Inside our System

An Integrated System for Maximum Efficiency
in Generating Single Cell Clones

The CellRaft AIR® System is efficiently designed for numerous applications and capabilities:

  • Cell line development

  • CRISPR gene editing

  • Stem cell culture

  • Organoid development

  • Single cell genomics

  • Direct sample analysis

  • On-array assays


The CellRaft AIR System consists of a customizable array, a platform with integrated three-channel fluorescence plus brightfield microscope, attached probe and movable stage, and the imaging software.

Watch the CellRaft Technology in action!

Three components, one platform

Microfabricated from an elastomeric material, the CellRaft Array is a high-density array with thousands of individual microwells. Precision soft lithography methods are used to obtain uniform dimensions across the array. Each microwell on the CellRaft Array contains an individual cell raft composed of a proprietary polystyrene formulation.

Cells are plated on the CellRaft Array in the same way as a standard Petri dish, making it familiar to the research community and easy to use. 

Raft release 3cells on a raft

Cells remain viable and localized on the CellRaft surface, allowing for it to act as a culture site. Each CellRaft is individually releasable from the array so that target cells and colonies can be identified and extracted. Different formats of the CellRaft array are available to match specific application needs.  

See our CellRaft Array Product Page to learn more.

After placing the CellRaft Arrayon the stage of the System, the software will automatically scan and capture each field of view within the array, providing detailed cell images sitting on each cell raft. The System contains a probe, mounted adjacent to a 10× microscope objective underneath an automated stage. A release needle mounted underneath the stage is used to release the raft from the array.



Cells can be tracked with images over time, allowing users to observe cell-to-cell interactions, cell morphology changes, and colony growth rates. 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. Using cell images, the user can manually designate target cells to be captured, or use the software to automatically choose targets.

Some criteria available for cell selection:

  • Cell morphology
  • Subcellular structures
  • Fluorescence levels
  • Temporal and spatial characteristics


To isolate target cells, the system drives the probe gently into the bottom layer of the polymer substrate of the array. This movement dislodges the individual CellRaft with attached cell(s) in a gentle enough manner to maintain cell viability and not disrupt further downstream application options.

The released CellRaft is recovered using a magnetic wand and transferred to a standard culture or 96-well PCR plate/tube. Recovered cells are able to be used for direct molecular analysis or clonal expression.

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For more information about the applications the AIR System is currently being used in, click here.

With four-channel imaging capabilities, users can see their single target cells like never before.  

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Built with the user in mind, the CellRaft AIR Imaging software is intuitive and easy-to-use. Once the CellRaft Array has been loaded in the imaging platform, the user is able to:

  • Adjust focus, position, and channel settings to produce optimal images
  • See individual channel intensity histograms
  • Image the entire plate or just individual wells
  • Track changes to target cells over time
  • Create a gating strategy for cell selection using a marker intensity scatterplot
  • Map out CellRaft collection plate for downstream analysis 

Similar to FACS, users are able to design a gating strategy for the automatic selection and retrieval of target cells.  But with the CellRaft AIR System, users can also designate specific phenotypic criteria based on the view of their target cells before collection.


Whether opting for automatic gating, or manual selection, the software has the ability to sort very rare cells (<1 per 1M).


To experience our software’s capabilities, we offer a free “Off the AIR” software demo.  Click here to learn more about our demo offer.


The additional incubator provides a temperature, CO2, and humidity controlled environment. This allows for single-point and time-course imaging in-unit. Limiting changes to the cell growth environment makes this add-on ideal for sensitive cell lines or multiple time-course imaging projects.


Click here to download the AIR System brochure with specifications

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