CloneSelect Imager

Objective and quantitative assessment of cell growth with label-free imaging

With high quality imaging and intelligent image analysis, CloneSelect™ Imager replaces time-consuming, subjective manual inspections with consistency and objectivity. Cell growth is viewed and tracked in every well in every plate.

  • Consistent determination of cell confluence and cell number estimation
  • Generation of growth curves
  • Label-free, white light imaging of living cells
  • Suitable for adherent and settled suspension cells

CloneSelect Imager has been successfully used on cells lines such as CHO (examples including DG44 and CHO-K1), HEK, Myeloma / Hybridoma, SupT1, Jurkat, H-4-II-E, MCF-7, PER.C6®, HT29, DLD1 and KB31.


Track confluence and cell number after fACS, limiting dilution or selection by clonePix


High Throughput Screening

  • Electronic data tracking ensures control of high throughput processes
  • Process up to 75 lidded plates in a single run
  • Recommended and supplied through Molecular Devices - optimized for CloneSelect Imager
See CloneSelect Imager in action in a high-throughput lab

Cell Line Development

Verification of Monoclonality

Focus Only On Single Colonies – Saving Time and Effort
After initial seeding, CloneSelect Imager can image every well, at any time point, using a ‘loci of growth’ functionality to highlight those wells that contain a single colony – the essential requirement for output from FACS and limiting dilutions. The user only needs to review wells with a single colony.


Confidently Verify Colony Origin
The growth (image) history of each well can be tracked back to its starting point – providing evidence of monoclonality



Data courtesy of CMC ICOS Biologics Inc., USA

Further Information

Monitor colony growth after selection of secreting cells

After screening and selection of cell lines using ClonePixSystem, CloneSelect Imager provides the ideal solution for monitoring and evaluating subsequent outgrowth and, eventually, productivity of the selected cell lines.

Track Colony Outgrowth

Outgrowth of a single well after 7 days - confluence overlay viewed for each imaging timepoint

Normalize Downstream Results to Cell Number

CloneSelect Imager estimates the number of cells per well. Data is then exported to enable normalization of results from ELISA or cell-based assays against cell number.


Correlate protein productivity and growth of cell line

Case study: Tecan-monoclonal antibody production, cell expansion

Read how the Tecan Integration Group integrated CloneSelect Imager with Freedom EVO®  to automate cell expansion and confluence measurement of MAb-producing cell lines at Monash University, Australia.

Further Information

  • Tecan Integration Group - Monoclonal Antibody Production, Cell Expansion. Part of the Monash system: Case Study Download

Case Study: Beckman Coulter - Automation of Cell Line Optimization

Read how CloneSelect Imager is utilized in a novel hardware solution for automating cell line optimization and expansion.

Further Information

  • Beckman Coulter - Cell Culture Automation in BioPharma: Cell Line Optimization and Monoclonal Antibody Production: Case Study Download

General Cell Culture

Colony Forming Assay

Save time by analyzing selected wells
(highlighted in green). Red wells are excluded.

Objective, Time-Saving Analysis

  • Every well can be imaged at any time point
  • Colony number and area quantified objectively
  • Focus on wells of interest, e.g. where growth is inhibited by test compounds

Review Results and Export Data

  • Dual gating for colony area and compactness
  • View each well at different time points
  • Export colony data
View number of colonies per well
Colonies are identified in well images

Assessment of Cell Viability (MTT Assay)

CloneSelect Imager offers several benefits over traditional MTT assays for assessing cell viability in response to a cytotoxic challenge.

  • Replace time-consuming conventional techniques
  • Monitor cell death over time
  • Ensure a permanent record of data
  • Avoid costly reagents - no staining required
Images of HeLa cells - wells exposed to
different level of cytotoxin
Dose response curve: decreasing cell
confluence with increasing exposure
to cytotoxin
High resolution images show growth of cells exposed to low, medium and high cytotoxin levels

Cell Migration Assay

CloneSelect Imager offers rapid, objective quantification of cell migration assays.

  • Determine migration rates, maximum migration rate and total migration area
  • Time-saving - scan a 96 well plate in <2 minutes
  • Convenient, label-free quantification
Export data to determine dose
response to cell mobility effectors

Review Results and Export Data

  • Obtain graphical display of migration area vs. time
  • Easy to read, numerical and graphical output



Wound healing time course

Case Study: using cloneSelect Imager for media and cell culture Optimization

Data courtesy of Ben Hughes Senior Bioprocess Engineer, NCRIS Biologics Facility, Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland
Acknowledgements to Warren Pilbrough and Dr. Trent Munro


  • Monitor serially-diluted cultures in a 96-well format to rapidly screen culture variables
    • Tissue culture ware (treated vs. non-treated, square vs. round bottom wells)
    • Media (volume, commercial vs. in-house formulations, supplementation)
    • Environment (sealed plates, humidification, effect of disturbances)


  • Load high-throughput 96-well plates
    • Add cells in exponential growth (~0.1 x106 cells/mL) to row 1
    • Serially dilute cells across plate to row 12 -  Eight replicates per dilution
  • Image plates on CloneSelect Imager
    • Initial “Day 0” time point
    • Periodically monitored over 1-2 weeks
  • CloneSelect Imager data review
    • “% confluence” data utilized to identify optimal conditions

Identifying low-cell density growth conditions

  • Significant improvements achieved in 2-week period with minimal effort by single FTE
Robust and extended growth range achieved over base-case (day-7 data)

Additional information gained on cellular morphology and understanding of growth characteristics

  • Multiple nucleation points vs. “edge only” growth
Wells showing multiple
nucleation growth points
Wells showing edge
growth characteristics


  • Identified sub-optimal environmental conditions or “edge-effects”
Plate demonstrating edge effects
Plate demonstrating environmental effects

Summary from AIBN:

  • Excellent workflow obtainable using CloneSelect Imager
    • Maximize success rate for serum-free colony outgrowth in chemically-defined media by prior optimization of growth conditions
    • Efficient tracking of cell confluence ensures high viability is maintained, leading to rapid expansion for evaluating clones in shake flasks (2-3 weeks from picking)
  • Use of the CloneSelect Imager is particularly useful for optimizing clonal outgrowth strategies when platform approaches are not suitable i.e., investigating new cell lines or variants

Related Videos

Non-subjective interpretation of colony formation with the CloneSelect Imager

Related Collateral



More Applications



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Product Support

For product configurations and pricing on CloneSelect Imager, please contact us

For instrument qualification services, please click here.

Latest Citations:
For a complete list of citations, please click here.


A high-throughput automated platform for the development of manufacturing cell lines for protein therapeutics

S Shuangping, C Russ GG, D Liang, S Jason… - Journal of Visualized …, 2011 -
... protein therapeutics from mammalian cell lines. Materials. Name, Company. BD FACS
Aria™ Cell Sorter, BD Bioscience. CloneSelect™ ImagerGenetix. TECAN Freedom
EVO® liquid handling system, Tecan Group. References. ...

Accurate non-invasive image-based cytotoxicity assays for cultured cells

P Marqués-Gallego, H den Dulk… - BMC …, 2010 -
... research. The CloneSelect™ Imager (Genetix Limited, New Milton,[9]) could offer
such an opportunity. The system was designed to be capable of screening cellular
confluence and growth in a range of microwell plates. For ...

Functional heterogeneity and heritability in CHO cell populations

SL Davies, CS Lovelady, RK Grainger… - Biotechnology and …, 2013 - Wiley Online Library
... Plates were incubated at 37°C in 10% CO 2 and individual wells were subjected to image analysis
(CloneSelect™ ImagerGenetix, Hampshire, UK) to rigorously identify those that contained a
single cell-derived colony—plates were screened at 18, 22, and 25 days post ...

Expression of g protein-coupled receptor 19 in human lung cancer cells is triggered by entry into s-phase and supports g2–m cell-cycle progression

S Kastner, T Voss, S Keuerleber, C Glöckel… - Molecular Cancer …, 2012 - AACR
... Experiments were done in 96-well culture plates. Fluorescence was recorded using a 2030
Multilabel Reader VICTOR X5 (PerkinElmer). In addition, proliferation of cells was assessed by
determining cellular confluence using a CloneSelect Imager (Molecular Devices). ...

Recombinant human albumin supports single cell cloning of CHO cells in chemically defined media

J Zhu, JW Wooh, JJC Hou, BS Hughes… - Biotechnology …, 2012 - Wiley Online Library
... For all experiments, plates were screened for growth using a CloneSelect™ Imager (CSI) system
(Molecular Devices). ... chemically defined media. CHO Chinese hamster ovary. FBS fetal bovine
serum. SFM serum-free media. CSI CloneSelect™ Imager. Literature Cited. ...

Strategies for clone detection, selection and isolation in Per. C6 cells-case for Rebmab100

FP Yeda, ML dos Santos, LR Tsuruta… - BMC …, 2013 -
... Cellular growth was assessed in plates, 96, 24 or 6-well plates, either by CloneSelect
Imager (Molecular Devices) or Guava EasyCyte cytometer (Merck-Millipore). Antibody
titers were measured by Biacore T100 (GE Healthcare, Sweden). ...

Sarsaparilla (Smilax Glabra Rhizome) Extract Inhibits Migration and Invasion of Cancer Cells by Suppressing TGF-β1 Pathway.

T She, C Zhao, J Feng, L Wang, L Qu, K Fang, S Cai… - PloS one, 2015 -
... then supplemented with 0.5% FBS before being seeded into matrigel pre-coated 96-well plates
at the density of 2×10 4 per well and allowed to adhere for 2 h. After removing non-adherent cells
by PBS, adherent cells were photographed with the CloneSelect Imager system ...

Generation of cell lines for monoclonal antibody production

K Alvin, J Ye - Monoclonal Antibodies, 2014 - Springer
... 12. Microscopic instruments, such as a standard inverted microscope with a 20× objective or
the CloneSelect Imager (CSI, Molecular Devices) system. 13. ... Automated microscopic screening
can also be performed using instruments, such as the CloneSelect Imager System. ...

Utilization of non‐AUG initiation codons in a flow cytometric method for efficient selection of recombinant cell lines

VR Cairns, CT DeMaria, F Poulin… - Biotechnology and …, 2011 - Wiley Online Library
... The unsorted MTX-withdrawn pools were also plated by limiting dilution into 96-well
plates at 0.5 cell per well. All 96-well plates were scanned using a CloneSelect Imager
(Genetix, UK) to determine clonality and confluence of each well. ...

Mycoplasma hyorhinis induces epithelial-mesenchymal transition in gastric cancer cell MGC803 via TLR4-NF-κB signaling

H Duan, L Qu, C Shou - Cancer letters, 2014 - Elsevier
... Cell confluence rates were measured by a CloneSelect Imager system (Molecular Devices,
New Milton, Hampshire, UK). Mycoplasma propagation and co-culture. M. hyorhinis was
grown for 72 h at 37 °C in a modified Hayflick's medium [18]. ...