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 use the multi-view reconstruction is as part of Fiji, it is part of BigStitcher.
You can also check the outdated Multiview-Reconstruction page on the ImageJ wiki.
For questions, bug reports, remarks and comments just use github here or send me an email: [email protected]
If you want to build the code you can use Maven calling mvn clean package on the command line after checking the project out. Important: you will need to install Java with JavaFX, for example available here in the Azul JDK.
Please note that the Multiview-Reconstruction/BigStitcher plugin available through Fiji, is based on publications. If you use it successfully for your research please be so kind to cite our work:
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D. Hörl, F.R. Rusak, F. Preusser, P. Tillberg, N. Randel, R.K. Chhetri, A. Cardona, P.J. Keller, H. Harz, H. Leonhardt, M. Treier & S. Preibisch, "BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples", Nature Methods, 16: 870–874. Webpage
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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
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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