FAQ Hub

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Instrument size: width: 27" | depth: 20" | height: 20" Bench space required for instrument and computer: width: 40" | depth: 26" | height: 26"

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

Yes. Brightfield-only analysis is supported.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Because BioFlux plates are Society for Biomolecular Screening (SBS) standard size, BioFlux systems are compatible with most inverted microscopes.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Scaling up 3D cultures requires a system that supports larger culture volumes without compromising uniformity. The CERO 3D supports expansion of 3D models in up to approximately 50 mL culture tubes, supporting biomass generation for screening, toxicity testing, and disease modeling applications.

Traditional shakers and spinner flasks can introduce shear stress that damages delicate aggregates. The CERO 3D uses a low-shear rotation system designed to protect developing spheroids and organoids while supporting uniform nutrient and oxygen exposure.

Reproducibility in 3D culture requires consistent environmental conditions and standardized vessel geometry. The CERO 3D uses identical disposable CEROtubes and closed-loop environmental control, which are designed to support experiment-to-experiment consistency.

Automated mixing and environmental monitoring reduce manual intervention. The CERO 3D is designed to support extended culture with only brief daily checks, helping labs reduce hands-on time per experiment.

Higher yields in 3D culture depend on stable conditions and consistent mixing. The CERO 3D is designed to support dense, viable 3D biomass with minimal cell death, relevant for applications such as drug discovery, disease modeling, and regenerative research.

The CERO 3D Incubator & Bioreactor is a rotation-based 3D culture system developed by Cell Microsystems. It is designed for long-term organoid and spheroid culture, supporting stable environmental conditions including CO₂, temperature, and low-shear rotation. CERO is relevant for researchers who need reproducible 3D culture workflows, multi-condition experimentation in a single system, and reduced dependence on large incubator infrastructure.