Biological Entities and Segmentation

The fundamental output of a MERFISH experiment is a list of the spatial locations of RNA molecules. In order to use this list of positions to understand biology, the RNA molecules need to be pooled together spatially. The goal of image segmentation for MERSCOPE data is to pool together RNA molecules that are in the same biological compartment or "Entity."

The Vizgen Post-processing Tool is concerned with membrane-bound biological entities that can be identified using fluorescent stains. In the flow of data through this tool, we preserve Entity-type information using column names and file names. While the most commonly identified Entity for most users is a cell, this user guide will refer to "Entities" whenever the specific entity type is not relevant to the processing step.