Methods and systems for multiplex assays

A method for conducting a multiplex assay comprising the steps of:

• a) contacting a sample with beads in an assay system, wherein each bead in the system comprises
• (1) a substantially transparent polymer layer having a first surface and a second surface, the first and the second surfaces being parallel to each other;
• (2) a substantially non-transparent polymer layer, wherein the substantially non-transparent polymer layer is affixed to the first surface of the substantially transparent polymer layer and encloses a center portion of the substantially transparent polymer layer, wherein the substantially non-transparent polymer layer comprises one or more ring(s) enclosing the center portion of the substantially transparent polymer layer and represents an analog code, and wherein at least one of the one or more rings comprises a discontinuity;
• wherein the system comprises (i) at least one bead with an analog code that is recognized by an imaging processor as a specific assay, specific analyte, manufacturing lot, individual, locational identifier, or calibration signal and does not correspond to a capture agent associated with the at least one bead, and (ii) a plurality of beads, wherein each bead of the plurality of beads comprises a capture agent that specifically binds to an analyte, wherein the capture agent is immobilized on at least one of the first surface and the second surface of the substantially transparent polymer layer in at least the center portion of the substantially transparent polymer layer, and wherein each bead of the plurality of beads comprises an analog code corresponding to the capture agent;
• and
• simultaneously or sequentially, in any order:
• b) identifying the analog code that is recognized by the imaging processor as the specific assay;
• and
• c) detecting the binding of the analyte in the sample by analyzing the binding of the analyte to the capture agent immobilized on the surface of the bead based on the identification of the analog code corresponding to the capture agent.