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.
Highlights
We introduce MosaicExplorerJ, an ImageJ macro to stitch 3D tiles from terabyte-size microscopy datasets organized on a regular 2D grid
We developed MosaicExplorerJ to address these shortcomings and bring a complementary alternative to ImageJ BigStitcher, the reference in the field
Implementation Whereas stitching the tiles of confocal microscopy datasets consists in compensating for the scanning head to sample stage tilt, stitching lightsheet microscopy datasets is compounded by the fact that the lightsheet is not necessarily perfectly collinear to the object plane of the detection objective
Summary
Any further responses from the reviewers can be found at the end of the article Introduction A number of open source tools are available to stitch mosaics from optical microscopy 3D tiled scans[1,2,3,4] but they systematically implement automated algorithms which results might depend on the starting positions of the tiles and potentially converge to a suboptimal solution. This is especially likely if the initial positions are far from the optimal positions, or if the data suffers from unexpected artifacts.
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