Example Assays: Opal Multiplex Kits, Phenocode Signature Panels, Ultivue Panels
Example Imagers: PhenoImager HT, Vectra Polaris
This guide aims to describe a recommended workflow for analyzing mid-plex (4-16 biomarkers) images acquired with assays like Opal Polaris Reagent Kits or the Opal 7 Color IHC Detection Kits, and scanners like the PhenoImager HT or Vectra Polaris. For example, the Opal Reagents allow simultaneous detection of up to 8 biomarkers plus a nuclear counterstain for the Polaris Kit, or up to 6 biomarkers plus a nuclear counterstain for the 7 Color Kit. Because of bleed over between different acquisition channels, the signals from individual markers are resolved through spectral unmixing. This pre-processing step is usually performed on the acquisition instrument (typically a Mantra, Vectra, or Vectra Polaris imaging system). The end result is that the signal for each individual biomarker as well as the nuclear counterstain is displayed as a different channel in a multi-channel image file.
This guide assumes that the user is importing pre-processed images that have already been stitched and undergone spectral unmixing. The images should be in a multi-channel format, where each channel corresponds to the signal for an individual biomarker (e.g., one channel for the DAPI nuclear counterstain, a second channel for PanCK signal, a third channel for CD45 signal, etc.). Starting from that point, the workflow on the Enable Medicine Platform is as follows:
Importing image files