Single Microbial
Cell Isolation

Access the microbial individual level

Single Microbial
Cell Isolation

Access the microbial individual level

cellenONE is the optimal tool for sorting and isolation of microorganisms for both single cell omics analyses and culture-based applications

A unique cell type range: any microbe, any size.

Here is what we have tried so far, and we will be very happy to try other microorganisms that you would like to isolate!

Bacteria and archaea, for instance:

  • Bacillus
  • Escherichia
  • Lactobacillus
  • Microccocus
  • Pseudomonas
  • Staphylococcus
  • Haloferax

Filamentous fungi spores and conidia, and yeasts, for instance:

  • Aspergillus Niger
  • Aspergillus Oryzae
  • Saccharomyces cerevisiae
  • Botrytis cinerea

Autofluorescent or not, for instance:

  • Alexandrium Minutum
  • Thalasiossira Weissflogii
  • Lauderia sp.
  • Dictyostelium
  • Leishmania

The optimal tool for clone isolation in synthetic biology

Synthetic biology is the new chemistry: bioengineered microbes can be used to produce any kind biomolecules, from drugs to fragrances.

  • cellenONE can dispense single clones directly in liquid cultures, scaling up mutant screening by automated pure culture generation.
  • Combine high performance on bacteria, fungal spores, yeasts and microalgae, easy sample prep and traceable post-isolation QC.
  • cellenONE goes HT, for integration in your production process and Cellenion engineering team helps you for an optimal and fast set-up of your process.

An open platform for microbial single cell omics

  • cellenONE is compatible with virtually any single cell -omics methods (single cell whole genome sequencing, RNA sequencing and proteomics) and can be combined with cutting edge –omics technologies (e.g., digital PCR).
  • Reduce cost and contamination in account of cellenONE nano-volume liquid dispensing ability.

Cellenion is collaborating with the University of Rennes and CNRS to develop single cell –omics solutions for microbial cells, within the framework of the funded project LabCom MICROSCALE.

Cellenion and ECOBIO laboratory (UMR CNRS-University of Rennes, expert in microbial ecology and environmental genomics) received a Labcom-2020 €360k grant by the French National Research Agency (ANR) for the creation of the joint MICROSCALE-Lab (MICRObial Single Cell AnaLysEs Laboratory). The overall objective of this 5-year project is to offer a complete solution for the isolation, library preparation and bioinformatic analysis of single microbial cells, creating a conceptual and technological breakthrough for the study of microbial communities. 

Labcom latest news:  

Solène Mauger, joint student of Ecobio lab and Cellenion, successfully defended her PhD thesis “Elaboration of innovative single-cell genomics approach and application to soil bacterial communities”. She will start in February 2024 a Post-doc at Ecogeno, dedicated to the development of microbial scRNAseq workflow. 

Check out our publication on the contribution of single microbe -omics to microbiology: 

High throughput culturomics

Culture-based approaches are rising back in microbiology. Classical methods for isolate library generation are tedious and time-consuming, therefore increase in throughput is now needed.

  • cellenONE can isolate any type of cells, and mixes of those types, including host and microbial cells in the same sample!
  • With no need for fluorescent staining, cellenONE ensures optimal post-isolation cultivability, for abundant and diverse culture libraries.

Unique single cell accuracy

  • Best-in-class single cell accuracy for all types of cells
  • With our microLIFE software, cellenONE is now able to reach up to 100% single cells for all types of microbes (even the smallest ones), both in bright field and fluorescence: no equivalent on the market.

Image-based cell isolation

  • User-defined sorting parameters (morphology and/or fluorescence)
  • 4-channel fluorescence (DAPI, FITC Cy3, Cy5)
  • Assurance of monoclonality: recorded images
  • Immediate visual feedback on sample preparation (e.g. presence of host cells, debris, etc…)
  • Link phenotypic and morphological information with omics data

Use any target labware

  • Microorganisms can be isolated onto or into any consumable, MTP, petri dish, microscope slide, etc.
  • Very high positional precision of cell isolation and reagent dispensing onto custom chips and microdevices

Nanoliter liquid dispensing for reaction miniaturization

  • Small droplet volume (150 to 600 pL)
  • Compatible with a wide range of reagents (incl. culture media, molecular biology reagents…)
  • Temperature and humidity control to prevent evaporation and enable on-deck incubations


cellenONE is a revolutionary technology with advanced visual processing solutions that provides real-time and high accuracy single cell isolation and dispensing.

cellenONE BSC

Single cell workflows under protection

microLIFE Software

Sorting and isolation of very small particles, from mitochondria to microbial cells

cellenONE® HT

True walk-away solution for efficient, automated and high throughput monoclonal cell line development