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CellCelector software

User friendly and powerful software for automated detection and isolation of single cells and colonies

The ALS CellCelector is a highly versatile and flexible system for the automated analysis and picking of individual single cells and colonies. This requires an equally flexible and powerful software giving access to the numerous features of the CellCelector.

An intuitive and easy-to-use graphical user interface is guiding the operator through every step of the experiment. Different user access levels allow easy access to the software without intensive training for new operators while offering advanced features, open access to all parameters, calibrations and customization capabilities for power users. This enables simple day-to-day use as well as performing sophisticated and complex experiments.

CellCelector standard experiment workflow:
The user interface of the CellCelector software is aligned with the standard experiment workflow of the system by separating the experiment into 5 different workflow steps:

  • Scanning of cell culture plates and dishes to acquire and store images in all required channels (bright field, phase contrast and fluorescence)
  • Analysis of those images and detection of cells or colonies of interest
  • (optional) Review of the analysis results by the operator
  • Picking of the detected single cells and colonies
  • Documentation and export of the experiment results

Each experiment step will be shown in a dedicated user interface giving access to just the right amount of features and data for the respective step. All options and features unrelated to the current experiment step are hidden from the operator hence reducing complexity.


Cellcelector software: scan
The plates and dishes containing the sample are scanned automatically by a high-resolution camera employing a motorized microscope stage. Plates are selected from a plate library containing the most common commercial plate formats as well as allowing creating customized formats. Additional plates, dishes or slides can be added easily if required.

Depending on application requirements scans can be done in bright field, phase contrast or up to 6 fluorescence channels. All imaging parameters from camera settings like exposure time to hardware settings like filter settings and illumination parameters are stored in predefined imaging configurations. This allows switching between different imaging setups with a simple mouse click. For scanning any combination of predefined imaging configurations can be chosen to acquire multispectral images over a variety of channels and illumination methods.

All stored images of the scan are combined by the software into an overview image of the scanned area:

Analysis and detection

During this step all stored images are analyzed and target cells and colonies are detected automatically based on parameters defined by the operator.

For each detected cells or colony in each recorded channel the software is calculating a panel of morphological measurements like area, diameter, shape, sphericity (roundness) and others.  Using filter gates on those parameters allows filtering of the analysis results to specifically detect only target cells and colonies.
A user-friendly preview functions allows real-time verification and adjustment of the analysis settings.
All parameters can be saved as predefined analysis settings that allow for easy routine analysis of standard experiments.
Analysis: morphological parameter

Review (optional)

During analysis the software is generating a list of all detected objects showing the data on all selected measurements for each detected cell or colony. If required these lists can now be revised by the operator by applying additional numerical filters or reviewing the images of detected cells in an image gallery. It is also possible to add additional items to the pick list by selecting interesting objects directly on the screen.
Manual selection
Detection: object list


Picking parameter
The ALS CellCelector facilitates a very gentle picking process with high rates of viability of the picked cells or colonies. Therefore the CellCelector is perfectly suited for further cell cultivation, single cell cloning or various molecular analysis methods.

The CellCelector software supports this by giving the operator access to a wide range of picking parameters (e.g. aspiration and dispensing speeds, volumes, picking height etc.). Those parameters can be adjusted and optimized individually for ideal picking results from individual single cells, clones from suspension or semi-solid media to adherent colonies.

Optimizing these parameters allow to not only pick objects from standard cell culture dishes or well plates but also from membranes, filters or microscope slides.
During picking cells are traced from their source position to their destination plate and well. The software is also showing a live image during picking giving the operator great microscopic visibility of the cell picking procedure facilitating easy picking parameter optimization.

For quality control purposes the software automatically saves images immediately before and after each pick allowing a later review of the picking results (in BF and/or any fluorescent channel).  Optionally the software can verify successful picking automatically recording the status of each pick in the pick list.
Quality control of the picking process
Microscopic high-quality before and after picking images are automatically acquired and can be easily exported.
Successful deposit can be visualized by scanning the destination plate.


The complete experiment data is listed and documented GLP-compliant on the documentation page of the software. All data can be exported quick and easily for documentation and archiving.

Each detected/picked object can be identified by its unique ID and can be tracked through the complete process from source to destination well.

All imaging and numeric data as well as microscopic high-quality before and after picking images of all picked cells and clones are stored in the CellCelector™ software database. Source and destination position of each cells are recorded in the same list. This way the imaging and picking data can be easily revisited later once downstream data (e.g. PCR or cultivation data) becomes available.
Documentation: result list

Benefits and features of the CellCelector™ Software

  • Perfectly suited for research and development application requirements by creating own protocols and open access to all parameters

  • Easy to use through a graphical experiment workflow and utilization of standard protocols for routine work

  • High flexibility through a large number of parameters for high-quality imaging, sophisticated image processing and analysis as well as sensitive and precise picking

  • Complete and GLP compliant documentation of the entire process

  • Data tracking for each object from source to destination plate

  • User-definable export of all experiment data for subsequent documentation and archiving

  • Continuous improvement of the software through adaptation of customer needs and suggestions by our own software development team

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