The Applied Biosystems QuantStudio 3D Digital PCR System is a simple, affordable platform that uses a sealed-chip technology, providing a streamlined, reliable, and robust method for performing digital PCR. The turn-key chip-based workflow lets you load the chip, seal and proceed to amplification.


Expanding the boundaries of traditional real-time PCR the QuantStudio 3D system supports absolute quantification without the use of a standard curve. 


The QuantStudio 3D Digital System offers: 

20,000 nanoscale reaction wells per chip

Enables more controlled sample loading and less reaction dropout than droplet-based approaches, ensuring higher precision for absolute quantification

Thermal cycle up to 24 chips at one time

Taking less than 30 seconds to read each chip, the QuantStudio 3D Digital PCR System enables a simple, streamlined workflow to perform digital PCR. 

Turn-key, chip-based workflow

Simple workflow; just load and seal and you’re ready for PCR and analysis as shown below:

Videos and demos

Sample data

QuantStudio 3D Digital PCR System precision

Five independent technical replicates were generated across an 8-assay panel of TaqMan Gene Expression Assays. All measurements were within ±10% (red lines) of the respective means (green lines). (A) Results for genes expressed at low level (HPRT1, MYC, and VEGFA). (B) Results for genes expressed at high levels (18S, B2M, GAPDH, GUSB, and PPIA).

Accuracy on the QuantStudio 3D Digital PCR System

The accuracy of absolute quantification on the QuantStudio 3D Digital PCR System was assessed by agreement with two orthogonal quantification methods. Using male genomic DNA, the number of copies/μL at two concentrations was measured and compared using UV spectrophotometer and digital PCR on QuantStudio 12K Flex OpenArray Digital PCR Plates (OA) and 5 replicates on the QuantStudio 3D Digital PCR System (QS3D). The expected target concentrations were 300 copies/μL and 1,500 copies/μL for the two samples, falling within the range of the expected value, with the measurements from the QuantStudio 3D Digital PCR System exhibiting the highest precision relative to the other methods.

Precision and accuracy demonstrated for copy number analysis of the CCL3L1 genetic locus on chromosome 17 across 9 independent DNA samples representing 0–8 copies.

(A) Experimental design and resulting data across the tested sample set. Each digital PCR measurement overlaps the expected value within the standard deviation achieved. It should be noted that all measurement coefficients of variation (CV) were below 2.55%, underscoring the high degree of precision achievable.

(B) Graphical representation of the same data displayed in A. With the achieved precision, digital PCR results made it possible to discern the difference between samples containing 7 and 8 copies.

Example of KRAS rare allele quantification by digital PCR. The KRAS G12V mutation was detected with a Custom TaqMan SNP Genotyping Assay optimized for digital PCR on the QuantStudio 3D Digital PCR System.

Each sample represents a fraction of mutant plasmid to wild type genomic DNA. The 0.1% target represents mutant genomic DNA from a mutant cell line in a wild type genomic DNA background. All samples were analyzed using QuantStudio 3D AnalysisSuite Cloud Software with the relative quantification module. (A) Targeted mutation rate of 10%. The mutation detection rate was 10.384% with a confidence interval of 8.235–13.076%. (B) Targeted mutation rate of 1%. The mutation detection rate was 1.393% with a confidence interval of 0.772–2.507%. (C) Targeted mutation rate of 0.1%. The mutation detection rate was 0.142% with a confidence interval of 0.064–0.310%. (D) Wild type control sample.

Kits and accessories


QuantStudio 3D Digital PCR Instrument

Time to read one sample

~30 seconds

PCR detection method


Sample illumination


Sample detection


Detection channels


Reader size (H x W x D)

8.3 x 5.3 x  9.15 in. (21 x 13.5 x 23.25 cm)


5.3 lb (2.4 kg)

QuantStudio 3D Digital PCR 20K Chip


Chip reaction wells

Samples per chip


Targets per chip


Chip capacity in thermal cycler


Reaction wells per sample


Loading volume

14.5 μL

Sealed workflow



Dynamic range

5 logs

Precision at 95% confidence interval


Compatible chemistries

TaqMan and SYBR Green chemistries



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