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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Bibliographic Details
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
Online Access:Get full text
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Description
Summary: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.
Bibliography:new_version
ObjectType-Article-1
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No competing interests were disclosed.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.27112.2