Next Generation Cytometry

High content cytometry for explorative analysis of cytometric and histological samples to understand structures, functions, and mechanisms on a cellular level.

Chipcytometry is a combination of unsurpassed quantitative phenotyping ability of flow cytometry with the unparalleled detailed imagery and functional insights of microscopy while maintaining cell and biomarker integrity over a period of 12 month.

Today, there is a great need for labs to improve sample preparation, shipping, storage and in-depth analysis of cell-containing samples. The inventors of Chipcytometry felt that when it comes to measuring the expression of cell-based biomarkers, it was always stressful, error-prone and time consuming to get significant and reliable answers from cellular samples:

1. Storage and logistics of cell samples:

When sending samples (e.g. blood, CSF) from study centers to the analysis facility, cellular composition and marker expression was not controllable and often did not mimic the in-vivo situation when finally analyzed. Thus, scientists always had to assure a very timely delivery to at least reduce these problems and always had only ‘one shot’ for analyzing the precious samples. Storing cells frozen often led to significant changes in biomarker expression.

2. Limitation in the numbers of markers that can be analyzed per sample

Normally, research and even diagnostic procedures are iterative/sequential processes: Step-by-step, the hypotheses are tested and rejected or proved until the solution/diagnosis is found. We often wished that we could somehow preserve our precious cell samples and re-analyze them with an unlimited set of markers in such an iterative process.

3. Flexibility and multiplexity

With the impressive advances resulting from the human genome project and many other successive studies, it became more and more clear that it is necessary to not only analyze protein- and nucleic acid-based biomarkers in body fluids or cell/tissue lysates, but (much more important) directly on and inside single cells. We often wished to be able to measure much more than 8-10 markers per cell without prior intensive markerset-establishing phases. It should be possible to have hundreds of markers in stock and flexibly use any combination of desired markers right out of the shelf and directly measure them on the sample.

Chipcytometry allows to generate cytometric data from up to 30 biomarkers at the same time from the same sample. Moreover Chipcytometry allows fixing biomarkers on cells at the site of sample preparation, to send and store them in a controlled format (ZellSafe chips) enabling sample re-analysis for about 12 month. This makes Chipcytometry the perfect technology to really study and understand cellular structures, functions, and mechanisms and discover new biomarkers. Chipcytometry therefore has become an extremely powerful tool for biomarker discovery in academic research. In a number of preclinical and clinical studies Chipcytometry has been validated for a broad range of clinical specimens and has delivered excellent results.


Principle of iterative chip-based imaging cytometry

Chipcytometry was first describes 2008 (Hennig et al.) enabling destruction-free analysis of cells and tissues. Thus, your cells are immobilized on microfluidic chips and are analyzed for biomarkers iteratively: After each round of (single- or multicolor) stain+scan, fluorescence is erased and fluorescence channels are free for a new round of biomarker analysis. Theoretically, this cyclic approach can be repeated for each chip endlessly. Therefore, you don’t need to establish fixed markersets – you can use each antibody with the SAME color and combine antibodies as needed, without time-consuming compensation tests. This cyclic approach (we call it ‘stain-think-stain’ cycles) enables very flexible research and significant shortening of knowledge generation times.


(1a) Cells in solution are pipetted into the microfluidic channels. The surface of area within the chips that will later be imaged contains a patented cell-attractive surface where any kind of cell self-adheres within seconds:


The image shows a part of the surface inside the microfluidic chip covered with differentiating human hematopoetic stem cells.

(1b) Cells that are recovered from organisms by tissue sectioning are directly ‘clicked’ into our microfluidic chips:

(2) After initial imaging of autofluorescence, cells are stained with dye-labeled antibodies, function-sensitive dyes (e.g. Fluo4 for calcium-flux) or histological stains like HE.

(3) High Dynamic Range microscopic imaging and our image processing pipeline enables a very sensitive measurement of cellular biomarker data with a theoretically unlimited dynamic range (see also ‘Chipcytometry Pipeline‘).

(4) We either use bleaching of remaining fluorescence or a patented technology named ‘Switch-Antibodies’ to switch-off remaining fluorescence. So another biomarker can be measured using the SAME dye. Therefore, the number of markers that can be measured on the same sample is virtually unlimited.

(5) This enables a cyclic measurement of biomarkers that can be stopped and resumed at any time, if cells are fixed (e.g., with paraformaldehyde).

We developed a technology platform to perform a completely automated workflow for this iterative chip-based imaging cytometry. Click here to visit our products page.

Further reading: Our seminal paper in Cytometry

Also visit our community site

So comparing different features of flowcytometry and Chipcytometry, it becomes clear that Chipcytometry is especially useful for the analysis for precious patient samples, small sample sizes and the need for explorative sample analysis, whereas flowcytometric approaches have their strength in analyzing large numbers of cells in short timeframes with a limited, predetermined markerset:



Sample Storage

ZellSafe Chips: Built-in Cell- & Tissue-Biorepository

There is no need to fear loosing your precious cell sample any more: ZellSafe chips have been designed to solve two major problems of current cell-analysis workflows:

1. Transport of cellular samples in a well-defined condition that preserves biomarkers in a near-to-in-vivo state

2. Storage of cellular samples under conditions that preserve the status-quo over several month and years, thus especially meeting the needs of biobanks and QC for regenerative cellular medicine.

Currently, two types of chips are available:

1. ZellSafe chips for immobilization and storage for cells in solution (e.g. PBMC, CSF-cells, bronchoalveolar lavage, joint fluid)

The surface inside these microfluidic chips is modified with a patented surface coating that leads to non-selective adherence of any kind of living cell.


Learn how to fix cells inside these chips:

2. ZellSafe chips for tissuesections

These chips have been designed to easily attach cryosections on coverslips to a microfluidic system for further analysis. See how it works:

ZellSafe chips are therefore the optimal tool to iteratively analyze cellular phenotypes and functions using a microscope-based imager. They seamlessly integrate with the Chipcytometry technology platform:

Click here to purchase ZellSafe chips.


The Chipcytometry Data-Pipeline: From Cells to Data

Usability of live science instrumentation and understanding of high-content data generated by those machines largely depends on well-designed software and userinterfaces behind these technologies. The software behind Chipcytometry was therefore based on a semantic data engine (EDL: Experiment description language) developed from scratch by our team. It enables every component of the Chipcytometry ecosystem (ZellScanner, Cytobot, userinterfaces, databases, image- and dataprocessing servers, datavizualisation tools) to ‘talk’ to each other. Using EDL we built software interfaces that hide the complexity of the technology from the user and helps to discover new biomarkers rather then to struggle with instrument calibration.


Technologies that produce complex and high-content data tend to let alone users with tons of unstructured, not annotated and therefore less useful data.

EDL data structure has been designed from scratch to generate highly structured data that assure for the first time the complete SEARCHABILITY, COMPARABILITY and EXCHANGEABILTY of all data generated by our technology.

We applied semantic web technologies to annotate every single step during pre-analysis, analysis and post-analysis, if requested by the customer.

Figure: Screenshot of pre-analytical workflow data acquisition interface


Figure: Screenshot of the project management interface


Cytometry data generated by Chipcytometry are fed into a automatic QC pipeline. After passing QC, data can be exported to CSV or FCS format to use the data in preexisting flow cytometry data processing software.

However, we developed R-based scripts to cluster and visualize the highly complex data generated by Chipcytometry.

Cytometric data produced by this technology meet high quality standards:


Data is handled using validated data encryption standards. No individual patient-specific data is stored. We are prepared to adapt our data handling and -transmission procedures according to your internal SOPs.


Chipcytometry was already used in a number of very different studies. In this section, a growing collection of usecases illustrates the many areas where Chipcytometry can be applied to.

Application Topics

Measuring the intracellular shutteling of EGF-Receptor in human tumor cells

Status: project ongoing

Project partner: Prof. Paul Span, PBG of the EORTC, UMC St Radbound, Netherlands

In this project, we make use of the ability of Chipcytometry to locate and quantify fluorescent signals inside the cell. We here monitor the ratio of cytoplasmatic vs nuclear EGFR in MDA-MB breast cancer cells.