home | purchase | services | contact | about


The Multiplex Assay Reader System (MARS) is a powerful but easy to use optical instrument that automatically analyzes multiplexed assays based on Parallume optical encoding technology.


The Multiplex Assay Reader System (MARS) is a powerful but easy to use optical instrument that automatically analyzes multiplexed assays based on Parallume optical encoding technology. The MARS instrument, which measures up to six Parallume encoding colors and three reporter colors, includes MARSoft software that designs the multiplex experiment, configures data acquisition, collects imaging data and provides the target signal level associated with each bead code. The MARS can also function as a general use, multicolor fluorescence microscope using standard 25mm x 75mm microscope slides.

The MARS Parallume bead analysis instrument (Fig. 1), is a small footprint (24cm x 35cm x 22cm H = 9.5” x 14” x 8.5” H), self-contained benchtop system which provides completely automatic data acquisition for bead-based, highly multiplexed assays built on the Parallume optical encoding platform (Parallume Beads). For each of 12 or 48 wells in the BLS, the MARS collects an image for each Parallume color on each bead and uses this information to sort each bead into its optical bin (Parallume Beads). The MARS also measures the reporter signal level for each bead and reports the target signal level for that optical code, i.e. for that particular probe. You just load the Bead Localization Slide (BLS) into the MARS and, using the refreshingly simple and intuitive MARSoft interface, you can quickly, simply and easily design, perform and analyze any nucleic acid or antibody-based multiplexed assay.

Multiplex Assay Reader System (MARS)
Fig. 1 The Multiplex Assay Reader System (MARS) instrument acquires imaging data on the Parallume encoded beads allowing interpretation of the multiplex assay results.

We are very pleased to say that the MARS instrument and the MARSoft software are both 100% designed and built in Santa Clara, CA. You won’t find inexpensive stamped chassis components, low grade optics and cameras, imprecise and irreproducible mechanical motion, software which is confusing, unclear or written in confusing English. Instead you will find a CCD camera from Digital Instruments, Mitutoyo objectives and locally designed and built printed circuit boards, wiring harnesses. Like the hardware, we developed and tested 100% of the control, acquisition and analysis software in house here in Santa Clara. We are very proud to offer this American designed and manufactured instrument built using locally-sourced California science, engineering and manufacturing talent.

The technical specifications of the MARS instrument may be found in Appendix 1. Additional operational details may be found in the User Manual. The discussion below provides information on the following MARS related topics:

  • How the MARS Measures Parallume Codes
  • Using the MARS
  • Technical Specifications

How the MARS Measures Parallume Codes and Reporter Levels

The Multiplex Assay Reader System (MARS) is a fluorescent bead reading instrument which (a) measures the Parallume optical code for each bead and (b) determines the reporter signal on the beads of a measured Parallume optical code which in turn provides information about the concentration of a particular target relative to a standard. The MARS performs these operations by imaging the beads using multiple excitation sources and emission filter combinations and then extracting relative fluorescent emission intensity information for various colors.

After the multiplex assay has been performed, the beads are simply loaded into the Bead Localization Slide (BLS) as described in Bead Handling Devices, the BLS placed into the MARS and, after designing the multiplex assay in MARSoft, the beads are scanned and analyzed in a completely automatic fashion. The wells in the archivable BLS, which are available with 12 3mm or 12 6mm wells on a 96-well format, or 48 wells on a 384 format, each contain the beads from a multiplex assay on a different multicomponent target mixture. For example, each well might contain a sample from a different patient, location or other singular event screened to determine the presence and amount of each target in the sample.

The MARS automatically moves the BLS from well to well imaging the beads in each well. The Parallume is imaged with a 320nm UV LED and the red, green or blue reporters are imaged at 632nm, 532nm and 488nm, respectively, with appropriate excitation and emission filters present. At each well the MARS measures the Parallume optical code, which identifies the capture probe for that particular bead set, and the reporter signal level that relates to target concentration for each bead/capture probe pair.

Each uniquely encoded Parallume bead set is permanently assigned an Code Designator Number (CDN) when manufactured. When the CDN for a given encoded bead set is input during the multiplex experimental design setup in MARSoft, the MARS automatically configures all optical components and acquires the bead images in each well using the appropriate excitation sources and emission filters. The MARS first images the beads under excitation from a 320nm UV LED and the appropriate emission filters used to separate and quantify the relative fluorescent emission intensity of the multiple Parallume colors which constitute the Parallume optical code. The relative fluorescent intensity of the Parallume colors are used subsequently to determine into which optical bin each bead is sorted, i.e., which probe is attached to that particular Parallume code.

The amount of up to three different reporter detected is proportional to the amount of target present. The MARS detects the reporter signal intensity on a given Parallume optical code by imaging the beads with appropriate excitation and emission filters.

Using the MARS

The MARS is extremely simple to use. You simply load the sample in the BLS, place the BLS in the MARS and, after configuring the experimental design and parameters in MARSoft, the MARS automatically scans the samples and analyzes the results.

More details can be found in the User Manual. The outline of the sequence of steps for data collection is as follows:

  1. Place BLS into MARS.
  2. Configure experimental setup in MARSoft.
  3. Input number and color of reporters used.
  4. Input which Parallume codes will be used and the MARS automatically configures all optical parameters
  5. MARS automatically collects data
  6. The analysis module of MARSoft analyzes the data and provides the reporter level statistics associated with each reporter/Parallume optical code.


The MARS instrument can conveniently, quickly and rapidly measure the results from any multiplex assay performed on optically encoded Parallume beads. The MARS has a flexible configuration in terms the optics and hardware required for a given number of Parallume codes (i.e., the multiplex depth desired) and reporter colors. The configuration and cost of the MARS instrument can match your experimental workflow in terms of number of Parallume codes and reporter colors. Please see the Purchase section for the options and configurations available for the MARS.

Appendix 1: Multiplex Assay Reader System (MARS) Technical Specifications

Specification or Item
Value, Range or Amount
Dimensions 24cm x 35cm x 22cm H = 9.5” x 14” x 8.5” H
Weight 10.5 Kg (~23Lb)
Power Requirements 4.0 Amps, 120V (or 1.5Amps, 240V) 50-60Hz
Sample Holder 25mm x 75mm Bead Localization Slide (BLS)
Microscope Objective 5X Mitutoyo ∞ Plan APO NA (0.14) WD(34 mm)
Camera SPOT camera from Diagnostic Instrument
  • 4MP monochrome CCD, gigabit Ethernet
  • >30 fps
Microscope Objective Stage 5X Mitutoyo motorized focus; other mag. optional
     Travel 7mm
     Accuracy 10µm
x, y Stage  
     Travel 100mm in x and 125mm in y
     Accuracy 10µm
Excitation Sources 2 UV LED standard for Parallume excitation; slots for up to 6 5W VIS LEDs for reporter excitation
Color Capability 6 Parallume colors and 3 reporter colors
PC Windows 7 and 8, 4GB RAM, 500GB Hard Drive, MARSoft

[back to top]