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Confocal Fluorescence Microscopy System 

Thorlabs' Confocal Microscope


Thorlabs' Confocal Laser Scanning (CLS) Microscopy Systems are compact imaging modules designed to bring powerful confocal imaging within reach of most research labs. By eliminating signals that originate from outside the focal plane, confocal microscopy provides the ability to acquire high resolution, optically sectioned images from within a thick sample or to reduce background fluorescence from thin cultures. The CLS systems offer turnkey integration to virtually any upright or inverted microscope with access to the intermediate image plane (e.g., camera port) via a C-Mount. The included ThorImageLS™ software provides an intuitive graphical user interface that drives the CLS hardware to quickly record and review data.

Our basic Confocal Laser Scanning System includes an electronics control unit, an expandable standard sensitivity dual PMT module, a 16-position pinhole wheel, a two-channel (488 nm & 642 nm) laser source, and the ThorImageLS™ acquisition software and computer workstation. For more sophisticated imaging requirements, systems are available with up to four laser lines and four high-sensitivity GaAsP PMTs.

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  • Turnkey Integration with Commercial Upright or Inverted Microscopes
  • Optimized for 400 - 750 nm
  • Compact, Modular Design
  • Video-Rate Image Acquisition (512 x 512 Pixels @ 30 fps)

Confocal Microscope System Components

  • Confocal Laser Scanner (Incudes ThorImageLSTM Software and Computer)
  • 16-Position Motorized Pinhole Wheel
  • Confocal Z-Stepper Motor (Sold Separately)
  • 4-Channel Fiber Coupled Laser Diode Source (Sold Separately)


For information concerning pricing and availability, contact

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Thorlabs' Confocal Microscopy System

 Thorlabs’ Confocal Laser Scanning (CLS) Microscopy Systems are comprised of compact, purpose built, imaging modules for infinity-corrected, compound microscopes. They add the ability to acquire high-resolution optical sections within a thick sample or to reduce background fluorescense from a thin culture. The CLS systems offer turnkey integration to almost any upright or inverted microscope with access to an intermediate image plane (e.g., a camera port) via a C-Mount thread. The included software has an intuitive graphical interface that allows data to be quickly recorded and reviewed while providing sophisticated peripheral controls for image acquisition. All CLS systems are user installable; however, on site installation is available.

All hardware components are directly controlled through the ThorImageLS™software, including automated Z stepping control for optical sectioning (via piezo or stepper motor) and automatic calculation of Airy disk units based on objective magnification and pinhole size combination. Our intuitive interface allows novice and experienced users alike to obtain high-resolution microscopic images quickly and easily.

All CLS complete systems include a multi-channel fiber-coupled laser source, control electronics, Scan Head, pinhole wheel, detectors, and all fibers and cables needed to interconnect the system. Additionally, each system includes a Windows® computer with a 24" monitor, data acquisition, and control boards as well as ThorImageLS™software. A comprehensive installation and operation manual is also included with basic preventative maintenance instructions to ensure that your system Confocal Fluorescence Microscopy Systems (Page 1 of 4) performs optimally for years to come. Also available are complete systems that combine the Thorlabs Confocal package with third party upright and inverted microscopes. For further details on this convenient option, please contact us at

Confocal Microscope

Confocal System Schematic

Confocal System Schematic



At the heart of our systems is an efficiently designed Scan Head that incorporates a resonant scanner and a galvanometer for fast image acquisition. This allows for high imaging speeds up to 100 frames per second (at 128 x 128 pixel resolution) or high spatial resolution images (4096 x 4096 pixel resolution at 2 fps). At either extreme, or anywhere inbetween, the control and acquisition system creates highquality, jitter-free images (see inset at left).

Located within the Scan Head is our new, kinematic fluorescence filter cube (DFMT1) for quick and repeatable exchange of the primary dichroic mirror. Our complete systems come standard with a primary dichroic that reflects four laser lines (405, 488, 532, and 642 nm). Other primary dichroics for use with other wavelengths are avalible upon request.

Confocal Scanner Head



The scan lens assembly has been designed for superior imaging performance, and is color corrected from 400 – 750 nm. This broad range adds to the functionality of the system enabling the use of laser sources down to 400 nm while color correcting fluorescence emissions from even the deepest of red emitting fluorophores. Coupled with ultra-sensitive, low noise detectors and control electronics, we are able to provide systems which redefine the boundaries of contrast, resolution and imaging speed at an affordable cost.


One of the great challenges in laser scanning microscopy has been keeping the lasers in a multi-channel source aligned and therefore at peak power. We have overcome this problem by creating a four-channel laser source based on four service-free fiber pigtailed laser sources. Three of the four wavelengths are combined into a single fiber using an advanced, fully integrated fiber optic device. This solid state coupling method provides lifetime, adjustment-free service from our laser source.

The combined visible output is contained in a single mode fiber with an FC/PC connector. The optional 405 nm laser output is delivered on its own single mode fiber and is combined after the beam expander in the Scan Head module. By combining the 405 nm light after the beam expander, we are able to couple the UV laser into the lightpath with a 4 mm beam diameter, which increases stability and maintains the color correction of the system.

Four-Channel CLS Laser Source
Four-Channel CLS Laser Source

We offer four standard wavelengths in our laser source (405, 488, 532, and 642 nm); others are availible upon request. The entire laser source is controlled by a single USB connection, which allows the user to turn each laser on and off as well as control its intensity.


CLS PMT Module
Expandable PMT Modules are designed for multi-channel laser scanning microscopy applications.

Pinhole: An automated 16-aperture Pinhole assembly with apertures ranging from Ø25 μm to Ø2 mm, enables the ultimate balance between resolution and signal (for further details, see the Laser Scanning Microscopy Tutorial on page 1654). The pinhole is conveniently powered and controlled through USB. Additionally, the motorized, encoded control of the pinhole ensures perfect alignment and vibration-free movement. The emission light is focused on the pinhole and then collected by a large-core multimode fiber for transmission to the PMT detector system.

Detector: Our systems provide two different detector options. The standard sensitivity multi-alkali PMTs provide a low-noise, high dynamic-range image that is appropriate for most life-science and industrial applications. If needed for weak or highly photosensitive samples, we also offer an option with high sensitivity, TEC-cooled GaAsP PMTs. With either choice, the gain of the detector as well as the dynamic range of the digitizer is controlled within the ThorImage software.


System Configurations

Confocal System Configurations

All Thorlabs CLS Confocal Laser Scanning Systems can be mounted on inverted and upright commercial microscopes on a standard C-mount camera port. For applications that do not require a commercial microscope, these systems are also compatible with Thorlabs’ T-Scopes. Thorlabs also offers a complete confocal imaging solution with motorized control and synchronization for Z stack image reconstruction with the use of the Motorized T-Scope.

ThorImageLS™ Software

The ThorImageLS software is a powerful Windows®-based acquisition software. The easy-to-use GUI interface coordinates system control, image acquisition, and animation playback through communication with all the hardware components driving the Thorlabs Confocal Imaging System.

For Windows XP and Windows 7
(32 & 64) Operating Systems

for more details.

Capture Setup

  • Flexible Framework of Peripheral Control
    • Multiphoton Scan Head Control
    • Z-Stepper Motor Control
    • Photomultiplier Gain Control
    • Excitation Laser Control (Power & Wavelength)
    • Beam Size Control
  • Real-Time Background and Flat Field Correction
  • User Control of Detection Channels
  • Flexible Image Size and Location Adjustment
  • Save and Recall Experimental Settings in XML Format
  • User-Selectable Color Assignments for Detection Channels



  • Selectable Color Channels
    • Up to Four Simultaneous Channels
  • Real-Time Capture
    • 30 Frames per Second (512 x 512 Pixels)
    • Streaming to Disk
  • Z Volume Capture
  • User-Defined Time-Lapse
  • Up to Five Dimensional Data Collection
    • X, Y, Z, Time, and Color
  • Hardware Triggering for Experimental Initiation
  • Image Formats: JPEG, TIFF, and AVI Movies


  • Experiment Playback
  • Image Histograms
  • Region of Interest (ROI) Measurements
  • Line Profile Measurements
  • AVI Movie Creator
    • Compress Image Sequences into an Easy-to-Share and Publish Format


Software Development Kit

  • Develop Custom Software for Full Control of Thorlabs' Multiphoton and Confocal Imaging Systems
  • Example Code Included to Simplify Application Development
  • Libraries Provided for C++ and LabVIEW Languages
  • Available Upon Request


Laser Wavelengths - Additional Wavelengths Available Upon Request 405 nm  YesYesYes
488 nmYesYesYesYesYes
532 nm  YesYesYes
642 nmYesYesYesYesYes
Primary Dichroic MirrorQuad Band Dichroic Beamsplitter
Scanning Speed @ Resolution100 fps @ 128 x 128 pixels (Max)
2 fps @ 4096 x 4096 pixels (Min)
ScannerX: 7.8 kHz Resonant Scanner
Y: Galvanometer Scan Mirror
Scan Zoom1X - 8X (Approximately)
Capture ResolutionUp to 2048 x 2048 Bi-Directional Acquisition
Up to 4096 x 4096 Uni-Directional Acquisition
Diffraction-Limited Field of View (FOV)FN25* = 442 µm x 442 µm FOV @ 40X
FN23* = 407 µm x 407 µm FOV @ 40X
Number of PMTs IncludedStandard Sensitivity2 4 2
High Sensitivity 2 4 
Emission Filters - CWL/FWHM447 nm/60 nm Bandpass  YesYesYes
514 nm/30 nm Bandpass  YesYesYes
525 nm/50 nm BandpassYesYesYesYesYes
559 nm/34 nm Bandpass  YesYesYes
645 nm/LongpassYesYesYesYesYes
Secondary Dichroic - CWL495 nm  YesYesYes
562 nmYesYesYesYesYes
605 nm  YesYesYes
*Field Number (FN) is the diameter of the image formed at the intermediate image plane: FN = FOV x Magnification

System Dimensions

Confocal Scanning System Dimensions

System Schematic

System Schematic

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Poster: bdada
Posted Date: 2012-02-06 15:06:00.0
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