Overview

Nornir is a collection of Python packages for building image mosaics and 3D volumes from serial-section imaging data. Components cover thread/process pools, shared utilities, image registration, and volume construction.

Mission

Nornir’s goal is to take large sets of overlapping images in 2D and 3D and produce registered (aligned) 2D and 3D volumes at any practical size and scale.

Theory and figures: for a guided walkthrough of mosaic capture, tile alignment, slice-to-slice registration, and volume mapping—with the original figures from the public manual—see Overview of volume building.

Documentation convention: narrative and API reference for the umbrella project live in this monodoc. Each nornir-* package also has a short README.md at its repository root with an introduction and links back here.

History

Nornir evolved from a collaboration between the Marc Lab and the Scientific Computing Institute (Tasdizen and Whitaker groups) at the University of Utah. The original tools, known as the NCR Toolset, were used to construct RC1, a 250 µm diameter, 33 µm tall cylinder of rabbit retina at a resolution of 2.18 nm/pixel.

Nornir is a work in progress. It supports importing images from transmission electron microscopes running SerialEM (.idoc files), light microscopes running Surveyor (.pmg files), and other volumes represented with a single image per section (.png files).

Related tools

Volume images frequently exceed reasonable sizes for single files. Viking is another Marc Lab tool for viewing and annotating huge datasets. Nornir output can be viewed with Viking when placed on a web server.

System notes

• 64-bit OS (development has focused on Windows).

• Rough guideline: about 2 GB RAM per CPU core for heavy pipelines (workload-dependent).

Terminology (short glossary)

Block — plastic-embedded sample before sectioning.

Section / slice — one thin physical slice from the block, typically tens of nanometres thick for TEM.

Mosaic — a set of overlapping microscope images covering an area larger than one field of view.

Tile — one image in a mosaic (with deliberate overlap between neighbors).

Slice-to-slice (STOS) — transforms that align one section’s image to an adjacent section.

Center section — the section chosen as the origin of the volume coordinate system; other sections map toward it through composed transforms.

Slice-to-volume — the composed mapping from a section’s mosaic space into the unified volume space.

For the same terms in the context of the full alignment walkthrough, see Overview of volume building.