What Is CellRaft Technology?

A paradigm shift in 2D and 3D cell culture for clonal isolation and cell line development

CellRaft® Technology provides a highly effective way of enabling single cell cloning, cell culture, analysis, and isolation that goes beyond dispensing a single cell into a well. The technology has been successfully applied to 2D as well as 3D complex multicellular systems. This unique platform for developing monoclonal colonies from single cells uses three components:

  • CellRaft® Array
  • CellRaft AIR® System
  • CellRaft Cytometry


  • Cell Line Development
  • Stem Cell Culture
  • Single Cell Genomics
  • Organoid Development
  • CRISPR Gene Editing

What Is a CellRaft Array?

The key to the technology is the CellRaft Array, a novel and proprietary cell culture dish containing thousands of microscale cell culture growth surfaces called CellRafts. Each CellRaft is housed within an individual microwell, allowing for gravity-based separation of a population into single cells.

Despite being spatially separated in the microwells, the novel design of the array allows the entire cell population to benefit from a shared media reservoir, mimicking the growing conditions of a flask. This feature leads to improved viability and proliferation of single cells compared to other single-cell culture and clonal propagation methods.

The flask-like culture feature is central to the Cell Raft Technology. Not only does this maintain the cell viability and vitality to ensure clonal propagation but it eliminates the need for excessive number of multiwell (96 or 384) plates, tips, and media, needed to isolate the precise target candidate.

CellRaft Array

The CellRafts are made of magnetic polystyrene, which enables them to be picked up by a specialized magnetic wand and moved into individual wells of a 96-well plate without the use of fluidics.

Learn more about CellRaft Arrays.

What Can the CellRaft AIR System Do?

How CellTech Works

The CellRaft AIR System is an all-in-one platform with an integrated three-channel fluorescence plus brightfield microscope providing an effective 20x magnification, release needle, magnetic wand, and a movable stage for the imaging, identification, and automated isolation of cells, colonies, or organoids.

The integration of image, analysis, and isolation in one platform provides unprecedented and unmatched efficiency in clonal isolation by excessively amplifying chances for success while utilizing remarkably reduced plastic consumables, media, reagents, and hands-on time.

With the optional add-on incubator, the cells’ growing environment can be controlled and maintained during time-course imaging projects, or for projects using rare or sensitive cell lines.

Learn more about the CellRaft AIR System.

The CellRaft Arrays are placed on the CellRaft AIR System for image-based verification of single cells to ensure monoclonality.

The CellRaft Array is serially scanned at the desired frequency to capture complete growth records of clonal development.

Once the cells have grown to the desired stage, the CellRafts of interest are gently dislodged from the Array by using a release needle and retrieved by a magnetic wand to gently transfer the CellRaft to a 96-well collection plate.

The fully automated CellRaft AIR System enables gentle, dissociation-free isolation of intact clones or organoids for downstream propagation with a high degree of outgrowth efficiency without the use of fluidics.

We have tested more than 100 Cell Lines: View Them HERE! 

What Is CellRaft Cytometry?

Finding and isolating selected cells, clones, or organoids is easy using the CellRaft Cytometry software. CellRafts can be analyzed for a wide range of parameters, including fluorescence intensity, cell morphology, or colony size over time to identify the desired phenotypes. The desired CellRafts can then be automatically identified and isolated using the CellRaft AIR System.

Learn more about the features of CellRaft Cytometry.

How Does CellRaft Technology Compare to Other Methods?

Limiting dilution and single cell sorting have been the primary methods for the development of monoclonal cell lines. These methods, however, are not without their problems: significant cellular damage, inefficient workflows, and lack of clonality. Newer single cell dispensers have provided significant improvements in the assurance of clonality, but yields can still be low due to cellular perturbation from the selection process. Furthermore, challenging cell lines, such as stem cells/iPSCs, organoids, and rare cells, are difficult to grow using standard methods, necessitating more gentle approaches that improve viability and efficiency.

See below for a quick look at how CellRaft Technology compares to Limiting Dilution and FACS.

> CellRaft Technology vs. Current Methods

LD Comparison 6

For an In-depth Overview of How CellRaft Technology Compares to Limiting Dilution, Click Here.

> CellRaft Technology vs. FACS

FACS v DtA 1

In a side-by-side comparison, CellRaft Technology delivers ~3X more viable clones in half the time compared to FACS with 1000X reduced input.

> Comparison of Cell Sorting & Isolation Methods

The CellRaft Technology is the basis for an integrated system that encompasses imaging, tracking, analysis, and automated isolation of monoclonal cultures. It offers significant cost-savings, viability, and high outgrowth advantages over other systems that require additional space, equipment, and manual labor. See the table below for a detailed comparison and learn more by downloading the white paper on Development of Monoclonal Cell Lines – Available Technologies and Overcoming Challenges.

Workflow comparison chart

Have questions about CellRaft Technology?
Please email me at allysa.stern@cellmicrosystems.com.

Allysa Stern Ph.D. scaled e1676468368845