Benchtop CQ1 Confocal System

With its compact footprint and lightweight, benchtop design, there is no need for a darkroom or specialized setup for the CellVoyager CQ1. The unit provides rich feature extractions, facilitating sophisticated cellular image analysis, and while the Nipkow Spinning Disk Confocal Technology allows high speed scanning, it reduces phototoxicity and photobleaching.

  • Easy to use, intuitive, simple acquisition software increases productivity
  • Compact design contains multiple, fully integrated functions
  • CSU W-1 confocal spinning disk technology results in higher scanning speeds and higher quality images
  • Systems open platform allows for integration for laboratory automation
  • Supports the CellPathfinder high content analysis system


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Enables measurement of spheroids, colonies, and tissue sections

  • No need to remove cells from the culture dish, in contrast to traditional flow cytometry
  • Nipkow spinning disk confocal technology allows high-speed yet gentle 3D image acquisition
  • Rich feature extraction to facilitate sophisticated cellular image analysis
  • Wide field of view and tiling capability enables easy imaging of large specimen

Enables analysis of time-lapse and live-cell

  • High precision stage incubator and low phototoxicity of our confocal makes the analysis of time-lapse and live-cell are possible
  • Max. 20fps option for fast time-lapse*1

Blue Spheroid Z StackHigh-quality image and similar operability to a traditional flow cytometer

  • Integration with CellPathfiner software can provide powerful analysis displayed in real-time with image acquisition
  • Usable high-quality image as confocal microscope image.
  • Interactive graphs make it easy to trace back the data points

Open platform

  • Connectable with external systems via handling robot*2
  • Expandable to the integrated system as image acquisition and quantification instrument
  • FCS/CSV/ICE data format readable by third-party data analysis software
  • A variety of cell culture and sample dishes are applicable

Compact footprint, lightweight bench-top device; no need for a darkroom


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*1 Option
*2 Contact to CQ1 partner for more information


CQ1Multiple functions fully integrated into a compact box

Compact design contains fully integrated functions to offer an easy-to-handle confocal imaging system, without a need for complicated system integration. You only need to set a sample and run the software. A user-friendly interface and versatile functions support your measurement and analysis.

Principles of the Microlens-enhanced Nipkow Disk Scanning Technology

A Nipkow spinning disk containing about 20,000 pinholes and a subsidiary spinning disk containing the same number of microlenses to focus excitation laser light into each corresponding pinhole are mechanically fixed on a motor, and very rapidly rotated. As a result, a high-speed raster scan of the excitation lights on the specimen can be achieved. The pinhole and microlenses are arranged on each disk in our proprietary design to optimize the raster scan. Multi-beam scanning not only increases scanning speed but also results in significantly lower photobleaching and phototoxicity because multi-beam excitation needs only a low level of laser power on the specimen to fully excite fluorescence.

CQ1 System integration with CQ1

Example of setup

Example of setup


Item Specifications
Optics Microlens enhanced dual wide Nipkow disk confocal,
Phase contrast (Optional add-on)
Laser/Filter Laser: Choose 2-4 lasers from 405/488/561/640nm,
10-position Filter wheel (built-in)
Camera sCMOS 2560×2160pixel, 16.6×14.0mm
Objective lens Max.6 lenses
(Dry: 2x, 4x, 10x, 20x, 40x Long working distance: 20x, 40x
Phase contrast: 10x, 20x )
Sample vessel Microplate (6, 24, 96, 384 well), Slide glass,
Cover glass chamber*1, Dish (35, 60mm*1)
XY stage High-precision XY stage, designated resolution 0.1µm
Z focus Electric Z motor, designated resolution 0.1µm
Autofocus Laser autofocus, Software autofocus
Feature data Number of cells/cellular granules, Intensity, Volume, Surface area, Area, Perimeter, Diameter, Sphericity, Circularity, etc
Data format Image: 16bit TIFF file (OME-TIFF), PNG
Numerical data : FCS, CSV, ICE
Workstation Measurement and analysis workstation
Size/weight Main unit: 600×400×298mm 38kg
Utility box: 275×432×298mm 18kg
Environment 15 - 30oC、20 - 70%RH No condensation
Power consumption Main unit and Utility box: 100-240VAC 800VAmax, Workstation: 100-240VAC 650VAmax

*1 Under development  *2 Display is not included with CQ1 system

CellPathfinderCellPathfinder, high content analysis software (Optional)

  • Preset analysis menus for a variety of applications
  • Flexible graph functions to display analysis results
  • Direct link between chart and object image

Machine learning

3D analysis

Label-free analysis

The software learns the features of the sample objects collected by users.



Digital phase contrast function is a powerful tool to analyze unstained bright field samples.


Simple, intuitive measurement procedures

Compare CQ1, Flourescent Imaging, and Flow Cytometry

  CQ1 General fluorescent imaging Flow cytometry
Cell removal/suspension treatment Not necessary Not necessary Necessary
Cell image confirmation Possible Possible Not possible
Display feature data and graphs in real-time with imaging Possible Depends on devices Possible
3D data measurement Possible Not possible Not possible
Time-lapse Possible Not possible Not possible
  • CellActivision

    CellActivision uses Machine Learning Technology and a unique digital filter to recognise cells or colonies directly from label free images. CellActivision can also classify and quantify these cells by the use of sample libraries which are easily prepared by the user.

    See More
  • CellPathfinder

    Cell imaging software supports label-free samples and provides multiple graphing options with a streamlined, easy-to-use interface.

    See More



PhenoVista Biosciences is the leading provider of custom, imaging-based, phenotypic assay services. With a collaborative and scientifically driven project design and management approach, PhenoVista has a proven track record of delivering high-quality data from robust and scalable assays. PhenoVista’s key advantage lies in the ability of their industry-trained scientists to combine world-class understanding of diverse biological systems with cutting-edge quantitative imaging to deliver clear, actionable output data.


drug discovery and drug development for an interrelated set of disorders that emanate from type II diabetes and obesity


world-class team with an unmatched combination of imaging experts, assay development experience and the latest technologies and data analysis capabilities

Application Note
Application Note
Application Note

The CQ1 confocal image acquisition mechanism with the distinctive CSU® unit has a function to sequentially acquire fine cell images along the Z-axis and capture information from the entire thickness of
cells which include heterogenic populations of various cell cycle stages. In addition, saved digital images can be useful for precise observation and analysis of spatial distribution of intracellular molecules.
The CQ1 capability to seamlessly analyze images and obtain data for things such as cell population statistics to individual cell morphology will provide benefits for both basic research and drug discovery
targetingM-cell cycle phase.


List of Selected Publications : CQ1

Application Note

Cell stage categorized using FucciTime lapse imaging of Fucci-added Hela cells was conducted over 48 hrs at 1 hr intervals. Gating was performed based on the mean intensities of 488 nm and 561 nm for each cell. They were categorized into four stages, and the cell count for each was calculated.

Application Note
Yokogawa Technical Report
1.0 MB
The CQ1 has a top opening for robotic integration and is remote control mode-compatible with many robotic arms and grippers. To learn more, click here. ...
The CQ1 has a remote operation mode that allows third-party robotic scheduling software to open and load plates and run protocols for measurement and analysis. To learn more, click here. ...
The additional computer workstation that comes with the CQ1 enables simultaneous acquisition and analysis of data. To learn more, click here.   ...
For neurite growth, consider using either the 20x or 40x objective lens for maximum lateral resolution. To learn more, click here. ...
You can request a CQ1 hardware or software manual by emailing Yokogawa Life Science at
The utility box is an accessory unit that provides power and lasers to the CQ1. To learn more, click here.




Yokogawa's CQ1 open platform integrates seamlessly with Advanced Solutions BioAssemblyBot® 400. With laboratory automation becoming a standard in research, Yokogawa's high content confocal system's ability to work with robots like Advanced Solutions' BioAssemblyBot® 400 is essential to advancing laboratory automation.


Are you looking to improve laboratory workflows, data management, and imaging analysis?


This webinar covers the integration of a high-content imager into a modern laboratory automation system and workflows built to utilize it. This on-demand webinar describes the integration topology used in the High Throughput Bioscience Center at St. Jude and the technical challenges that emerged pertaining to data handling and analysis. The webinar addresses the variety of ways we have used our high-content imager in the context of a high throughput screening center, using examples of experiment workflows from recent users.


Key Topics:

  • Body Copy:
    • Key considerations for integrating a high-content imager into a laboratory robot system
    • Methods for interfacing between robots and the imager
    • Important considerations for imaging data management and analysis
    • How the St. Jude High Throughput Bioscience Center supports the diverse imaging needs of its projects

In this webinar, Professor Jonny Sexton discusses a pipeline, developed in the Sexton lab, for the quantitative high-throughput image-based screening of SARS-CoV-2 infection to identify potential antiviral mechanisms and allow selection of appropriate drug combinations to treat COVID-19. This webinar presents evidence that morphological profiling can robustly identify new potential therapeutics against SARS-CoV-2 infection as well as drugs that potentially worsen COVID-19 outcomes.


3D imaging experts from Yokogawa and Insphero have come together to provide helpful tips and tricks on acquiring the best 3D spheroid and organoid imaging. This webinar focuses on sample preparation, imaging, and analysis for both fixed and live cells in High Content Screening assays. The experts also discuss automated tools that can help researchers understand the large volume of data in these High Content Imaging Analysis Systems.


Physiologically relevant 3D cell models are being adopted for disease modeling, drug discovery and preclinical research due to their functional and architectural similarity to their tissue/sample of origin, especially for oncology research. Multifunctional profiling and assays using 3D cell models such as tumoroids tend to be manual and tedious. Further, high-content imaging of biomarkers in 3D cell models can be difficult.
In this two-part webinar present to you streamlined technologies which can bring consistent timesaving, ease-of-use, and high-quality data to your 3D cell-based workflows:

(A)  The Pu·MA System is a microfluidics-based benchtop automated device for performing “hands-off” 3D cell-based assays. In this webinar, application scientist Dr. Katya Nikolov will present data from optimized assays using tumoroids followed by Yokogawa’s high-content imaging systems for biomarker detection.

(B) Yokogawa’s high-content imaging systems such as CellVoyager CQ1 provide superior confocal imaging using the Nipkow Spinning Disk Confocal Technology. Here, application scientist, Dan Collins will present details of the high-content imaging capabilities, easy to use and intuitive image acquisition software, especially for increasing productivity and a streamlined workflow.

Learn How:

  • The open platform, Pu·MA System can be used to automate your 3D cell-based assays
  • To perform automated IF staining for biomarkers using tumoroid models without perturbing your precious samples
  • Image acquisition from 3D cell models using Yokogawa’s high-content imaging platforms
  • Image analysis from cells, complex spheroids, colonies, or tissues using the CellPathfinder high content analysis software

Physiologically relevant 3D cell models are essential for drug discovery and preclinical research due to their functional and architectural similarity to solid tumors. One of the challenges faced by researchers is that many of the assays using these precious samples tend to be manual and tedious.

Using proprietary microfluidics technology, Protein Fluidics has created the Pu·MA System for automated complex 3D cell-based assays. In this webinar, application scientist Dr. Katya Nikolov will present her work on combining this novel automation technology with Yokogawa’s high-content imaging systems for biomarker detection in 3D cell models. Nikolov will demonstrate the utility of an automated immunofluorescence staining workflow followed by confocal imaging within the Pu·MA System flowchips. This automated workflow enables quantitative assessment of biomarkers which provides valuable data for further understanding disease mechanisms, preclinical drug efficacy studies, and in personalized medicine.

This webinar will explore:

  • The Pu·MA System and novel technology for automated 3D cell-based assays
  • How to perform automated immunofluorescence staining for biomarkers with a “hands-off” assay workflow
  • How to visualize biomarkers after the assay with high-content imaging within the flowchip

Generating translatable high-content imaging data from physiologically-relevant cell models, including 2D and 3D structures, is extremely valuable for drug discovery and pre-clinical research. In this webinar, James Evans, CEO of PhenoVista Biosciences presents case studies on how Yokogawa’s Benchtop CQ1 Confocal System can improve throughput and standardize processes for complex 3D cell-based phenotypic assays.

Key learning objectives:

  • Strategies for designing and implementing high-content screening assays
  • Approaches for deciding between 2D and 3D model systems

Visualizing the complex spatiotemporal dynamics of human stem cells as they proliferate and make cell fate decisions is key to improving our understanding of how to robustly engineer differentiated tissues for therapeutic applications.

In this webinar, Dr. Rafael Carazo Salas will describe multicolor, multiday high-content microscopy pipelines that his group has recently developed to visualize the dynamical cell fate changes of human Pluripotent Stem Cells (hPSCs).

Key Topics:

  • Visualizing how human Pluripotent Stem Cells (hPSCs) proliferate and undergo early differentiation in vitro, by high content microscopy
  • Learning about experimental and computational pipelines that enable monitoring single-cell fate dynamics
  • Learning about novel “live” reporters of hPSC cell fate

Rafael Carazo Salas, PhD
Professor, School of Cellular and Molecular Medicine
University of Bristol


This webinar highlights Yokogawa’s High Content Solutions, the benchtop confocal CellVoyager CQ1, and CellVoyager CV8000. Utilizing Yokogawa’s dual-wide microlens spinning disk confocal technology, these automated HCA systems provide remarkable image quality while increasing your output. This frees up time to complete other research activities. Also, recent additions to the CSU-W1 confocal upgrade is discussed. The SoRa, a super-resolution solution, and the Uniformizer, an image flattening device. Both of which can be added to the lightpath of your CSU-W1-enhanced microscope.

Introduction to Yokogawa
SoRa for CSU-W1 super-resolution with confocal
Two high content instruments from Yokogawa: The CQ1 and the CV8000

Dan J. Collins, Applications Scientist, Yokogawa Life Science


In the last few decades, the pharmaceutical industry has transformed people’s lives. However, the development of new drugs is becoming increasingly difficult and a paradigm shift in the drug discovery workflow is required to reduce attrition and transform conventional drug screening assays into translatable analytical techniques for the analysis of drugs in complex environments, both in-vitro and ex-vivo. The ability to visualize unlabelled compounds inside the cell at physiological dosages can offer valuable insight into the compound behavior both on and off-target.

SiLC-MS is a semi-automated methodology that allows the collection of intracellular contents using a modified CQ1 imaging system developed by Yokowaga. The instrument is equipped with a confocal microscope that allows bright field imaging as well as fluorescence imaging with 4 lasers (405, 488, 561, and 640 nm). Sampling is performed using the tips developed by Professor Masujima (1-4).

In this study, we show the applicability of the SiLC-MS technology to drug discovery, as it is crucial to identify compound and its metabolites when incubated in a mammalian cell at a therapeutic dose. We report on the validation studies performed using the SiLC-MS platform, in these validation studies we assess the ability to distinguish different cell types based on their metabolomic fingerprint, furthermore, we have also evaluated if this assay was sensitive enough to detect drugs intracellularly.

Presenter: Carla Newman, Scientific Leader (Celluar Imaging and Dynamics), GSK


Image-based phenotypic screening relies on the extraction of multivariate information from cells cultured in a large number of screened conditions. In this webinar, we explored the application of complex and biologically relevant model systems for drug screening, such as small intestinal organoids.

Key topics include:

  • Learn how to upscale, streamline, and automate intestinal organoid handling
  • Learn how to image in complex three-dimensional (3D) model systems and how to approach large imaging datasets
  • Understand the basics of multivariate analysis on image-inferred features


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