Single-Cell Analysis with Microfluidics

Why study single cells?

Bulk assays average over millions of cells, hiding rare cell types and cell-to-cell variation. Single-cell methods resolve each cell's individual state — essential in immunology, oncology and developmental biology, where the interesting biology is often in the outliers.

How microfluidics isolates single cells

• Droplet encapsulation — one cell and one barcoded bead per droplet, using droplet microfluidics.
• Microwell arrays — cells settle into thousands of tiny wells, one per well.
• Traps and valves — geometry captures and holds individual cells for imaging or treatment.

Single occupancy is governed by Poisson statistics and careful design of cell concentration and droplet/well size.

The barcoding trick

Each cell's molecules are tagged with a unique barcode inside its compartment. All compartments are then pooled and sequenced together, and software uses the barcodes to assign every read back to its cell of origin — allowing thousands of cells to be processed in one run.

Applications

Single-cell RNA sequencing (scRNA-seq), single-cell genomics, immune-repertoire profiling and multi-omics methods such as CITE-seq all rely on microfluidic single-cell isolation.

Chip requirements

These devices need precise, reproducible droplet generation, clean and biocompatible surfaces, and tight control of flows. They are typically prototyped in PDMS and scaled in thermoplastics — see prototype to scale.

Frequently asked questions