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SPIM Workflow Manager For HPC

1 byte removed, 05:38, 31 August 2018
SPIM data processing pipeline
== SPIM data processing pipeline ==
SPIM ("Selective/Single Plane Illumination Microscopy") typically images living biological samples from multiple angles (views) collecting several 3D image stacks to cover the entire biological specimen. The 3D image stacks, representing one time point in a long-term time-lapse acquisition, need to be registered to each other which is typically achieved using fluorescent beads as fiduciary markers .
After the registration, the individual views within one time point need to be combined into a single output image either by content-based fusion or multi-view deconvolution [https://imagej.net/Multiview-Reconstruction]. The living specimen can move during acquisition, necessitating an intermediate step of time-lapse registration. Whereas parallel processing of individual time points has proven to be beneficial, the time-lapse registration takes only a few seconds and can therefore be performed on a single computing node without the need for parallelization.
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