Concepts

Overview states what Nornir is for. Overview of volume building walks through mosaic capture, slice-to-slice registration, and slice-to-volume mapping, and names the nornir-build command for each stage.

Glossary

Block: Plastic-embedded sample before sectioning. In the volume tree, a block groups sections and is the unit of batch processing.
Section / slice: One thin physical slice from the block, typically tens of nanometres thick for TEM. One Z level in the volume.
Channel: A named image set on a section, such as TEM or a derived filter stack.
Filter: An image-processing product of a channel (raw tiles, leveled tiles, a blob image). Pipelines select filters by name.
Tile: One microscope image in a mosaic. Neighbors overlap on purpose.
Mosaic: The set of tiles that covers an area larger than one field of view, plus the transform that lays them out. Stored as a .mosaic file.
Pyramid level: A downsampled copy of a tile or assembled image. Lower levels are smaller and are what registration usually measures.
Prune: Drop tiles that do not have enough texture to align. The Prune pipeline does this before Mosaic.
Slice-to-slice (STOS): A transform that aligns one section to an adjacent section. Stored as a .stos file.
Blob: A texture filter that keeps features visible after downsampling. CreateBlobFilter builds it. TEM brute alignment uses it.
Grid / mesh: After a rigid or translation step, a grid of cells is measured and the mesh records a local offset at each cell. Mosaic refine and slice-to-slice refine both do this. In Pyre, a refined grid does not support adding or deleting control points the way a triangulation transform does.
Center section: The section chosen as the origin of the volume coordinate system. Other sections map toward it.
Slice-to-volume: The composed mapping from a section’s mosaic space into that shared volume space. SliceToVolume builds it from the slice-to-slice chain.
VikingXML: The manifest CreateVikingXML writes so Viking can open the volume. The StosGroup name is the label in Viking’s transform menu.