Glossary of terms in context

To build a 3D volume using our transmission electron microscopes we begin by taking a sample and embedding it in a block of plastic resin. This block is then cut into thin, about 70-90nm, sections. Each section is placed on a grid or a slide. At 5000X our transmission electron microscope can produce an image representing an 8um square. To collect a larger area we collect a mosaic of images with a 10%-12% overlap. We refer to an image in a mosaic as a tile even though proper tiles wouldn’t overlap. Nornir figures out how to layout the tiles so we can assemble a single image of the entire mosaic.

We assemble a mosaic image for each section cut from the block. Sometimes we call a section a slice. Each section is then registered to the adjacent sections to produce slice-to-slice (stos) transformations. We decide which mosaic is the center of the volume. Transforms can then be added such that any point on a mosaic can be mapped through stos transforms until the center is reached. This produces a mapping for each section to the volume. The slice-to-volume transforms can be used with Viking or if the mosaic images are small enough volume aligned section images can be produced.