CloneSelect Single-Cell Printer - Cytena

CloneSelect Single-Cell Printer

Demonstrate monoclonality with greater confidence

The CloneSelect™ Single-Cell Printer™ by Cytena and Molecular Devices is a fully automated system that utilizes proprietary microfluidics-based technology and real-time image analysis to sort and deposit single cells into standard microplates—while simultaneously providing assurance of monoclonality through image documentation. 

  • Isolate single cells with high efficiency (>80%) and high cell viability (75%) 
  • Provide consistent, high-quality image evidence of monoclonality to the FDA
  • Minimize cross contamination with disposable cell printing cartridges
  • Print a variety of cell types (CHO, HEK, hybridoma, etc) into standard 96- or 384-well plates


Demonstrate monoclonality for cell line development

Cell line development is a critical step in the generation of biologics such as monoclonal antibodies. This process involves the isolation of single cells and downstream characterization of clones for productivity, quality, and stability.

Current workflows in cell line development have drawbacks including reduced cell viability, inefficient single cell isolation, and limited evidence for clonality:

  • Limiting dilution, the standard technique most often used to isolate single cells, relies solely on statistical probabilities to achieve single cell deposition. At best, limiting dilution yields only 30% single cell-containing wells; the majority will be void or doublet wells. Additionally, slight inaccuracies in cell counting and/or dilutions can significantly reduce the probability that a single cell was seeded. 
  • Flow cytometry-based single-cell sorting, in contrast to limiting dilution, offers the inverse advantages and disadvantages: strong evidence of monoclonality and high efficiency, but low viability due to shear stress and pressures cells are exposed to.

The CloneSelect Single-Cell Printer (SCP) addresses the limitations described above with a technology that provides image-based evidence for monoclonality, efficient and fast single-cell seeding combined with excellent cell viability, and low risk of cross-contamination. 

Single cell printing efficiency greater than 80%, better than other traditional methods

Traditional methods of single cell isolation are compared with that of the CloneSelect SCP. The SCP provides significant advantages over those techniques in efficiency of deposition and viability of clones.

Comparison of single cell isolation and deposit efficiency between limiting dilution, single-cell printing, and flow cytometry
96-well microplates containing cells isolated using different methods are shown.  The CloneSelect SCP provides significant advantages over those techniques in efficiency of deposition and viability of clones. (A) 64% of wells contain viable single cells. (B) 20% of wells contain viable single cells. (C) 25% of wells contain viable single cells.

Instantaneous evidence for monoclonality

Equipped with a high resolution and large depth-of-field camera that ensures cells appear in focus >99% of the time, the CloneSelect SCP can capture images of single cells at the cartridge nozzle as they are being deposited into microplates. Combining together with the CloneSelect Imager, researchers can now capture the journey of a single cell from the moment it is dispensed to the formation of a colony several days later, thus providing additional evidence of monoclonality. 

showing single cell deposition by CloneSelect Single-Cell Printer
These images illustrate the path of a single cell prior to and following ejection from the nozzle tip. Images 1-3 show the cell approaching the nozzle. Image 4 shows the detection of a single cell (inner circle) and the absence of any cells in the vicinity (outer circle). Finally, image 5 shows the nozzle after droplet ejection to provide evidence that the single cell was expelled from the nozzle.
Images of colony formation are captured by the CloneSelect Imager after single cell deposition via single-cell printing
Example image of a single cell printed on the SCP and imaged on the CloneSelect Imager for several days post-print. The viability of a single cell clone can be monitored with label-free imaging following single-cell printing.

Isolate more viable clones with confidence

One drawback of the current methods is low cell viability observed post sorting and isolation. For example, cell viability is commonly <25% with flow cytometry-based methods. The CloneSelect SCP’s unique microfluidics-based print technology is as gentle as pipetting. The cell-containing microdroplets are dispensed slowly and delicately in the absence of any pressure, electric fields, or lasers observed in other technologies. These features make the SCP’s performance on par with limiting dilution when it comes to isolating healthy cells.

viability Data Comparing Limiting Dilution with Single Cell Printing
(A) Following single-cell deposition with the CloneSelect SCP, the printed single cells remain viable and form a monoclonal colony with a span of several days. The cells were imaged at high resolution directly after single-cell printing (day 0) on the CloneSelect Imager and subsequently for a number of days to follow the growth characteristics of the candidate clones. (B) Single cell colonies (shown in green) derived from limiting dilution are compared to equivalent colonies from the CloneSelect Single-Cell Printer by imaging on day 10 with the CloneSelect Imager. A representative 96-well plate imaged on the CloneSelect Imager is shown for limiting dilution and SCP. A total of 28 single-cell clones resulted from limiting dilution, while 68 colonies resulted from single-cell printing. The higher efficiency of single cell deposition along with similar viabilities allow researchers to characterize more clones per plate, significantly increasing throughput and reducing time. 


Clonal Outgrowth from Limiting Dilution Compared with Single Cell Printing
(C) Clonal outgrowth from limiting dilution is compared with that of single cell printing.  (D) The viabilities of single cell wells obtained from different cell types are compared. Single-cell printing can be used to print a wide variety of cells, resulting in high viability. Note that cell viability can vary based on cell type and sample preparation, cell media, gating parameters, and other external factors. A typical viability of 75% was observed when using CHO-K1, HEK, and other common cell lines.


Instrument specifications

Instrument dimensions (mm) 550 (W) x 510 (H) X 400 (D)
Instrument weight 30 kg
Computer dimensions (mm) 270 (W) x 325 (H) X 270 (D)
Computer weight 6.5 kg
Additional space considerations Biological Safety Cabinets
• BSC depth > 400 mm
• BSC width > 600 mm
• Max. front window opening > 400 mm
• External table with 600 x 600 mm space for control PC and peripherals
Power requirements Three power sockets with 100 - 240 VAC, 50-60 Hz
Maximum power consumptions are:
• Lab Robot: ca. 1.34 - 0.55 A (100-240 VAC); max. 135 W
• Computer: ca. 0.41 - 0.21 A (100-240 VAC); max. 41W
Environmental conditions Temperature: 10o - 30o C
Humidity: 10 - 80% (non-condensing)
Axis system and precision Open three-axis Gantry system with ca. 100 mm precision or less (not including backlash); print-head mounted on z-axis, which includes optics, dispenser, agitation, etc.
Optics ca. 10x magnification with 90o beam deflector, bright-field, c-mount
Cell camera 8-bit greyscale, 1280-1024 pixels
Droplet camera 32-bit RGB, 1280-1024 pixels
Microplate compatibility • SBS or SLAS standard cell culture well plates (96 and 384 well format*)
• Not compatible with deep well plates, PCR plates, or skirt-less/frameless plates 

*May be customizable with additional formats (6-well to 24-well, tubes)
Microplate capacity 2 destination plates
Disposable compatibility SCP cartridges and Eppendorf 200 mL pipette tips (Eppendorf Order No. 0030 073.428 for agitation)
Instrument sterility Resistant against 70% Ethanol, Resistant against UV (254 nm CWL)
Component sterility Metal piston guide, tubing (agitation and shutter), and Luer-Lock connectors are resistant to ethanol and isopropanol. Piston guide and tubing can be autoclaved (121o C)
Status lights • Green: shows power status of the device
• Yellow: indicates dispensing
• Blue: indicates axes movement
Sterile filters Sterile filters must support Luer-Lock in and out connections. Pore sizes can be 0.2 μm, 0.45 μm, 0.8 μm, or 1.2 μm

SCP cartridges

Cartridge dimensions (mm) ca. 8.8 (W) x ca.16 (H) x ca. 5 (D)
Nozzle dimensions (mm) ca. 40 x 40
Reservoir volume 80 µL
Chip material Glass and silicon
Cartridge compatibility PBS and cell growth media (depends)
Cell concentrations Recommended 0.5 – 1x106 cells/mL
Recommended cell/bead sizes 40 µm nozzle width (5-35 µm beads or cells)
Cartridge sterility UV sterilized, TSE/BSE-free


Printing efficiency Average single-cell deposit efficiency >80%*
Printing speed Average 5-10 min for 96 well plate**
Cell viability Average cell viability of 75%***
Image focus >99% of images in focus
Conformity CE and QPS

Computer Specifications

Operating system Windows 7 64-bit Professional (language: English)
Software Included: SCP control software and License
Data storage 120 GB solid state drive
Networking 2x GigE network slots
Processor AMD Quadcore 4x 2.0 GHz


Image tracking 5 per well. 4 prior to deposit, 1 post-deposit
Image format, size JPEG, 1280x1024 pixels, 200 kb per image
Data size 110 MB per 96 well plate

*Deposit efficiency can vary based on cell type, cell density, gating parameters, and cell media used. The efficiency of bead deposit under more controlled conditions typically exceeded 90%

**Print time can vary based on cell density and gating parameters used. The average print time for beads at 1x10beads/mL concentration was 5 - 10 minutes.

***Cell viability can vary based on cell type, sample prep, gating parameters, cell media, and other external factors. A typical viability of 75% was observed when using CHO, HEK, and other common cell lines.

North America

To get pricing information, please submit a quote request.


Other Regions

The CloneSelect Single-Cell Printer is available only in North America. For information about single-cell printing products outside of North America, please contact cytena GmbH.

cytena GmbH
Georges-Koehler-Allee 103
D-79110 Freiburg

 Cytena GmbH

CloneSelect Single-Cell Printer Cartridges

CloneSelect Single-Cell Printer Cartridges

Disposable printing cartridges

CloneSelect Imager

CloneSelect Imager

Colony imager for imaging cells growing in the microplates