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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,...

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Detalles Bibliográficos
Autores principales: Tosi, Sébastien, Lladó, Anna, Bardia, Lídia, Rebollo, Elena, Godo, Anna, Stockinger, Petra, Colombelli, Julien
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
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.
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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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