Glossary

Below is a glossary of terms related to MERFISH, imaging, etc. that are used throughout the MERFISH Tools documentation.

FOV (Field of view)

Because the entire tissue section cannot be captured in a single image at the magnification required for MERFISH imaging, an experiment consists of hundreds or even thousands of separate images that each contain a small portion of the tissue. Each of these is referred to as a field of view, often abbreviated as FOV.

MERlin

MERlin is the software created in the Zhuang lab for processing MERFISH data. The MERSCOPE runs a version of this software to process the data it collects and produce the output folders.

Z-slice, Z-stack

MERFISH images are pseudo-3D. Multiple 2D images are taken within the same FOV, each focused at a different depth into the tissue section. Each of these are called a z-slice or z-stack.