Streamlined cytoplasmic biopsy extraction 
with the FluidFM OMNIUM Platform

Sequence your cells while keeping them alive.

FluidFM biopsy solution for cytoplasmic extraction of single cells

FluidFM biopsy solution for cytoplasmic extraction of single cells

A FluidFM Nanosyringe, compared to regular liquid biopsy needle used to aspirate a small sample from patients, here is miniaturized to the dimensions where it can be used to aspirate a sample from the cytoplasm of a living cell. FluidFM Nanosyringes have a sharp pyramidal tip with a 600nm opening that gently inserts into the cell.

A biopsy is a cytoplasmic extract taken from an individual living cell. 


The RNA comprised in a single-cell biopsy represents a snapshot of a cell’s transcriptome at a given point in time. As such, a single cell biopsy makes it possible to profile a cell over time and correlate the downstream transcriptome of a specific, living cell directly to its phenotype without removing it from its native culture environment. 


The biopsy solution on the FluidFM OMNIUM platform, is a streamlined workflow to collect cytoplasmic biopsies for live-cell sequencing or Live-seq, using a FluidFM Nanosyringe.

The streamlined FluidFM biopsy workflow provides a delicate procedure to systematically collect a small portion of a chosen cell’s cytoplasm.


The workflow, facilitated through the FluidFM technology, enables users to precisely control the biopsy volume and pressure exerted on the cell to minimize cell perturbation and ensure high cell viability. During the entire experiment, cells can remain in their cellular context under visual control.

FluidFM biopsy solution for cytoplasmic extraction of single cells

The FluidFM OMNIUM platform is a semi-automated single-cell manipulation system developed for the non-destructive injection and extraction of individual cells.

FluidFM biopsy solution for cytoplasmic extraction of single cells

Keep your cells alive. 

Gentle cytoplasmic extraction workflow with minimal cell perturbation.

FluidFM biopsy solution for cytoplasmic extraction of single cells

Time-resolved transcriptomics.

Monitor specific cells in their 2D environment. 

& obtain transcriptional snapshots of a living cell.

Phenome - Transcriptome correlation

Real-time recording of both slow and long cell state transitions while directly correlating a cell’s transcriptome and phenome.

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Cytoplasmic Biopsy Collection Workflow & Features

The single-cell cytoplasmic biopsy collection workflow consists of three main steps detailed below.


Read our latest post "LUTHOR HD: Pushing the boundaries of single cell transcriptome analysis by in vitro mRNA amplification."

Use Cases

Investigate the effect of cell-cell interactions or external stimuli.

Select a specific cell within a 2D cell culture based on its neighbor or assess a cell’s response to a specific stimulus.

FluidFM biopsy solution for cytoplasmic extraction of single cells

Select & extract from a specific cell based on its morphology.

Use live imaging to obtain an extract of a specific cell based on its morphology. Then follow it over time.

Collect consecutive biopsies from the same cell.

Each biopsy represents a snapshot of a cell’s transcriptome at a specific time point. Subsequent sequencing enables direct tracking of cell state transitions. Learn more.

Biopsies from the cytoplasm of a single cell

In this video, a picoliter biopsy is taken from a specific HeLa cell with a FluidFM Nanosyringe. The gentle insertion into the cell is facilitated by the pyramidal tip of the FluidFM Nanosyringe.

The precision of the FluidFM OMNIUM Platform enables extraction from the cytoplasm of a cell of choice under visual control. Cells can be selected based on morphology or specific (fluorescent) tracers. The high precision and gentle nature of the biopsy comes from the force feedback provided by the FluidFM technology in combination with the Nanosyringe and its sharp pyramidal tip.

Live-cell imaging to record morphological changes of individual cells after biopsies.

The FluidFM biopsy solution allows to collect biopsies from individual cells and track them over time by recording of the coordinates using the ARYA software. This allows the researcher to study the response of an individual cell to a stimulus without disturbing the cellular microenvironment and correlate the response to the previously collected transcriptome. Furthermore, repetitive sampling of the same cell enables to generate time resolved transcriptional trajectories of the same cell. The FluidFM OMNIUM comes with an inverted microscope (Olympus IX83) that is fully integrated with the FluidFM ARYA operator software and is equipped with a temperature and CO2-controlled incubator. It is possible to collect images of the targeted cells before and after taking a biopsy to directly compare the generated transcriptome to morphological data.

Panc-1 cells are selected for extraction based on specific cell morphology.

Efficient collection of single cell biopsies for further downstream processing. 

The FluidFM Biopsy Solution comes with a custom Biopsy kit for efficient collection of cytoplasmic biopsies. The picoliter extracts are ejected from the FluidFM Nanopipette into a 1μL droplet of buffer on the droplet slide. From there, the droplet can be efficiently transferred to vials for snap freezing or direct library preparation for transcriptomic analysis. 

The single-cell biopsy kit - to be used with the FluidFM OMNIUM Platform to perform cytoplasmic biopsy collection.

The single-cell biopsy kit contains:

  • 35mm ibidi® dish with an imprinted grid to support alignment and position recovery of the platform. 
  • Droplet slide and holder, for precise positioning of the buffer droplet and sample collection. 
  • Drying station for automatically removing the droplet around the FluidFM Nanosyringe, in preparation for the buffer pre-load or biopsy disposition steps.

More questions or Interested in a demo? 

Further reading


Our collaborators from ETH Zurich and EPFL Lausanne successfully demonstrated that using a FluidFM Nanosyringe, it is possible to take an extract from a cell’s cytoplasm without killing it (Cell, 2016 [1]) and that this “single-cell Biopsy” is a representable snapshot of a cell’s transcriptome at a given point in time (Nature, 2022 [2]). Learn more about their findings when pioneering Live-seq using FluidFM cytoplasmic biopsies. 


Additional resources available: 


[1] O. Guillaume-Gentil, R.V. Grindberg, R. Kooger, L. Dorwling-Carter, V. Martinez, D. Ossola, M. Pilhofer, T. Zambelli & J.A. Vorholt. Tunable Single-Cell Extraction for Molecular Analyses. (Jul 2016) Cell, 166(2), 506-516. doi: 10.1016/j.cell.2016.06.025.

[2] W. Chen, O. Guillaume-Gentil, P. Yde Rainer, C. G. Gäbelein, W. Saelens, V. Gardeaux, A. Klaeger, R. Dainese, M. Zachara, T. Zambelli, J. A. Vorholt & B. Deplancke. Live-seq enables temporal transcriptomic recording of single cells. (Aug 2022) Nature, doi:10.1038/s41586-022-050

The total RNA content of a cell ranges between 1pg up to 50pg per cell, depending on the cell type. This comes down to an RNA content of a few pg of RNA per biopsy. Live-Seq as published by Chen et al. (Nature, 2022 [1]) is a combination of a cytoplasmic biopsy taken with a FluidFM Nanosyringe, and a low-input RNA sequencing protocol that is an enhanced version of SmartSeq2. Together with Lexogen, Cytosurge is developing a streamlined, commercially available workflow for biopsy collection and analysis using Lexogen’s LUTHOR HD kit. LUTHOR HD is a high-definition single-cell 3’ mRNA-seq library prep kit based on their proprietary THOR technology for direct RNA amplification. 


Related resources:

[1] W. Chen, O. Guillaume-Gentil, P. Yde Rainer, C. G. Gäbelein, W. Saelens, V. Gardeaux, A. Klaeger, R. Dainese, M. Zachara, T. Zambelli, J. A. Vorholt & B. Deplancke. Live-seq enables temporal transcriptomic recording of single cells. (Aug 2022) Nature, doi:10.1038/s41586-022-05046-9

Our proprietary FluidFM (Fluidic Force Microscopy) technology integrates the best features of force microscopy and micro-channeled probes. The FluidFM probes, of which the FluidFM Nanosyringe is one example, “senses” the surface which enables highly gentle interactions with cells. The FluidFM Nanosyringe has a sharp tip and an aperture of 600nm that allows to simultaneously sense interaction forces with the cell membrane and to aspirate exact femtoliters.

Find out more about:

[1] O. Guillaume-Gentil, R.V. Grindberg, R. Kooger, L. Dorwling-Carter, V. Martinez, D. Ossola, M. Pilhofer, T. Zambelli & J.A. Vorholt. Tunable Single-Cell Extraction for Molecular Analyses. (Jul 2016) Cell, 166(2), 506-516. doi: 10.1016/j.cell.2016.06.025.