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Introduction & Overview

Selective Plane Illumination Microscopy (SPIM, Science, 305(5686):1007-9) allows in toto imaging of large specimens by acquiring image stacks from multiple angles. However, to realize the full potential of these acquisitions the data needs to be reconstructed. This project implements several algorithms for the registration and fusion of multi-angle SPIM acquisitions.


The easiest is to get the SPIM Reconstruction as part of Fiji.

See also the SPIM Registration page on the ImageJ wiki.

For questions, bug reports, remarks and comments just use github here or send me an email:


Please note that the SPIM reconstruction plugin available through Fiji, is based on publications. If you use it successfully for your research please be so kind to cite our work:

  • S. Preibisch, S. Saalfeld, J. Schindelin and P. Tomancak (2010) "Software for bead-based registration of selective plane illumination microscopy data", Nature Methods, 7(6):418-419. Webpage

  • S. Preibisch, F. Amat, E. Stamataki, M. Sarov, R.H. Singer, E. Myers and P. Tomancak (2014) “Efficient Bayesian-based Multiview Deconvolution”, Nature Methods, 11(6):645-648. Webpage

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