The nCounter

I’ve been thinking a bunch about the nCounter for various reasons. This, Bionano’s instrument, the OpGen instruments… they all interest me as commercial implementations of single molecule visualization platforms.

Of course, none of them have been great commercial successes…

Typically single molecule imaging requires complex optics and includes TIRF excitation often using expensive ($10K) high-NA objective lenses, lasers, sCMOS cameras etc.

To investigate how the nCounter handles these challenges I picked up an old one of eBay. In this post I’m going to take a brief look at the approach and instrument.

The nCounter Approach

At the fundamental level the nCounter is a single molecule hybridization counting platform. Most typically this is used for counting transcripts.

The original NanoString Approach used an M13 backbone¹ with RNA tags this allowed them to build up a barcode using tags which incorporated multiple dyes:

These barcodes are then stretched out under an electric field and imaged:

The use of these multi-dye tags is part of what enables a more practical imaging system than would traditionally be used for single molecule imaging. For this original patent they used a 63x 1.4NA objective and a mercury lamp light source. Alongside a Orca-ER CCD camera.

As optical setups go, nothing particularly fancy.

After their original work on M13 they moved to a different reporter, but the concept essentially remains the same:

What’s In The Instrument?

A number of NanoString instruments have been developed. Most notably the original series and the NanoString SPRINT. The Sprint moves away from a field based stretching approach to a flow driven system (I assume something like DNA combing). It integrates both the fluidic and imaging components in the same instrument and uses a dry objective.

But the original instrument series used a fluidic prep box and a separate imager. I picked up one of the imagers on eBay: