naica® System Workflow

Crystal Digital PCR™: Ease of use, transparency of data

Crystal Digital PCR™, the next generation of DNA amplification, is based on a patented technology to partition the fully assembled PCR sample mix into thousands of individual reaction compartments prior to amplification, in a single step. Nucleic acid molecules are thus distributed across partitions, and amplified separately, alleviating any potential competition, and enabling absolute quantification of the DNA or RNA molecules.

Digital PCR Workflow. Click image to enlarge.

The naica® system

With the naica® system, Stilla Technologies makes the experience of digital PCR accessible across applications and markets, featuring ready-to-use digital PCR reagents as well as a selection of chip consumables for optimized throughput and flexible sensitivity. Easy-to-use instrument operation and intuitive software analysis enable fast time-to-results. Scroll down to learn more about the naica® system workflow for Crystal Digital PCR™.

Lab hardware

The path to good analysis starts with good sample preparation

As the saying goes, “good data in, good data out.” Whether using precious samples from liquid biopsies to test for oncological mutations  or testing wastewater samples for the presence of SARS-CoV-2, be sure to begin any digital PCR experiment with a clean sample preparation processThe Maxwell Systems from Promega Corporation provide benchtop automated DNA/RNA extraction from any sample.

Mix and load

Once your sample extraction is complete, use the ready-to-use naica® PCR MIX reagents optimized for Crystal Digital PCR™ to prepare the sample mix. There is no need for multiple buffers or chemistries, simply mix your reaction, pipette it onto a chip consumable, and load it into the naica® system.

Start your reaction

Prepare your reaction mix with optimized reagents such as naica® PCR MIX or naica® multiplex PCR MIX. 

Load your mix

Samples are loaded onto patented chip consumables with just a single pipetting step. Stilla Technologies offers two different chip consumables – the Ruby Chip and the Sapphire Chip – designed with varying sample throughput, and sensitivity in mind. 

Amplify and read

The naica® system for Crystal Digital PCRTM is composed of two instruments: the first performs droplet generation and amplification, and the second enables imaging of the Droplet Crystal in up to six detection channels. 


After pipetting the reaction onto the chips, the chips are loaded into the naica® system’s thermocycler, known as the Geode. While in the thermocycler instrument, pressure pushes the sample through channels in the chips to create tens of  thousands of droplet crystals. Each droplet  undergoes its own PCR amplification.


After PCR amplification of the sample droplets, the chips are placed into a 3-color or a 6-color fluorescence reader, known as the Prism. Using intuitive Crystal Reader software, the scanning parameters are defined with just a couple of commands, and the droplets are imaged in up to six fluorescent channels.

Easy to read results

Measure the concentrations of targeted nucleic acids with Crystal Miner software. This intuitive tool allows for visual inspection and analysis of Crystal Digital PCR™ experiments. The software provides automatic quality control for experiment performance, as well as automation identification of positive and negative droplets for all fluorescence channels.

  • Analyze data using 1D, 2D, or 3D dot plots
  • Explore Droplet Crystals and link any dot on the dot platos to its corresponding droplet in the Droplet Crystal
  • Obtain targeted nucleic acids concentrations
  • Access raw data and export all experiment details and results

For Research Use Only. Not for use in diagnostic procedures.