Scripts for Intelligent Microscopy Tosi, Sébastien Lladó, Anna Bardia, Lídia Rebollo, Elena Godo, Anna Stockinger, Petra Colombelli, Julien Front Bioinform Bioinformatics We developed AutoscanJ, a suite of ImageJ scripts enabling to image targets of interest by automatically driving a motorized microscope at the corresponding locations. For live samples, our software can sequentially detect biological events from their onset and further image them at high resolution, an action that would be impractical by user operation. For fixed samples, the software can dramatically reduce the amount of data acquired and the acquisition duration in situations where statistically few targets of interest are observed per field of view. AutoScanJ is compatible with motorized fluorescence microscopes controlled by Leica LAS AF/X or Micro-Manager. The software is straightforward to set up and new custom image analysis workflows to detect targets of interest can be simply implemented and shared with minimal efforts as independent ImageJ macro functions. We illustrate five different application scenarios with the system ranging from samples fixed on micropatterned surfaces to live cells undergoing several rounds of division. The target detection functions for these applications are provided and can be used as a starting point and a source of inspiration for new applications. Overall, AutoScanJ helps to optimize microscope usage by autonomous operation, and it opens up new experimental avenues by enabling the real-time detection and selective imaging of transient events in live microscopy. Frontiers Media S.A. 2021-03-18 /pmc/articles/PMC9581036/ /pubmed/36303768 http://dx.doi.org/10.3389/fbinf.2021.627626 Text en Copyright © 2021 Tosi, Lladó, Bardia, Rebollo, Godo, Stockinger and Colombelli. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Bioinformatics Tosi, Sébastien Lladó, Anna Bardia, Lídia Rebollo, Elena Godo, Anna Stockinger, Petra Colombelli, Julien AutoScanJ: A Suite of ImageJ Scripts for Intelligent Microscopy |
title | AutoScanJ: A Suite of ImageJ Scripts for Intelligent Microscopy |
title_full | AutoScanJ: A Suite of ImageJ Scripts for Intelligent Microscopy |
title_fullStr | AutoScanJ: A Suite of ImageJ Scripts for Intelligent Microscopy |
title_full_unstemmed | AutoScanJ: A Suite of ImageJ Scripts for Intelligent Microscopy |
title_short | AutoScanJ: A Suite of ImageJ Scripts for Intelligent Microscopy |
title_sort | autoscanj: a suite of imagej scripts for intelligent microscopy |
topic | Bioinformatics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9581036/ https://www.ncbi.nlm.nih.gov/pubmed/36303768 http://dx.doi.org/10.3389/fbinf.2021.627626 |
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