Flow Alignment and Scanning of Encoded Microparticles

Techniques are provided for high precision scanning of hydrogel microparticles. The high precision is achieved by one or more modifications to the microparticle composition, or microfluidics apparatus that align the microparticles in a detection channel, or method of preparing a sample for introduction into the apparatus, or some combination. An apparatus comprises a body structure having formed therein a central channel and multiple focusing channels in fluid communication with the central channel through multiple junctions. A width of the central channel is smaller in a portion downstream of each junction. A particle comprises a hydrogel matrix and a probe molecule. The particle has an aspect ratio greater than about three. A method includes loading into a sample fluid inlet a mixture, wherein a number of particles lies within a range from about 15 to about 20 particles/μl.