MosaicExplorerJ: Interactive stitching of terabyte-size tiled datasets from lightsheet microscopy [version 2; peer review: 2 approved]

MosaicExplorerJ: Interactive stitching of terabyte-size tiled datasets from lightsheet microscopy [version 2; peer review: 2 approved]

We introduce MosaicExplorerJ, an ImageJ macro to stitch 3D tiles from terabyte-size microscopy datasets organized on a regular 2D grid. As opposed to existing software, stitching does not require any prior information on the actual positions of the tiles, or conversion of raw TIFF images to a multi-...

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Published in:F1000 research Vol. 9; p. 1308
Main Authors: Tosi, Sébastien, Bardia, Lídia, Barallobre, Maria Jose, Muñoz-Barrutia, Arrate, Soto-Montenegro, María Luisa, Colombelli, Julien
Format: Journal Article
Language:English
Published: London Faculty of 1000 Ltd 2021
F1000 Research Limited
F1000 Research Ltd
Subjects:
Algorithms
Datasets
Microscopy
Software
Software Tool
Madrid Spain
Spain
ImageJ
Lightsheet microscopy
Tiled scan
Mosaic
3D stitching
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Abstract We introduce MosaicExplorerJ, an ImageJ macro to stitch 3D tiles from terabyte-size microscopy datasets organized on a regular 2D grid. As opposed to existing software, stitching does not require any prior information on the actual positions of the tiles, or conversion of raw TIFF images to a multi-resolution format for interactive exploration and fast processing. MosaicExplorerJ was specifically designed to process lightsheet microscopy datasets from optically cleared samples. It can handle multiple fluorescence channels, dual-sided lightsheet illumination and dual-sided camera detection.
AbstractList We introduce MosaicExplorerJ, an ImageJ macro to stitch 3D tiles from terabyte-size microscopy datasets organized on a regular 2D grid. As opposed to existing software, stitching does not require any prior information on the actual positions of the tiles, or conversion of raw TIFF images to a multi-resolution format for interactive exploration and fast processing. MosaicExplorerJ was specifically designed to process lightsheet microscopy datasets from optically cleared samples. It can handle multiple fluorescence channels, dual-sided lightsheet illumination and dual-sided camera detection.
Author Colombelli, Julien
Bardia, Lídia
Tosi, Sébastien
Barallobre, Maria Jose
Soto-Montenegro, María Luisa
Muñoz-Barrutia, Arrate
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  organization: Institute for Research in Biomedicine - IRB Barcelona, the Barcelona Institute for Science and Technology - BIST, Barcelona, Spain
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  givenname: Maria Jose
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  surname: Colombelli
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  organization: Institute for Research in Biomedicine - IRB Barcelona, the Barcelona Institute for Science and Technology - BIST, Barcelona, Spain
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Cites_doi 10.1038/s41592-019-0501-0
10.1186/1471-2105-13-316
10.1111/j.1365-2818.2008.03094.x
10.1126/science.1100035
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Copyright Copyright: © 2021 Tosi S et al.
Copyright: © 2021 Tosi S et al. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
Copyright: © 2021 Tosi S et al. 2021
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Keywords ImageJ
Lightsheet microscopy
Tiled scan
Mosaic
3D stitching
Language English
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S Tosi (ref-6) 2021
S Tosi (ref-7) 2021
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D Hörl (ref-4) 2019; 16
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Software
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Title MosaicExplorerJ: Interactive stitching of terabyte-size tiled datasets from lightsheet microscopy [version 2; peer review: 2 approved]
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