Build a volume

The science behind each stage is in Overview of volume building. The lab commands, with the flags the TEM scripts actually pass, are in TEM build scripts. This page is the order of the work, not a second recipe. Host sizing is in Host requirements. Deploy the machine that runs the scripts with Deploy the build container.

1. Import. For SerialEM that is TEMImport (ImportIDoc). VolumeData.xml is written at several levels of the tree, not only at the volume root. Those paths are on nornir-buildmanager.

2. Build each mosaic with TEMBuild: prune, histogram, contrast, tile layout, image pyramids, a mosaic report, and a mosaic VikingXML file.

3. Align sections with TEMAlign: blob filter, brute-force slice-to-slice, grid refine, slice-to-volume, then a VikingXML file whose StosGroup names show up in Viking. A bad brute-force pair is fixed in Pyre (Using Pyre) before the later grid passes are treated as final.

4. View and annotate in Viking. Analyze those annotations in SBFSEM-tools.

nornir-build <Pipeline> --help lists flags for one stage. The grouped names are Pipeline catalogue. Those help examples are not the TEM script.