→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.
The sheer amount of the SPIM data requires conversion from raw microscopy data to Hierarchical Data Format (HDF5) for efficient input/output access and visualization in Fiji's BigDataViewer (BDV) [https://imagej.net/BigDataViewer#Publication]. BDV uses an XML file to store experiment metadata (i.e. number of angles, time points, channels etc.). Although the conversion to HDF5 is a parallelizable procedure, further updating the XML file downstream in the pipeline is not; and per-time point XML files have to be created and then merged after completion of the registration and fusion steps. Consequently, the parallel processing of individual time points on an HPC resource (conversion to HDF5, registration, fusion and deconvolution) is interrupted by non-parallelizable steps (time-lapse registration and XML merging).