Lightsheet Microscopy (LSFM, SPIM) allows in toto imaging of large specimens by acquiring image stacks from multiple angles. To realize its full potential the data needs to be reconstructed. This software allows registration of multiview data, sample drift correction, multichannel alignment, sample-induced aberration correcting using external markers or sample inherent features. The registered data can be interactively viewed (using the BigDataViewer by Tobias Pietzsch), resaved, fused, and/or deconvolved. Standard confocal data is also supported.

A detailed video tutorial: https://www.youtube.com/watch?v=0IkaSwfPYw0

Developers webpage: http://www.preibisch.net

The software is distributed as Fiji plugin (http://fiji.sc/) using the Fiji Updater, just add the BigDataViewer Update Site. Source code is also available on GitHub (https://github.com/fiji/SPIM_Registration). Any issues, comments & feature requests can be discussed here. Documentation is available on the Fiji Wiki:

Features

  • Multiview registration
  • Multichannel alignment
  • Timelapse stabilization
  • Multiview deconvolution
  • Multiview fusion

Project Samples

Play Video Illustration of a typical multiview acquisition. Four views were acquired in different orientations and need to be reconstructed Principle of geometric local descriptors on the example of a Drosophila embryo expressing His-YFP Registration result after global optimization based on geometric local descriptor matching of external landmarks Comparison of multiview fusion and multiview deconvolution on a registered dataset of C. elegans consisting of 6 views Illustrates the effect of multiview deconvolution compared to two input views as acquired by the microscope after registration

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Registered

2014-09-02
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