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Fiji MVR (Multiview Reconstruction)
This software is for registering and fusing the datasets from two views. It was originally developed for OpenSPIM-like setups but works well for diSPIM data as well.
See homepage at http://fiji.sc/Multiview-Reconstruction.
As of April 2015 the MVR plugin allows for direct importing of Micro-Manager datasets, rendering the plugin's export function obsolete for MVR analysis (it is still required for MIPAV GenerateFusion).