What Is CellRaft Technology?

A Unique, Integrated System for Maximum Efficiency in Generating Single Cell Clones

CellRaft® Technology is a highly effective and seamless way of enabling single cell cloning, cell culture, analysis, and isolation that goes beyond trypsinization and dispensing a single cell into a well. This unique method for developing monoclonal colonies from single cells uses three components:

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

What Is a CellRaft?

The key to the technology is the CellRaft Array, a novel proprietary tissue 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, which leads to improved viability and proliferation of single cells compared to other single-cell culture methods.

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.


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

What Can the CellRaft AIR Do?

The CellRaft AIR System is an all-in-one platform with an integrated three-channel fluorescence plus brightfield microscope with a 10X objective, release needle, magnetic wand, and a movable stage for the imaging, identification, and automated isolation of cells, colonies, or organoids.

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 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 CellRaft Array by using a release needle and retrieved from the array 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 fully intact clones or organoids for propagation without the use of fluidics with a high degree of efficiency.

What Is CellRaft Cytometry?

Finding and isolating precious 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 cells 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. However, these methods 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 and confluence, 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.

CellRaft Technology is an integrated system that encompasses imaging, tracking, analysis, and automated isolation of verified 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.

Comparison of Cell Sorting & Isolation Methods

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