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Isolation of precise numbers of cells

Get an exact cell count for your validation experiments

In many applications like measuring enrichment rates or assessing sensitivity and specificity a precise number of cells is required to create high-quality spike-ins for reference samples. Conventional cell sorting techniques like FACS or single cell printing cannot guarantee the deposition of such exact numbers of cells to a destination well/tube.

The ALS CellCelector platform combined with our nanowell plate technology allows for an extremely precise and gentle isolation of a precise number of cells. So if for example a precise count of 1, 5, 10, 50 or 100 cells is necessary for your assay the CellCelector will precisely retrieve exactly those 1, 5, 10, 50 or 100 intact cells.
Single cell module in 96 well microtiter plate
Fig. 1. The ALS CellCelector™ allows isolating cells to any standard or custom plates, tubes or vials.


Our CellCelector approach for isolation of precise numbers of cells consists in (i) seeding cells in a CellCelector™ S200 ULA nanowell plate at a cell density corresponding to the target cell number per nanowell; (ii) automated scanning and counting of the cells in the nanowells; (iii) automated selection of the nanowells populated with the target cell number; (iv) validation of the list by the operator; (v) automated tranfer of selected sets of cells to the destination tubes/wells with complete tracking of the whole process (Fig. 2).
Workflow for isolation of fixed numbers of cells
Fig. 2. The CellCelector™ workflow for automated isolation of precise numbers of cells.

Cell seeding statistics

When seeding a single cell suspension into a nanowell plate the cells are randomly captured inside the nanowells. Ideally a uniform seeding of a perfect single cell suspension follows a standard Poisson distribution. Here the probability (p) to randomly capture a given number of cells (k) in a nanowell is described by the equation

where λ is the average number of seeded cells per nanowell. Fig. 3 shows both the theoretical and measured cell distributions in one well of a S200 24-well nanowell plate for several cell seeding densities. This allows to calculate the number of cells to be seeded into each well of a 24 well plate that is needed in order to maximize the probability of capturing the required amount of cells inside the nanowells.
Poisson distribution for fixed cell number isolation
Fig. 3. Theoretical (lines) and experimental (dots) Poisson distributions for seeded cell densities of 1, 5, 10 and 20 cells per nanowell. Total number of scanned and analyzed nanowells has been 2,500.

Automated well scanning and cell counting

The seeded wells can be scanned in BF and any fluorescence channel (Fig. 3 and Fig. 4) if the cells are fluorescently labelled (e.g. with CellTracker™ dyes). Cell counting can be done both in BF and fluorescence modes. After cell counting the user can review the images of all nanowells in a gallery of nanowell images.
Overview Nanowells after cell loading
Fig. 4. Overview image of one well scanned in FITC channel. The circle visualizes the scan and analysis area.
Isolation of fixed numbers of cells - Cell distribution example
Fig. 5. A typical cell distribution in 200 µm nanowells with an average cell density of 20 stained SK-BR-3 cells per nanowell. Left: bright field, right: FITC.
Isolation of fixed numbers of cells - Selection of sets of 5 cells
Fig. 6. Example of 12 nanowells with 5 cells automatically selected by the CellCelector software.

Automated recovery (picking)

Once the operator has validated the list of nanowells to be recovered the system is automatically picking from all the selected nanowells. During picking the system is automatically saving before and after picking images for quality control purposes. The system also allows pooling the content of several nanowells into one destination tube leading to a deposit of larger numbers of cells, e.g. 20 cells = 2 nanowells x 10 cells, 100 cells = 5 nanowells x 20 cells.
Before and after cell recovery from nanowell plate
Fig. 7. Example of picking a set of 20 cells. Before and after picking images are saved automatically.
CellCelector - Imaging deposited cells in the destination well
Fig. 8. Detection of 20 cells deposited in an optical flat bottom PCR tube.
100% of the picked cells are deposited in the destination well. If the cells are transferred in a flat bottom plate or tube the deposited cells can be easily visualized and counted using the CellCelector (Fig. 8).


The user can export all numerical data including full tracking information for source and destination plates as well as all images (scan, before/after picking etc.) related to the picked nanowells.
Gallery of before-picking nanowell images in destination plate layout
Fig. 9. Example of a gallery of before-picking nanowell images corresponding to sets of cells isolated to specific wells of a destination 96-well plate.

Benefits of the CellCelector™ workflow for the isolation of precise numbers of cells


  • The only system guaranteeing isolation of the very exact number of cells down to a single cell.
  • Reliable image-based confirmation: no hidden cells.
  • 100 % picking efficiency: no cells left behind or lost.
  • Very gentle to cells.


  • Compatible with any cell size and type.
  • Works both with fixed and live cells.
  • Automated cell counting in bright field and/or fluorescence.
  • Flexible isolation scenarios: identical cell numbers throughout the destination plate or creation of cell number series, e.g. 1, 2, 5, 10, 20, cells.
  • Mixing of several cell populations in fixed proportions.

Easy to use

  • Simple sample preparation.
  • User-friendly software.
  • No routine maintenance necessary.
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