[OpenSPIM] real time projections, batch processing

[Ulrik Günther]

Hi Stephanie,


Regarding your first question, you can use ClearVolume (http://imagej.net/ClearVolume). We originally had a version of the OpenSPIM acquisition plugin with ClearVolume directly integrated, but as ClearVolume is a Fiji plugin on its own now, we have to handle this in a different way. We’ll have an updated version of that ready soon(ish).


Regarding your second question, Christopher Schmied created an updated and automated version of the workflow. The guide is available at http://imagej.net/Automated_workflow_for_parallel_Multiview_Reconstruction, with source code on GitHub: https://github.com/mpicbg-scicomp/snakemake-workflows


I hope this is helpful for you!


cheers!


ulrik




  —
Ulrik Günther, Dipl.-Phys.
PhD Student
MOSAIC Group & Tomancak Lab, Center of Systems Biology Dresden
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108, D-01307 Dresden, Germany


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