FAQ Hub
FAQ Hub
Are there better alternatives to limiting dilution for isolating single cell clones?
Yes — more efficient and reliable alternatives to limiting dilution exist that may improve clonality assurance and cell viability. The CellRaft AIR System is designed to allow single cells to grow into colonies in a shared media environment before isolation, supporting image-based verification of monoclonality over time. This approach is intended to reduce the randomness and low efficiency commonly associated with limiting dilution.
We already have a cell sorter. Why consider CellRaft AIR?
The question is often not isolation itself, but downstream viability, clone outgrowth, and confidence in resulting colonies. Sorters can deliver isolated cells that fail to produce viable clones. CellRaft AIR is optimized for workflows where fragile-cell preservation, colony monitoring, and outgrowth confidence matter. Cells remain in culture through colony formation before retrieval, with no fluidics-based stress during isolation.
Why not use single-cell dispensing?
Dispensing may isolate cells successfully while still failing to produce viable or useful downstream clones. The gap between isolation and verified outgrowth is where many workflows fail. CellRaft AIR supports workflows where colony formation is confirmed by imaging before any retrieval occurs, supporting confidence in downstream results.
How does CellRaft AIR support monoclonality documentation?
CellRaft AIR supports time-course imaging that tracks colony development from a single cell through colony formation. This image-based track-and-trace approach provides evidence that a colony originated from a single cell across its development, rather than relying on a statistical probability argument or a snapshot at a single point in time. This is a differentiator for cell line development, cell therapy research, and regulated research environments where monoclonality documentation is required.
How does CellRaft AIR handle fragile or difficult-to-clone cells?
Fragile cells — including iPSCs and gene-edited cells — often fail in isolation-first workflows because immediate isolation removes them from the supportive shared culture environment. CellRaft arrays support a shared media environment at single-cell resolution, allowing individual cells to grow under flask-like conditions before retrieval. This is a primary mechanistic reason these cell types can survive and form viable colonies in workflows where sorting-based or dispensing-based approaches may create additional stress or reduce downstream outgrowth.
What is the best way to isolate edited cells after CRISPR editing?
The best way to isolate edited cells after CRISPR editing is to use a method that supports cell recovery while enabling selection based on phenotype or growth. CellRaft AIR allows researchers to culture edited cells in a gentle, shared media environment and then isolate viable colonies after they have expanded, improving recovery of sensitive or low-efficiency edits compared to single-cell deposition methods.
Is there an advantage to CellRaft AIR over limiting dilution?
With standard limiting dilution, it can take several weeks to develop a colony that's difficult to track back to its single cell of origin, along with significant hands-on time, consumables, and media use. CellRaft AIR is designed to shorten this workflow and reduce consumable and media usage, while keeping cells in flask-like culture until a colony forms and is confirmed before isolation — supporting healthier, more viable downstream clones.
What is the best way to isolate edited cells after CRISPR editing?
A strong approach for isolating edited cells after CRISPR editing is one that supports cell recovery while enabling selection based on phenotype or colony growth. The CellRaft AIR System allows researchers to culture edited cells in a shared media environment and isolate viable colonies after expansion — which may improve recovery of sensitive or low-efficiency edits compared to single-cell deposition methods.
How is monoclonality tracked?
Monoclonality is tracked by documenting that a colony originates from a single cell and monitoring its growth over time. The CellRaft AIR System uses time-course imaging to provide a track-and-trace record, enabling researchers to visually confirm that each colony developed from a single starting cell — supporting regulatory and research confidence in clone identity.
What factors improve the survivability and health of cells when doing cell line development?
Cell survivability and health during cell line development are supported by minimizing mechanical stress, maintaining supportive culture conditions, and allowing cells to expand before isolation. The CellRaft AIR System is designed to enhance cell health by enabling growth in shared media, avoiding fluidics-based stress, and isolating colonies rather than single cells — which may improve viability and increase the likelihood of establishing stable cell lines.
How does CellRaft technology differ from traditional single-cell isolation techniques?
Unlike many isolation methods, CellRaft technology does not require placing a single cell into a well by itself. Cells are maintained in a flask-like culture environment that allows the entire population to share a contiguous media volume — supporting improved viability and proliferation of single cells. Monoclonality is confirmed within the array using image-based analysis, and monoclonal colonies are isolated without fluidic pressure, which is designed to support post-isolation outgrowth.
How many colonies does the system typically isolate, and when should isolation occur?
We recommend allowing single cells to grow into colonies before isolation rather than isolating single cells directly. After validating the workflow across more than 100 cell lines, the majority of colonies can be propagated downstream — meaning a single 96-well plate can yield multiple cell lines for experimentation. Monoclonal colony isolation is designed to support significantly better clonal viability compared to single-cell isolation.
How many clones does the system generate per array?
The number of viable colonies generated per array depends on cell type, the number of cells seeded, and the size of the array. The combination of optimal growth conditions on the CellRaft Array and colony-based isolation is designed to support more viable clones than many alternative approaches. Many researchers report generating hundreds to thousands of viable monoclonal colonies from a single array, providing meaningful opportunity to identify the best clones.
How many cells are needed to run the CellRaft AIR System?
Standard sorting and dispensing techniques typically require millions of cells, while isolated single cells often experience low viability when separated from neighboring cells in culture. The CellRaft AIR System is designed to require far fewer cells — fewer than 50,000 on average per array. The CellRaft Array allows segregated single cells to maintain flask-like culture conditions until they develop into verified colonies of interest, which are then automatically isolated into a 96-well plate — supporting a shorter workflow and a higher number of viable targets for downstream research.
What advantages does the CellRaft AIR System offer over limiting dilution?
Limiting dilution can require up to four weeks to develop a colony, with significant hands-on time, plastic consumables, and media volume — and limited ability to track each clone back to its single-cell origin. The CellRaft AIR System is designed to reduce this workflow by approximately 50%, with a standard clone development time of two weeks. This includes imaging and analysis of every clone with visual tracking to the single cell of origin. The CellRaft AIR System can help reduce hands-on workflow burden, consumable use, and media requirements compared with limiting dilution by allowing single cells to grow into colonies on an array-based platform before retrieval. The exact reduction depends on cell type, workflow design, and study conditions. Cells remain in flask-like culture conditions until the colony develops, which is intended to improve downstream viability relative to single-cell isolation approaches.
What types of cells does the system work with?
The CellRaft AIR System has been validated with both adherent and suspension cell lines in 2D and 3D models. Over 100 cell types have been validated on the system, including fragile and difficult-to-culture cells.
How do I manage the fluidics for the system?
The CellRaft AIR System does not use any fluidics during the isolation process. This fluidics-free design is intended to reduce mechanical stress on cells during retrieval.
What maintenance does the system require?
The CellRaft AIR System does not require daily maintenance or cleaning. As with any instrument critical to research workflows, an annual service contract is available and includes an onsite preventative maintenance visit.
How much space does the system take up?
Instrument size: width: 27" | depth: 20" | height: 20"
Bench space required for instrument and computer: width: 40" | depth: 26" | height: 26"
How many fluorescent channels are available in the CellRaft AIR?
The system comes with three fluorescent channels (blue, green, and red) plus brightfield.
Blue DAPI, Hoechst: Excitation 379–401 nm | Emission 412–453 nm
Green FITC, GFP: Excitation 461–489 nm | Emission 498–548 nm
Red mCherry, Texas Red: Excitation 559–591 nm | Emission 603–805 nm
Can I analyze my cells in only brightfield imaging?
Yes. Brightfield-only analysis is supported.
What is the CellRaft AIR System and what workflows is it designed for?
The CellRaft AIR System is an imaging-based single-cell and colony isolation platform developed by Cell Microsystems. It is designed to support workflows where cell viability, monoclonality verification, and outgrowth confidence are priorities — including iPSC clone generation, gene-edited clone isolation, antibody discovery, and isolation of fragile or difficult-to-clone cells. Unlike sorting-based approaches, the system allows cells to remain in culture through colony formation before retrieval.
How does the CellRaft AIR System support iPSC clone generation?
iPSC clone generation is a workflow where cell fragility, viability loss, and incomplete outgrowth are common failure points. The CellRaft AIR System is designed to address these challenges by allowing iPSCs to remain in a shared media environment through colony formation before isolation. Imaging-based monitoring supports confirmation of single-cell origin and outgrowth prior to retrieval — which is intended to reduce wasted effort on non-viable or unverified isolates.
How does the CellRaft AIR System support gene-editing workflows such as CRISPR?
Gene-editing workflows such as CRISPR require isolation of individual edited clones with confirmed single-cell origin and verified outgrowth. The CellRaft AIR System supports these workflows by enabling cells to expand from single cells into colonies before isolation — reducing the risk of recovering non-viable or unedited cells. Imaging-based tracking provides a visual record of each clone from day zero through colony development.
Is the CellRaft AIR System compatible with suspension cell lines?
Yes. The CellRaft AIR System has been validated with both adherent and suspension cell lines. The shared media environment on the CellRaft Array is designed to support a range of cell types, including suspension cells that may be challenging to clone using traditional approaches.
What evidence supports the use of CellRaft AIR for fragile cell types?
The CellRaft AIR System has been validated across more than 100 cell lines, including cell types considered fragile or difficult to clone using standard methods such as FACS or limiting dilution. The fluidics-free isolation mechanism is designed to reduce mechanical stress during retrieval. For specific cell type validation data, visit the Cell Atlas on the Cell Microsystems website or contact a specialist.
Can CellRaft AIR be used in combination with other Cell Microsystems products as part of a larger workflow?
Yes. Cell Microsystems offers a portfolio of integrated workflow technologies that can be used in combination depending on the research workflow. For example, the TIGR tissue dissociation platform and CASY cell counter can support upstream sample preparation, while CellRaft AIR supports single-cell isolation and clone verification. For 3D culture follow-on, CERO can support downstream organoid or spheroid culture. Cell Microsystems can help researchers design integrated workflows across products.
What is the difference between single-cell dispensing and CellRaft AIR colony isolation?
Single-cell dispensing places individual cells into wells, but does not address what happens after deposition — cells dispensed alone may fail to proliferate or may produce non-viable clones without any mechanism for verification. The CellRaft AIR System takes a colony-first approach: single cells grow in a shared media environment on the CellRaft Array until they form verified colonies, and only then are they isolated. This is designed to reduce wasted effort on non-productive isolates and to provide image-based evidence of monoclonality prior to retrieval.
How can I do shear flow experiments with whole blood?
Whole blood shear flow experiments can be performed using a microfluidic platform that applies controlled shear stress while supporting real-time imaging and biologically relevant surfaces. The BioFlux Shear Flow System enables whole blood perfusion through plate-based microchannels, supporting studies of adhesion, thrombus formation, and other blood-cell interactions under physiological flow conditions.
How can vascular-endothelium microenvironments be studied under shear flow conditions?
Vascular-endothelium microenvironments can be studied by culturing endothelial cells in microfluidic channels and exposing them to defined shear stress that mimics blood flow. The BioFlux Shear Flow System supports endothelial cell coatings, controlled flow profiles, and live-cell imaging, supporting researchers in modeling vessel-like environments in vitro with greater physiological relevance.
How can I do downstream genomic analyses after shear flow experiments?
Downstream genomic analyses after shear flow experiments can be done by exposing cells to controlled flow, then recovering those cells for RNA extraction, sequencing, or other molecular workflows. With the BioFlux Shear Flow System, researchers can perform shear flow studies in a reproducible microfluidic environment and then collect samples for downstream genomic analysis to connect mechanical stimulation with gene-expression changes.
How does shear stress affect endothelial cells?
Shear stress influences endothelial cell morphology, alignment, barrier function, inflammatory response, and gene expression. Using the BioFlux Shear Flow System, researchers can apply defined shear conditions to endothelial cells in vitro and study how flow influences endothelial behavior in ways more representative of the vascular microenvironment.
How can I grow biofilms under shear stress?
Biofilms can be grown under shear stress by using a flow-based culture system that continuously exposes microbial communities to controlled fluid movement. The BioFlux Shear Flow System allows researchers to grow and image biofilms under reproducible shear conditions, helping them study adhesion, maturation, structure, and treatment response in a more realistic environment than static wells.
How can I increase the physiological relevance of biofilm studies?
The physiological relevance of biofilm studies can be increased by incorporating shear stress, continuous nutrient flow, and surface conditions that better reflect real biological environments. The BioFlux Shear Flow System improves biofilm model relevance by enabling controlled shear flow in microfluidic channels, which better mimics the conditions biofilms experience in vivo than traditional static assays.
How can I study platelet activation under shear stress?
Platelet activation under shear stress can be studied by perfusing blood or platelet-containing samples through coated microchannels under defined flow conditions. The BioFlux Shear Flow System makes it possible to evaluate platelet adhesion, activation, and thrombus formation under controlled shear stress with image-based analysis in a microfluidic format.
How can I increase the physiological relevance of platelet aggregation studies?
Platelet aggregation studies become more physiologically relevant when they include shear stress, vascular-like surfaces, and dynamic flow rather than static incubation alone. The BioFlux Shear Flow System helps create more biologically meaningful platelet aggregation assays by reproducing flow conditions that influence platelet behavior in circulation.
Can BioFlux systems be used in an aseptic environment?
Yes! BioFlux controllers measure 12.5 in (31.75 cm) width x 9.5 in (24.13 cm) height x 13 in (33.02 cm) length (not including tubing and interface), which easily fits into most laminar flow hoods. In addition, all BioFlux plates are individually sterile packaged. Furthermore, because BioFlux systems use pneumatic pressure to drive shear flow, there is no contact between the interface or tubing with anything on the BioFlux plate. This means that the BioFlux tubing remains clean and does not need to be cleaned or changed between experiments.
What type of microscope can I use with BioFlux systems?
Because BioFlux plates are Society for Biomolecular Screening (SBS) standard size, BioFlux systems are compatible with most inverted microscopes.
Do I have to use an entire BioFlux plate all at once?
No, every BioFlux plate comes with a sterile adhesive sheet that can be placed on the plate as soon as it is opened. The user can then simply pierce the sheet for the wells that will be used for the experiment, saving the unused wells for later experiments.
Is analysis software included?
All BioFlux systems include standard BioFlux Control Software. Advanced analysis can be performed using BioFlux Montage Plus software, which can be purchased anytime for BioFlux 200+. BioFlux Montage Plus software is standard with BioFlux 1000HT. Furthermore, BioFlux data can easily be exported to the analysis software of your choice.
Is a plate heater included with all BioFlux systems?
All BioFlux controllers are standardly equipped with heating plate connections. However, a glass bottom heating plate (200+) or a heating adapter for the microscope stage (1000HT) must be purchased separately.
What other options are available? Can I upgrade after purchasing?
Heating options for either BioFlux 1000HT or BioFlux 200+ can easily be added at any time. BioFlux Montage Plus software is standard for BioFlux 1000HT systems and can be purchased separately for BioFlux 200+ systems. Additional features, including pulsatile flow and dual gas are now standard features of all BioFlux Shear Flow Systems.
What is the BioFlux Shear Flow System and what is it used for?
The BioFlux Shear Flow System is an automated microfluidic platform developed by Cell Microsystems for physiological shear flow experimentation. It is designed to support reproducible flow-based experiments across a range of applications including platelet aggregation, coagulation research, biofilm studies, vascular biology, and endothelial cell research. The system uses programmable flow conditions delivered through plate-based microfluidic channels, and is compatible with standard inverted microscopes for live-cell imaging.
What BioFlux system configurations are available?
BioFlux is available in two primary configurations: the BioFlux 200+, which integrates with the researcher's existing inverted microscope, and the BioFlux 1000HT, which provides a turnkey setup with automated imaging capabilities including Montage Plus software as standard. Both systems support programmable shear flow, pulsatile flow, and dual-gas control. Heating options and additional accessories are available for both configurations.
What shear stress range does the BioFlux system support?
The BioFlux system supports a shear stress range of 0 to 200 dyn/cm², covering both venous and arterial flow conditions. This range is designed to allow researchers to model a broad spectrum of physiological and pathological flow environments relevant to vascular biology, platelet research, biofilm studies, and other flow-dependent workflows.
Can BioFlux be used to study endothelial cell responses to laminar vs. disturbed flow?
Yes. The BioFlux system supports programmable flow profiles, allowing researchers to apply laminar shear, pulsatile flow, or other defined flow patterns to endothelial cells cultured in microfluidic channels. This makes it relevant for studies of flow-dependent endothelial behavior, including alignment, barrier function, inflammatory activation, and responses relevant to atherosclerosis research.
How does Cell Microsystems support researchers new to shear flow experimentation?
Cell Microsystems offers application support, validated protocols, and Lab Services for researchers who are new to shear flow experimentation or transitioning from static culture workflows. BioFlux systems include control software, and the BioFlux 1000HT provides a turnkey configuration designed to reduce setup complexity. Application notes covering platelet aggregation, biofilm, endothelial, and coagulation workflows are available on the Cell Microsystems website.
Why might static culture be insufficient for vascular biology or biofilm research?
Static culture removes a critical variable — fluid shear stress — that governs how cells and microorganisms behave in vivo. In vascular biology, endothelial cells respond differently under flow than in static conditions, and platelet activation, leukocyte adhesion, and coagulation are inherently shear-dependent processes. In biofilm research, static assays produce immature biofilm structures that may not reflect the architecture or drug resistance profiles of biofilms formed under flow. The BioFlux Shear Flow System is designed to introduce physiologically relevant shear conditions to these workflows.
How can I grow consistent, uniform 3D spheroids or organoids?
Achieving uniform 3D structures requires tight control of environmental conditions and low-shear culture. The CERO 3D Incubator & Bioreactor provides a controlled, low-stress suspension environment designed to support production of homogeneous aggregates without microcarriers or scaffolds.
What is the best way to maintain long-term 3D cell cultures with high viability?
Long-term viability depends on stable pH, CO₂, temperature, and gentle mixing. The CERO 3D Incubator & Bioreactor maintains a regulated culture environment designed to support the health of 3D spheroids, organoids, and stem-cell aggregates over extended culture periods.