QIAcuity Digital PCR System

For nanoplate-based digital PCR applications

QIAcuity in action

Explore QIAcuity inside and out while learning more about dPCR.

QIAcuity One, 2plex Device

Cat no. / ID. 911001

One-plate digital PCR instrument (cat.no 911000 QIAcuity One, 2plex instrument) for detecting up to 2 fluorescent dyes, roller, USB flash memory and QIAcuity Software Suite: includes 1 preventive maintenance visit. 1 year warranty on labor, travel, and parts also included.

Format

One

Four

Eight

Multi-channel detection

2 channels (up to 4plex)

8 channels (up to 12plex)

Service Options

Device

System

System FUL-2

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The QIAcuity is intended for molecular biology applications. This product is not intended for the diagnosis, prevention or treatment of a disease. Therefore, the performance characteristics of the product for clinical use (i.e., diagnostic, prognostic, therapeutic or blood banking) is unknown. For diagnostic applications of digital PCR, please use the QIAcuityDx Digital PCR System.

QIAcuity in action

Explore QIAcuity inside and out while learning more about dPCR.

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Features

Fully integrated system
Scalable format (1-, 4- and 8-plate instruments)
Advanced multiplexing capabilities (up to 12 plex)
Up to six standard channels plus two hybrid channels for LSS dyes
Flexible sample throughput
Comprehensive results in approx. 2 hours

Product Details

The QIAcuity Digital PCR System is designed to deliver precise and multiplexed quantification results for mutation detection, copy number variation (CNV), gene expression studies, gene-editing analysis, and many more. This nanoplate-based system seamlessly integrates a standard dPCR workflow of partitioning, thermocycling and imaging into a walk-away automated platform with minimal hands-on time.

The system is used in conjunction with the QIAcuity nanoplates, reagents and assays.

Explore the virtual demo to learn more about QIAcuity.

Performance

The QIAcuity Digital PCR System makes absolute quantification accessible and affordable for all laboratories. The walk-away automation integrates and streamlines the entire digital PCR workflow of partitioning, thermocycling and imaging into a single instrument with minimal hands-on time. It is also easy to adapt your current qPCR assays to the QIAcuity Digital PCR System. No change in plate handling is required when coming from qPCR, assuring fast assay setup and quick results in approx. 2 hours.

QIAcuity Instruments – features and specifications

Feature	QIAcuity One 2plex	QIAcuity One 5plex	QIAcuity Four	QIAcuity Eight
Plates processed	1	1	4	8
Detection channels	2	8¹) (6+2 hybrid²)	8¹) (6+2 hybrid²)	8¹) (6+2 hybrid²)
Multiplexing capability	4	12³⁾¹⁾	12³⁾¹⁾	12³⁾¹⁾
Thermocycler(s)	1	1	1	2
Time to result	Approx. 2 h	Approx. 2 h	First plate approx. 2 h Every ∼80 min a following plate	First plate approx. 2 h Every ∼40 min a following plate
Throughput (samples processed in 8-hour shift, including overnight run)	Up to 480 (96-well) Up to 120 (24-well)	Up to 480 (96-well) Up to 120 (24-well)	Up to 768 (96-well) Up to 192 (24-well)	Up to 1536 (96-well) Up to 384 (24-well)

1) Requires use of QIAcuity High Multiplex Probe PCR Kit in case of multiplexing >5plex
2) Hybrid channels are used for Long Stokes Shift (LSS) dyes
3) Detection of 12 targets in parallel can be achieved by using amplitude multiplexing in the six standard channels. When combining hybrid channels for single plex LSS dyes and amplitude multiplexing, the total possible multiplex can be increased to 14. However, this combination is not recommended due to the optimization demand for all assays used in a reaction mix and their corresponding crosstalk compensation.

Principle

In just 3 simple steps, you can have the dPCR result you want in approx. 2 hours: pipette and load, run the experiment, analyze results.

The principle of the dPCR reaction in the nanoplates is described here.

Procedure

Just like in qPCR experiments, sample preparation includes the transfer of master mix, probes and primers to a 96- or 24-well nanoplate, followed by the addition of samples. The system integrates partitioning, thermocycling and imaging into a single fully automated instrument that takes users from the sample to result in under 2 hours. One can perform analysis on the Software Suite, providing the concentration in copies per microliter of your target sequence as well as for quality control such as positive samples or NTC. This analysis can also be extended to remote computers within the same local area network (LAN).

Applications

The QIAcuity instruments, together with the QIAcuity Nanoplates and the QIAcuity PCR kits, enable digital PCR applications, including:

Rare mutation detection
Copy number variation analysis
Gene expression analysis
Pathogen detection
Genotyping
miRNA research
Cell and gene therapy

Software

The QIAcuity Software Suite provided with the instrument and installed on a separate computer controls one or multiple QIAcuity instruments, either connected directly to one instrument or using an existing local area network (LAN). Using the QIAcuity Software Suite, digital PCR experiments, samples and reaction mixes can be defined, assigned to Nanoplates, and transferred to the QIAcuity instrument. After the run, data can be analyzed, reports can be created and data can be exported for external analysis. The software provides multiple template functionalities to make repeating plate layouts or plate run parameters easily accessible, further transforming your digital PCR experience.

When integrated into a local area network, the computer is hosting the QIAcuity Software Suite function as a server that is accessible via LAN to other computers serving as clients. This enables multiple users to access the software from other rooms or offices and analyze data via a standard browser without the need to install the software on multiple computers or access and exchange data via internet connections.

Services

Protect your instrument with diverse service solutions from QIAGEN. Learn more about a specific service agreement to match your needs.

Supporting data and figures

A simple and rapid plate-based workflow

Partitioning, thermocycling and imaging are all integrated into a single fully automated instrument, delivering results in under two hours. Nanoplate formats are amenable to front-end automation for sample preparation, further reducing hands-on time.

Data accuracy was demonstrated by repeatable results in two independent runs using the QIAcuity Nanoplate dPCR.

Comparable quantification in singleplex and 5plex setups.

Multiplexing feasibility of cDNA targets of strongly varying abundance was confirmed.

Quantifying twelve targets in parallel on the QIAcuity Digital PCR System.

QIAcuity quantifications using single, duplex or 12-plex reactions are highly concordant.

Kits & Consumables

dPCR accessories

Master mixes & reagents

Assays & kits

QIAcuity Nanoplate 26k 8-well (10)

Cat. No.: 250031

QIAcuity Nanoplate 8.5k 24-well (10)

Cat. No.: 250011

QIAcuity Nanoplate 26k 24-well (10)

Cat. No.: 250001

QIAcuity Nanoplate 8.5k 96-well (10)

Cat. No.: 250021

Nanoplate Seals (11)

Cat. No.: 250099

Nanoplate Tray (2)

Cat. No.: 250098

QIAcuity Nanoplate Adapter (1)

Cat. No.: 9027242

Service Plans

QIAcuity One 2plex, Full Agreement

Cat no. / ID. 9245362

On-site instrument repair, including travel, labor and parts, for a period of one year. Response time of two business days. Includes one Planned Maintenance during the Full Agreement period.

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QIAcuity One, Preventive Subscription

Cat no. / ID. 9245355

One on-site Planned Maintenance (PM) visit, including travel, labor and PM parts. Includes a 10% discount on repair services during the Preventive Subscription period.

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QIAcuity Four, Preventive Subscription

Cat no. / ID. 9245356

One on-site Planned Maintenance (PM) visit, including travel, labor and PM parts. Includes a 10% discount on repair services during the Preventive Subscription period.

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QIAcuity Eight, Preventive Subscription

Cat no. / ID. 9245357

One on-site Planned Maintenance (PM) visit, including travel, labor and PM parts. Includes a 10% discount on repair services during the Preventive Subscription period.

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QIAcuity One 2plex, Core Agreement

Cat no. / ID. 9245358

One on-site instrument repair, including travel, labor and parts, for a period of one year. Response time of 5 business days. Includes one Planned Maintenance during the Core Agreement period.

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QIAcuity One 5plex, Core Agreement

Cat no. / ID. 9245359

One on-site instrument repair, including travel, labor and parts, for a period of one year. Response time of 5 business days. Includes one Planned Maintenance during the Core Agreement period.

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QIAcuity Four, Core Agreement

Cat no. / ID. 9245360

One on-site instrument repair, including travel, labor and parts, for a period of one year. Response time of 5 business days. Includes one Planned Maintenance during the Core Agreement period.

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QIAcuity Eight, Core Agreement

Cat no. / ID. 9245361

One on-site instrument repair, including travel, labor and parts, for a period of one year. Response time of 5 business days. Includes one Planned Maintenance during the Core Agreement period.

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QIAcuity One 5plex, Full Agreement

Cat no. / ID. 9245363

On-site instrument repair, including travel, labor and parts, for a period of one year. Response time of two business days. Includes one Planned Maintenance during the Full Agreement period.

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QIAcuity Four, Full Agreement

Cat no. / ID. 9245364

On-site instrument repair, including travel, labor and parts, for a period of one year. Response time of two business days. Includes one Planned Maintenance during the Full Agreement period.

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QIAcuity Eight, Full Agreement

Cat no. / ID. 9245365

On-site instrument repair, including travel, labor and parts, for a period of one year. Response time of two business days. Includes one Planned Maintenance during the Full Agreement period.

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QIAcuity One, Installation & Training

Cat no. / ID. 9245352

On-site service that includes the setup of instrument hardware and system software along with hands-on application training for up to four lab staff members to ensure smooth integration into laboratory workflows.

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QIAcuity Four, Installation & Training

Cat no. / ID. 9245353

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QIAcuity Eight, Installation & Training

Cat no. / ID. 9245354

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Resources

Fast. Scalable. Reliable.

A versatile workflow for the detection of low-abundance microbes

Version 11

The Volume Precision Factor (VPF) offers a unique feature to secure precision of concentration results obtained from a QIAcuity dPCR run.

In general, Nanoplates provide partitions of fixed sizes that enable a very precise way of sample concentration calculation. Potential variation of partition sizes in Nanoplate batches, caused by different microstructure molding forms, can be addressed by applying the batch specific VPF. Furthermore, the VPF includes well-specific volume information and therefore further increases precision of concentration calculation in each well of the Nanoplates.

The QIAcuity dPCR System, complemented by the QIAcuity Software Suite version 2.5 and higher, offers a powerful solution for determining DNA integrity and stability. Analyzing up to 5 targets simultaneously enables accurate and precise integrity assessment. The importance of determining genome integrity becomes particularly evident in analyzing viral vectors such as AAVs, which are known for their susceptibility to packaging errors. Moreover, dPCR is a valuable tool for assessing DNA stability, providing valuable insights into storage and processing impacts.

Here we demonstrate how to optimize your assays on a microfluidic nanoplate-based digital PCR system, the QIAcuity, and provide recommendations for a seamless transfer. Moreover, the QIAcuity dPCR workflow is very similar to qPCR.

Digital PCR (dPCR) is a powerful technique that detects and quantifies ultra-rare mutations in a high background of wild-type cfDNA down to 0.1% variant allele frequency. Here, we describe end-to-end manual and automated workflows that enable accurate detection and absolute quantification of ultra-rare PIK3CA variants in cfDNA using the QIAcuity Digital PCR System.

With the cellenONE-QIAcuity workflow, we achieved high-throughput absolute quantification of low-abundance targets at the single-cell level. cellenONE’s single-cell isolation platform enabled real-time and 100% accurate single-cell isolation without compromising viability and transcript expression. This allowed us to use the exact number of intact cells for RT-dPCR reactions. Moreover, the elimination of the RNA purification step significantly reduced hands-on time, and QIAcuity’s probe-based chemistry allowed the multiplexing of up to five targets in a one-step RT-dPCR format with no or minimal optimization.

Here we compared the performance of qPCR and the nanoplate dPCR techniques. The digital PCR method on the QIAcuity significantly improved precision when measuring copy number states and sensitivity of mutation detection through absolute quantification and reduced standard error. This is advantageous in various applications, including copy number variation analysis, small fold-change and rare mutation detection.

Here, we present a workflow that combines two technologies, cellenONE and QIAcuity Digital PCR, which accelerate and streamline high-throughput analyses of target copy numbers in cultured cells. The workflow starts with detecting and sorting defined populations of cells as well as individual cells using cellenONE, followed by multiplexing dPCR on the QIAcuity platform. Copy number variations of target regions are then analyzed using the QIAcuity Software Suite, providing an intuitive and fast interpretation of results.

Here, we present a highly efficient, high-throughput workflow that combines two technologies, cellenONE and QIAcuity Digital PCR, to accurately analyze miRNAs in well-defined individual cells and populations of cells.

Q-Solution is an innovative and versatile PCR additive that works in part by lowering the melting temperature of DNA. Adjusting template melting properties can be useful when interrogating DNA with high-GC content or with complex secondary structures, such as adeno-associated virus (AAV) genomes. Q-Solution has additional properties that can be used to mitigate the carryover of various PCR inhibitors. This application note will highlight a few examples of how the Q-Solution Kit can be used in QIAcuity workflows.

The goal of this work was to compare performance of quantitative PCR (qPCR) and digital PCR (dPCR) in the quantification of gene expression and Wolbachia abundances in Nasonia parasitoid wasps.

The QIAcuity digital PCR system combined with the QIAcuity One-Step Viral RT-PCR Kit enables precise detection and quantitation of vector-borne viruses in mosquitoes. The results presented in this comparison study showed that digital PCR is a powerful tool for absolute quantitation of low abundant targets and is a more reliable detection method than qPCR. Multiplexing allows detection and quantitation of multiple targets in a single reaction more efficiently by increasing sample throughput at a reduced cost per target.

This study tested a workflow for quantitation and qualification of AAV samples using a duplex assay on the QIAcuity dPCR instrument targeting both an insert (GFP) and the viral backbone (AAV2-ITR). With very low intra-assay and inter-assay CVs <6.5%, we demonstrate one of the main benefits of dPCR: reproducibility.

The QIAgility instrument is a liquid handler designed for automating PCR setup. For compatibility with the QIAcuity, we developed an adapter to secure up to two nanoplates onto the deck of the QIAgility. Using the QIAgility software, we have optimized a protocol that works for all nanoplate types and QIAcuity applications. Here we report the performance of a front end automated QIAgility dPCR nanoplate setup procedure for use with the QIAcuity dPCR system.

Here we provide an integrated rAAV genome titer method using the QIAcuity Digital PCR (dPCR) System with detailed parameters for high assay performance. Using this optimized method for pre-PCR handling of in-process rAAV samples, the results demonstrated that QIAcuity dPCR system generates the same level of accuracy and precision as the current gold standard ddPCR system but with much faster sample-to-result times (2 hours vs 7 hours) and higher overall throughput and scalability.

Here we report the use of saliva samples in combination with dPCR as a suitable alternative to screen for individuals infected with SARS-CoV-2.

Compliance with 21 CFR Part 11 involves both technical (i.e., hardware and software) and procedural requirements. This document explains how the QIAcuity system contributes to fulfilling those technical requirements.

A new temperature gradient functionality to determine the optimal primer annealing temperature of a digital PCR assay

Version 2.1.8

Version 2.5

Version 3.0

Version 3.1.1

Version 2.1.8

Version 3.2

Version 2.1

For Version 2

Version 3.0

Version 3.2

Version 2.2

Version 3.1

For Version 1.0

Version 2.5.0.0

For Version 2.0

Version 3.1.3

Version 2.2

Version 2.1

Version 3.1

For Version 1.2

Version 2.5.0.1

December 2025

Guidance on resolving audit trail logging issues in QIAcuity Software Suite versions 3.1 and 3.2

July 2024

Note about a known issue of the remaining PostgreSQL database after updating to the QIAcuity Software Suite version 2.5.0.0 and 2.5.0.1

November 2025

User manual for QIAcuity instruments and QIAcuity Software 3.0

User manual for QIAcuity instruments and QIAcuity Software 2.1

Extension to the QIAcuity User Manual for QIAcuity Software version 3.1.1

User manual for QIAcuity instruments and QIAcuity Software 3.1

May 2025

User manual for QIAcuity instruments and QIAcuity Software 2.0

User manual for QIAcuity instruments and QIAcuity Software 1.2

User manual for QIAcuity instruments and QIAcuity Software 2.5

QIAcuity backup and restore scripts for QIAcuity Software Suite versions 2.0, 2.1.7, 2.1.8, and 2.2

User manual for QIAcuity instruments and QIAcuity Software 3.2

Extension to the QIAcuity User Manual for QIAcuity Software version 3.2

User manual for QIAcuity instruments and QIAcuity Software 2.1.8

For QIAcuity Software Suite version 3.1 or higher

QIAcuity backup and restore scripts for QIAcuity Software Suite version 2.5

User manual for QIAcuity instruments and QIAcuity Software 2.2

For QIAcuity Software Suite version 3.0

For QIAcuity User Manual – Updated QIAcuity Nanoplate Partition Volumes

For QIAcuity Software Suite 1.2: Updating VPF for archived or exported plates

Updating QIAcuity Software Suite 1.1.3 and Control Software 0.5.2.18 to QIAcuity Software 2.0

Network connection of QIAcuity instruments

For software version 3.1.1.0

Download Safety Data Sheets for QIAGEN product components.

FAQ

This is not needed. The QIAcuity is equipped with a flexible power supply technology and operates within a range of 100–240V AC, 50/60 Hz, 1500 VA (max).

FAQ-3761

The instrument software GUI shows error codes including a description and information how to resolve the error. The instrument touchscreen shows an alarm icon in the upper right corner that turns red in case of an instrument failure. Accessing the System Status in the Tool tab allows users to clear errors. Rebooting of the instrument is required to complete the removal of the error. Please do not skip this step. You may always contact QIAGEN Technical Services in case of any question.

FAQ-3763

The user manual contains instructions on how to perform a regular cleaning and decontamination, and how to replace air filters on the QIAcuity instruments. A regular maintenance reduces the dust in the instrument and therefore minimizes the presence of dust particles on the nanoplate, which might interfere with the plate analysis.

FAQ-3765

If you had run a nanoplate for which the installed VPF misses the specific factor, the software will notify you. If you then analyze without the specific VPF, the impact depends on the variation of the partition volume of the new Nanoplate batch compared to the latest. Typically this variation is ±6–7% (approx. 5% CV over the entire plate). The analysis may be repeated after updating the VPF file. After installing the latest VPF and re-analysis of the run, a copy of the plate is generated in the QIAcuity Software Suite including the new results.

FAQ-3769

Yes, the report includes a notification if the matching VPF was missing and, therefore, not applied to the analysis. If the matching VPF was applied there is no notification on the report.

FAQ-3770

If you had analyzed your nanoplates without VFP, the impact depends on the variation of the partition volume of the new nanoplate batch compared to the latest. The VPF reduces the CV from approximately 5% to 2%. We recommend to reanalyze results in case the data originated from different wells (e.g., copy number variations or gene expression data sets for which the reference sample was measured in a different well). Results obtained across different plates should also be r-analyzed. A reanalysis is not required for assay data that were analyzed within the same well (e.g., mutation rate determination using two channels within the same well).

FAQ-3771

A standard PCR plate is required to set up dPCR reaction before transferring it to the nanoplate to ensure a proper mixing of the reaction mix before partitioning.

FAQ-3774

QIAGEN master mixes are optimized for nanoplate microfluidics and are recommended to be used with our dPCR system. They also include an optimized reference dye required for proper analysis.

FAQ-3777

All DNA samples used in reaction mixes should show similar quality and quantity, which can easily be assessed using UV spectrophotometry. DNA samples with an average length of ≥20 kb (e.g., genomic DNA purified via spin column with silica membrane) should be fragmented by restriction digestion before partitioning. Enzymatic fragmentation of larger DNA ensures an even distribution of template throughout the QIAcuity Nanoplate, which in turn leads to an accurate and precise quantification.

FAQ-3778

The QIAcuity Probe PCR Kit should be stored immediately upon receipt at –30 to –15°C in a constant-temperature freezer and protected from light. The QIAcuity Probe PCR master mix can also be stored protected from light at 2–8°C. Components are stable for 12 months, unless otherwise indicated on the label.
The QIAcuity EG PCR Kit should be stored immediately upon receipt at –30 to –15°C in a constant-temperature freezer and protected from light. The QIAcuity EG PCR master mix can also be stored protected from light at 2–8°C. Components are stable for 6 months, unless otherwise indicated on the label.
The QIAcuity Nanoplates does not have expiry date and are stable for at least 1 year when stored at RT.

FAQ-3780

The plate is designed for a single use run. For example, even if only 30 samples are loaded into the 96-well plate, a whole plate will be sealed by the roller. It can't be unsealed and used for another run. The QIAcuity Software won’t allow to set up a separate experiment for the same nanoplate to avoid that previously processed plates being not partitioned a second time.

FAQ-3781

An essential temperature gradient functionality was introduced with software version 2.5. When updating older software versions to 2.5, each QIAcuity instrument will offer the temperature gradient and may be used to find the best cycling temperature for new dPCR assays. When running a QIAcuity Four or a QIAcuity Eight, all plates may have their own temperature profile, including the option for a temperature gradient.

FAQ-3783

The VPF provides a set of well-specific and molding form-specific factors used to specify the exact reaction volume of a nanoplate, thus increasing the concentration calculation of each well.

FAQ-3784

In general, nanoplates provide partitions of fixed sizes that enable a very precise way of sample concentration calculation. If a new molding form is used for nanoplate manufacturing, potential variation of partition sizes can be addressed by applying the molding form-specific VPF. Thus, each time a new molding form is used, a new VPF is created and made available. Currently, the VPF is updated once every 3–6 months.

FAQ-3785

In dPCR we measure the absolute concentration of targets at endpoint reaction. Concentrations of unknowns can be determined based on dPCR results observed (number of negatives, number of positives, and partition volume analyzed).

FAQ-3786

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Solutions for Laboratory-Developed Tests

QIAcuity Digital PCR System

For nanoplate-based digital PCR applications

QIAcuity One, 2plex Device

Features

Product Details

Performance

Principle

Procedure

Applications

Software

Services

Supporting data and figures

A simple and rapid plate-based workflow

Kits & Consumables

Service Plans

QIAcuity One 2plex, Full Agreement

QIAcuity One, Preventive Subscription

QIAcuity Four, Preventive Subscription

QIAcuity Eight, Preventive Subscription

QIAcuity One 2plex, Core Agreement

QIAcuity One 5plex, Core Agreement

QIAcuity Four, Core Agreement

QIAcuity Eight, Core Agreement

QIAcuity One 5plex, Full Agreement

QIAcuity Four, Full Agreement

QIAcuity Eight, Full Agreement

QIAcuity One, Installation & Training

QIAcuity Four, Installation & Training

QIAcuity Eight, Installation & Training

Resources

FAQ