Single plane illumination microscopy analysis software tools | Bioimaging

Selective Plane Illumination Microscopy (SPIM) allows to image developing organisms in 3D at unprecedented temporal resolution over long periods of time. The resulting massive amounts of raw image data requires extensive processing interactively via dedicated graphical user interface (GUI) applications. The consecutive processing steps can be easily automated and the individual time points can be processed independently, which lends itself to trivial parallelization on a high performance computing (HPC) cluster.

Source text:
(Schmied et al., 2015.) An automated workflow for parallel processing of large multiview SPIM recordings. Bioinformatics.

Image preprocessing

Image processing

Structural analysis