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.


Pipette 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.

  1. Transfer
  2. Run
  3. Read


Pipette samples and assays into the designated inlets on the IFC.


Place the IFC in Juno and press Start.



View the IFC results on your Biomark™ HD system.



IFCs, Assays and Reagents

Dynamic Array IFCs

Experience a new level of efficiency and throughput for genotyping applications with Fluidigm’s Dynamic Array IFCs.

Digital Array IFCs

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

Juno 96.96 Genotyping IFC

Transform your workflow with this innovative IFC, which leverages multiple layers and advanced valve controls to achieve preamplification and SNP genotyping in one step.


SNP Type Assays

Leverage a flexible, economical solution for single nucleotide polymorphism (SNP) genotyping with Fluidigm's SNP Type™ assays.

D3 Assay Design

Simplify your assay design with our D3™ tool, which enables you to easily define parameters for customized gene expression, genotyping and targeted DNA sequencing.

Delta Gene Assays

Specify your genes of interest and target species to order our custom high-quality, economical and MIQE-compliant Delta Gene™ assays.

SNP Trace™ Panel

Ensure accurate sample identification with an authoritative panel of 96 SNPs that determine specific attributes around gender, ancestry or polymorphism across populations.

  1. Dynamic Array IFCs
  2. Digital Array IFCs
  3. Juno 96.96 Genotyping IFC
  4. SNP Type Assays
  5. D3 Assay Design
  6. Delta Gene Assays
  7. SNP Trace™ Panel

Related Systems

Biomark HD

Biomark HD Analyze single-cell gene expression with real-time PCR, industry-leading flexibility and consistently high-quality results on the Biomark™ HD system.

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. Biomark HD
  2. IFC Controllers


SNP Genotyping Analysis

Highly accurate genotyping analysis software addresses genotyping's specific needs with an advanced automatic cluster-calling algorithm, multiple chip scoring and automatic confidence score. Created for use with Biomark, EP1™ and Juno™ systems.

Singular Analysis Toolset

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.

Real-Time PCR Analysis

Quick and efficient Real-Time PCR Analysis software helps you easily establish standard curves, calculate delta delta Ct and automatically determine the ideal threshold setting for each run. Specifically created for Biomark systems. 

Digital PCR Analysis

Featuring tools specific to digital PCR, our innovative software offers real-time analysis, automated copy number variation, end-point imaging and the ability to quantitate up to four targets per sample using multiple reporter dyes. Designed for use with Biomark and EP1 systems. 

  1. SNP Genotyping Analysis
  2. Singular Analysis Toolset
  3. Real-Time PCR Analysis
  4. Digital PCR Analysis


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 4ºC - 99ºC
Max heating rate: > 4ºC/sec
Max cooling rate: > 3ºC/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


Height 19.7in (50 cm)
Width 17.3 in (43.9 cm)
Depth 27.5 in (69.8 cm)
Weight 137 lb (62 kg)

Thermal Control

Peltier-based 4–99 ºC
Max heating rate >4 ºC/sec
Max cooling rate >3 ºC/sec

IFC Compatibility

Dynamic Array™ IFCs 48.48, 96.96, 192.24, Flex Six
Digital Array™ IFCs 12.765, 48.770, qdPCR 37K

Data Storage

Ethernet connection 1GB/sec
Hard drive 40GB
Port USB port
Computer Internal CPU
touchscreen interface