Biomark HD

Production-scale throughput with exquisite single-cell sensitivity and consistent results


High-Definition Biology

No more compromising for quality. With the Biomark™ HD system, you get reliable production-scale throughput and exquisite single-cell sensitivity, with a wide variety of sample types and chemistry choices to accommodate the most genomic applications. Now you can run entire projects from research to validation to routine screening on a single system with the flexibility you want and the consistency you need. Anything else we can help with?


Design experiments to match your needs across the widest range of genomic applications.


Detect unique molecular signatures in individual cells and rare cell populations.


Accelerate discovery with a higher throughput and automated workflow.


Conserve precious samples—and funding—with lower reagent use and nanoliter reactions.


Fluidigm’s revolutionary integrated fluidic circuits (IFCs) empower life science research by automating PCR reactions in nanoliter volumes. This means using less sample and reagent, and a single microfluidic device, to achieve the high-quality, consistent results your work depends on. The Biomark HD system runs IFCs in either real-time or end-point read modes, bringing flexible, efficient and economical PCR solutions to a range of applications.


  1. Prime
  2. Transfer
  3. Load
  4. Run
  5. Analyze


Prime the Dynamic Array IFC to prepare it for sample transfer.


Pipet samples and primer-probe sets into the designated inlets on the IFC.


Load the IFC on the controller, which prepares the reactions.


Place the IFC into Biomark for thermal cycling and end-point or real-time fluorescence detection.


View and analyze color-coded expression heat maps, allele maps and cluster plots for single or multiple runs with our analysis software.


Biomark & EP1 Support

Explore tutorials and publications, browse frequently asked questions, download technical documents, review training programs and service plans and locate the right IFCs, kits and reagents for your research. Still need help? Reach out to one of our support specialists here


IFCs, Assays and Reagents

Digital Array IFCs

Ensure a precise determination of copy number variation with this innovative IFC designed specifically for digital PCR experiments.

Dynamic Array IFCs

Experience a new level of efficiency and throughput for gene expression and genotyping applications with the Fluidigm Dynamic Array™ IFCs used together with the Juno and Biomark HD systems.

D3 Assay Design

Simplify your assay design with our D3™ tool, which enables you to easily define parameters for customized targeted DNA sequencing, gene expression and genotyping. For species not supported online, support is available from the D3 expert design team.

SNP Type Assays

Leverage the high-throughput and economical single-nucleotide polymorphism (SNP) genotyping solution made possible by allele-specific PCR with our SNP Type™ assays (formerly SNPtype). Designed especially for use with Dynamic Array™ IFCs.

Delta Gene Assays

Realize the full potential of your Biomark™ HD system with minimal setup time and validated protocols that yield quality gene expression results. Just specify your genes of interest and target species to order our exclusive, high-quality, economical and MIQE-compliant Delta Gene™ assays (formerly DELTAgene). Designed specifically for use with Dynamic Array IFCs.

  1. Digital Array IFCs
  2. Dynamic Array IFCs
  3. D3 Assay Design
  4. SNP Type Assays
  5. Delta Gene Assays

Related Systems

IFC Controllers

IFC Controllers Benefit from fewer steps and automated setup of our Dynamic Array™ and Digital Array™ IFCs with Fluidigm’s highly efficient IFC controllers.
  1. IFC Controllers


Biomark & EP1 Software

The Biomark/EP1 software package includes:

Data Collection Software v4.2.2


SNP Genotyping Analysis v4.3.2
SNP Genotyping software analyzes genotyping data acquired from Biomark™ or EP1 systems. Advanced features include a cluster-calling algorithm, multiple IFC scoring and automatic confidence score ratings.


Real-Time PCR Analysis v4.3.1
Real-Time PCR Analysis software helps you quickly and easily create standard curves, calculate DDCt and automatically determine the ideal threshold setting for each run. Specifically created for Biomark™  systems.


Digital PCR Analysis v4.1.2
Our innovative Digital PCR Analysis software offers real-time and endpoint dPCR analysis,
automated copy number variation, and the ability to quantitate up to four targets per sample.
Designed for use with Biomark™ and EP1™ systems.


Melt Curve Analysis v4.1.3

Singular Analysis Toolset Software v3.5.2

An innovative, open-source solution for analyzing and visualizing data, the Singular™ Analysis Toolset offers powerful methods for identifying gene expression and mutation patterns at the single-cell level. Designed for use with Biomark and C1 systems.

  1. Biomark & EP1 Software
  2. Singular Analysis Toolset Software v3.5.2


Dimensions as Shipped

Height 58 in (147 cm)
Width 40 in (102 cm)
Depth 40 in (102 cm)
Weight 459 lb (208 kg)


Height 39.4 in (100 cm)
Width 29.5 in (75 cm)
Depth 29.5 in (75 cm)
Weight 308 lb (140 kg)

IFC Controller

Height 13 in (33 cm)
Width 9.5 in (24 cm)
Depth 19 in (48 cm)


IFC Throughput (reactions per run)
48.48 Dynamic Array™ 2,304
96.96 Dynamic Array 9,216
12.765 Digital Array™ 9,180
48.770 Digital Array 36,960
192.24 Dynamic Array 4,608
Flex Six™ Dynamic Array 144 x 6 separate partitions


LED excitation Sources (center, in nm)

475-41, 530-16, 575-31
Optional: 632-27

Emission filters (center, in nm)

525-25, 570-30, 630-30
Optional: 700-30

Detection CCD camera; 9MPixel, 12 µm; 12 µm pixel size
Thermal control

Peltier-based, ranging from 4 ºC to 99 ºC
Max heating rate: >4 ºC/sec
Max cooling rate: >3 ºC/sec


Fluidigm Real-Time PCR Analysis software
Fluidigm SNP Genotyping Analysis software
Fluidigm Digital PCR Analysis software
Fluidigm Data Collection software

Computer and accessories Windows® XP PRO, having at least 2 GB memory, 300 GB hard drive, 4 USB ports, LCD flat screen monitor, keyboard and mouse
Data storage options 1 GB/sec Ethernet connection; 40 GB hard disk space; USB port for memory stick