Build a volume

nornir-build runs one named pipeline against a volume directory. The science behind each stage is in Overview of volume building. Flags below are the examples already shipped in Pipelines.xml and the buildmanager README. Run nornir-build <Pipeline> --help before changing them. Host sizing is in Host requirements.

Import

Pick the importer that matches the microscope:

  • SerialEM .idoc:

    nornir-build ImportIDoc /data/volume /data/idoc -Sections 1-10 -CameraBpp 14

  • Digital Micrograph .dm4:

    nornir-build ImportDM4 /data/volume /data/dm4 -Sections 1-20 -overlap 10,20

  • Surveyor .pmg:

    nornir-build ImportPMG /data/volume /data/pmg -Scale 4.0

VolumeData.xml is written at several levels of the tree (volume, block, section, channel), not only at the volume root. The locations are on nornir-buildmanager.

Prune and mosaic

Prune drops tiles that do not have enough texture. Mosaic then lays the remaining tiles out and writes an assembled mosaic.

nornir-build Prune /data/volume -InputFilter Raw8 -DefaultThreshold 0.2 -Sections 1-10
nornir-build Mosaic /data/volume -InputFilter Raw8 -InputTransform Prune -OutputTransform Grid -RegistrationDownsample 4

Slice-to-slice

CreateBlobFilter builds the texture image used when downsampled TEM sections would otherwise lose features. AlignSections brute-force aligns adjacent sections and records a center section. RefineSectionAlignment applies the grid refine, often in passes at finer downsampling.

nornir-build AlignSections /data/volume -Downsample 8 -Channels .* -Filters Raw8 -OutputStosMap PotentialRegistrationChain

This brute-force step is the usual place to open Pyre and correct a bad pair before refine. Controls are in Using Pyre.

Slice-to-volume and export

SliceToVolume composes the slice-to-slice chain into one transform per section onto the center section. Assemble builds images from a transform and a filter. CreateVikingXML writes the manifest Viking reads. The -StosGroup name is the label in Viking’s File → Transform → SliceToVolume menu.

nornir-build CreateVikingXML /data/volume -OutputFile MyVolume -StosMap FinalStosMap -StosGroup Grid32 -StosGroup SliceToVolume1

The Version 2 XML and zip layout is documented on nornir-buildmanager. Put the volume where Viking can read it.

View and analyze

Nornir stops at the VikingXML manifest and the image pyramids.

  1. View and annotate the volume in Viking.

  2. Analyze those annotations in SBFSEM-tools (MATLAB).

Build in Nornir, view and annotate in Viking, analyze in SBFSEM-tools.