Cerna® Series: Modular Microscopy Systems and Components


Cerna® Series: Modular Microscopy Systems and Components


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Example Configurations &
Images Taken Using Cerna® Microscope Systems

Thorlabs' Cerna® Microscopy Platform

  • Supports Conventional Widefield Microscopy Techniques
    • Epi-Fluorescence
    • Brightfield
    • Dodt and DIC
  • Modular Design with a Slim Profile and Large Working Volume Underneath and Around
    the Objective
  • Broad Compatibility with Thorlabs' Ø1" Lens Tubes, Ø2" Lens Tubes, 30 mm Cage Systems, and 60 mm Cage Systems
  • Add-Ons for Confocal Imaging, Hyperspectral Imaging, and System Developers

Cerna is a modular microscopy platform for applications ranging from routine experiments to advanced optical systems. This platform is designed for users to configure or modify their system to exact experimental requirements, and is especially useful for setups that require large-range adjustment for positioning of the sample or wide-angle access to the objective and other optical components.

Fully Customizable Design

Our modular Cerna components make it simple to adapt this microscopy platform for a wide variety of imaging modalities and experimental applications. We provide several high-performance products, including epi-illuminator modules for one to six filter sets, Dodt gradient contrast and differential interference contrast (DIC) modules for transmitted light imaging, as well as scientific cameras and accessories for widefield and fluorescence imaging. Additionally, this platform's open design is ideal for electrophysiology applications, as it provides access to the focal plane from the front, sides, and even behind.

The backbone of every Cerna microscope is the microscope body, which is engineered around Thorlabs' 95 mm optical construction rails. Our microscope bodies enable a vertical construction that consumes a minimal amount of space in the horizontal dimension, preserving valuable table space for experimental apparatuses. The microscope body rail offers a linear dovetail mounting surface, excellent vibrational damping, and stable long-term support. Modules such as motorized condensers, sample holders, and our transmitted light imaging modules can be positioned along the rail using a balldriver. The dovetail centers the modules along the optical axis so that the user can minimize painstaking optical alignment procedures.

Easily Expandable with Thorlabs, Industry-Standard, or User-Constructed Add-Ons

For system developers who wish to build microscopes entirely from Thorlabs' catalog of parts (see the For Developers tab for an example), we offer body attachments and extensions that provide connections to our standard mechanical interfaces, including SM1 threads (1.035"-40), SM2 threads (2.035"-40), and taps for 30 mm and 60 mm cage compatibility. Breadboard accessories with either 1/4"-20 or M6 x 1.0 tapped holes attach to the top of the support rail to allow the construction of custom illumination pathways.

Options at a Glance
Widefield Imaging Epi-Illumination Trans-Illumination Objective Mounting & Focus Control  Sample Holders &
Motion Control		 Body Attachments & Extensions



Trinoculars with 10X Eyepieces

CCD, CMOS, or Scientific-Grade Cameras

Optional Double Camera Port		 Modular, User Configurable Epi-Illuminator Modules 

25 mm × 36 mm Dichroics & Ø25 mm Filters

LEDs & Ø3 mm Liquid Light Guides		 Brightfield, DIC Imaging, and Dodt Contrast Modules

DIC Polarizers, Condenser Prisms, & Objective Prisms

Air Condensers		 Objective Holders for RMS-, M25 x 0.75-, or M32 x 0.75-Threaded Objectives

Motorized Focusing Modules with 1" Travel

Piezo Objective Scanner for Fast Z-Stacks		 Rigid Stands Mount Samples & Experimental Apparatuses

Motorized XY Scanning Stages for Scanning Up to 250 mm/s

XY Platforms for 2" (50 mm) Manual or Motorized Travel		 Integrate Thorlabs' Optomechanical Components into a Cerna Microscope

Breadboard Tops, Fixed Arms, and Adapters Provide Compatibility with Lens Tubes and Cage Systems

Acknowledgements
The red false-colored image on computer screens in the above image and elsewhere is courtesy of Dr. Lei Zhang and Professor Joshua Singer, University of Maryland.

Example Cerna® System: Cerna Microscope for Epi- and Trans-Illumination

Cerna
Click for Details
This Cerna Microscope has been configured for epi-fluorescence and differential interference contrast (DIC) imaging. This preconfigured microscope is available for purchase here.
  • Sliding Nosepiece Accommodates Two Objectives
  • Large Throat Depth Supports Free-Standing or Attached Sample Holders
  • Capable of Epi-Fluorescence, Brightfield Illumination (Epi or Trans), Differential Interference Contrast (DIC), or Phase Contrast Imaging
  • Double Camera Port Enables Two Scientific Cameras to be Individually Dedicated to Widefield Fluorescence and DIC Imaging

This Cerna microscope is configured for both epi-fluorescence and multiple trans-illumination imaging modalities. The preconfigured microscope kit is available for purchase here.

To support epi-fluorescence studies, we have designed this microscope to be compatible with light sources using a liquid light guide. The microscope also utilizes an epi-illuminator module with a removable turret, which enables up to six filter sets to be rotated through the optical path.

For DIC and other trans-illumination modalities, we have outfitted the microscope with several DIC components, including a condenser, polarizers, and prisms. The condenser features an exchangeable tray to mount optics, such as a prism for DIC imaging or condenser mask, inside the condenser. Transmitted illumination is provided by two of Thorlabs' mounted LEDs: a white light LED for brightfield imaging and an 850 nm LED for NIR DIC. Alternate LEDs are available with single wavelength peaks as well as broad spectra. Cerna microscopes are also compatible with Dodt contrast, phase contrast, darkfield, and oblique illumination.

To explore this and our other preconfigured microscope options, see the Preconfigured Microscopes presentation.

Epi-Fluorescence Accessories
Scientific Cameras Scientific Cameras
Thorlabs' sCMOS and scientific CCD cameras are based on high-quantum-efficiency, low-noise imagers, which make them ideal for high-performance imaging techniques.
Objectives Objectives
Thorlabs offers several types of objective lenses: infinity-corrected visible imaging objectives, focusing objectives for laser sources, super apochromatic objectives, phase contrast objectives, and reflective objectives.
Rigid Stands Rigid Stand with Slide Holder
Thorlabs' Rigid Stands are ideal for mounting our micromanipulators and other electrophysiology accessories such as slide or chamber holders.
LED Light Sources LED Light Sources
Thorlabs provides a range of mounted LEDs that emit in the UV, visible, NIR, and IR spectral ranges for brightfield illumination, Dodt contrast, and DIC imaging.

Thorlabs recognizes that each imaging application has unique requirements.
If you have any feedback, questions, or need a quotation, please contact ImagingSales@thorlabs.com or call (703) 651-1700.

Hyperspectral Imaging with Cerna
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Schematic of Hyperspectral Imaging
Hyperspectral Imaging Cerna Microscope
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A hyperspectral imaging system built using Thorlabs' Cerna® Microscopy Platform, KURIOS-VB1(/M) Tunable Bandpass Filter, and Monochrome Scientific Camera. Several components shown here were modified from their stock configuration.

Application Idea: Hyperspectral Imaging

In hyperspectral imaging, a stack of spectrally separated, two-dimensional images is acquired. This technique is frequently used in microscopy, biomedical imaging, and machine vision, as it allows quick sample identification and analysis.

Hyperspectral imaging obtains images with significantly better spectral resolution than that provided by standalone color cameras. Color cameras represent the entire spectral range of an image by using three relatively wide spectral channels—red, green, and blue. In contrast, hyperspectral imaging systems incorporate optical elements such as liquid crystal tunable bandpass filters or diffraction gratings, which create spectral channels with significantly narrower bandwidths.

Thorlabs' Cerna® microscopy platform, Kurios® tunable filters, and scientific-grade cameras are easily adapted to hyperspectral imaging. The Cerna platform is a modular microscopy system that integrates with Thorlabs' SM lens tube construction systems and supports transmitted light illumination. Kurios tunable filters have SM-threaded interfaces for connections to the Cerna platform and our cameras. In addition, Kurios filters include software and a benchtop controller with external triggers, which enable fast, automated, synchronized wavelength switching and image capture.

Example Image Stack
The data in the images and video below demonstrate the hyperspectral imaging technique. Figure 1 depicts two images of a mature capsella bursa-pastoris embryo (also known as shepherd's-purse) taken with a Kurios filter set to center wavelengths of 500 nm and 650 nm. These two images show that an entire field of view is acquired at each spectral channel. Figure 2 is a video containing 31 images of the same sample, taken at center wavelengths from 420 nm to 730 nm in 10 nm steps. (10 nm is not the spectral resolution; the spectral resolution is set by the FWHM bandwidth at each wavelength.) In Figure 3, images from each spectral channel are used to determine the color of each pixel and assemble a color image. Figure 3 also demonstrates that a broadband spectrum is acquired at each pixel, permitting spectroscopic identification of different sample features within the field of view.

Kurios tunable filters offer a number of advantages for hyperspectral imaging. Unlike approaches that rely upon angle-tunable filters or manual filter swapping, Kurios filters use no moving parts, enabling vibrationless wavelength switching on millisecond timescales. Because the filter is not moved or exchanged during the measurement, the data is not subject to "pixel shift" image registration issues. Our filters also include software and a benchtop controller with external triggers, making them easy to integrate with data acquisition and analysis programs.

LCTF Spectrum
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Figure 3: A color image of the mature capsella bursa-pastoris embryo, assembled using the entire field of view acquired in each spectral channel, as shown in Figure 1. By acquiring across multiple channels, a spectrum for each pixel in the image is obtained.
LCTF Spectrum
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Figure 1: Two images of a mature capsella bursa-pastoris embryo taken at different center wavelengths. The entire field of view is acquired for each spectral channel.

Figure 2: This video shows the image obtained from the sample as a function of the center wavelength of the KURIOS-WB1 tunable filter. The center wavelength was incremented in 10 nm steps from 420 nm to 730 nm. (10 nm is not the spectral resolution; the spectral resolution is set by the FWHM bandwidth at each wavelength.)

Example Cerna® System: Developers' Configuration

Cerna
Click for Details
Through the Use of Fixed Arm Attachments, a Selection of Thorlabs'
Optomechanical Components Are Integrated Into this Cerna® System
  • Fixed Arms Integrate Thorlabs' SM1, SM2, 30 mm Cage, and 60 mm Cage Construction Standards with the 95 mm Support Rail
  • Breadboard Tops Enable User-Designed Widefield Viewing Schemes
    • Ø1.5" Through Hole for Optical Path
    • Array of 154 1/4"-20 or M6 x 1.0 Taps
    • Two-Position Slider Option to Integrate Multiple Optical Paths
  • Custom-Built Illumination Apparatuses Using Thorlabs' Selection of Light Accessories

The configuration shown here contains several microscope body attachments and extensions that are specifically designed for expanding the microscope's functionality using Thorlabs' mechanical construction systems. Intended for system developers, these accessories enable a high degree of system customization.

For instance, the 95 mm support rail has been capped with a breadboard that has a Ø1.5" through hole and an array of 1/4"-20 taps, which here have been used to build a widefield viewing apparatus with our scientific camera and previous-generation plasma light source. Taking advantage of the linear dovetail mounting surface on the support rail, we have attached an SM1-threaded (1.035"-40), 30-mm-cage-compatible fixed arm and an SM2-threaded (2.035"-40), 60-mm-cage-compatible fixed arm in the optical path underneath the objective, allowing us to construct custom transmitted light illumination apparatuses. Please see the full web presentation to explore DIY Cerna options for custom constructions.

Accessories for DIY Microscopy Construction
Cage System 30 mm and 60 mm Cage Systems
Thorlabs' cage systems use four rigid steel rods on which optical components can be mounted along a common optical axis.
Lens Tubes Lens Tubes
Lens tubes securely contain custom optical assemblies along the optical axis and can be easily integrated with Cerna components.
Fiber-Coupled Lasers Fiber-Coupled Lasers
Thorlabs' extensive line of fiber-coupled laser sources includes both single channel and four channel options.
LED Light Sources LED Light Sources
Thorlabs provides a range of mounted LEDs that emit in the UV, visible, NIR, and IR spectral ranges for brightfield illumination, Dodt contrast, and DIC imaging.

360° Video of Cerna Series Developers' Configuration

Thorlabs is eager to assist with custom system builds, starting from either the catalog configurations shown here
or parts from our components catalog. Please contact ImagingSales@thorlabs.com to start a conversation.

Building a Cerna® Microscope

The Cerna microscopy platform's large working volume and system of dovetails make it straightforward to connect and position the components of the microscope. This flexibility enables simple and stable set up of a preconfigured microscope, and provides easy paths for later upgrades and modification. See below for a couple examples of the assembly of some DIY Cerna microscopes.

DIY Cerna Design and Assembly


Walkthrough of a DIY Microscope Configuration
This DIY microscope uses a CSA3000(/M) Breadboard Top, a CSA2001 Dovetail Adapter, our CSA1001 and CSA1002 Fixed Arms, and other body attachments and extensions. These components provide interfaces to our lens tube and cage construction systems, allowing the rig to incorporate two independent trans-illumination modules, a home-built epi-illumination path, and a custom sample viewing optical path.

DIY Microscope Configuration Assembly
The simplicity of Thorlabs optomechanical interfaces allows a custom DIY microscope to be quickly assembled and reconfigured for custom imaging applications.

To schedule an in-person or virtual demo appointment, please email ImagingSales@thorlabs.com.

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China Demo Room
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China Demo Room

Try Our Microscopes In Person or Virtually

Thorlabs' sales engineers and field service staff are based out of eight offices across four continents. We look forward to helping you determine the best imaging system to meet your specific experimental needs. Our customers are attempting to solve biology's most important problems; these endeavors require matching systems that drive industry standards for ease of use, reliability, and raw capability.

Thorlabs' worldwide network allows us to operate demo rooms in a number of locations where you can see our systems in action. We welcome the opportunity to work with you in person or virtually. A demo can be scheduled at any of our showrooms or virtually by contacting ImagingSales@thorlabs.com.

Customer Support Sites
(Click Each Location for More Details)

Demo Rooms and Customer Support Sites
(Click Each Location for More Details)

Click on the different parts of the microscope to explore their functions.

Explore the Cerna MicroscopeSample Viewing/RecordingSample MountingIllumination SourcesIllumination SourcesObjectives and MountingEpi-IlluminationEpi-IlluminationTrans-IlluminationMicroscope BodyMicroscope BodyMicroscope BodyMicroscope Body

Elements of a Microscope

This overview was developed to provide a general understanding of a Cerna® microscope. Click on the different portions of the microscope graphic to the right or use the links below to learn how a Cerna microscope visualizes a sample.

 

Terminology

Arm: Holds components in the optical path of the microscope.

Bayonet Mount: A form of mechanical attachment with tabs on the male end that fit into L-shaped slots on the female end.

Bellows: A tube with accordion-shaped rubber sides for a flexible, light-tight extension between the microscope body and the objective.

Breadboard: A flat structure with regularly spaced tapped holes for DIY construction.

Dovetail: A form of mechanical attachment for many microscopy components. A linear dovetail allows flexible positioning along one dimension before being locked down, while a circular dovetail secures the component in one position. See the Microscope Dovetails tab or here for details.

Epi-Illumination: Illumination on the same side of the sample as the viewing apparatus. Epi-fluorescence, reflected light, and confocal microscopy are some examples of imaging modalities that utilize epi-illumination.

Filter Cube: A cube that holds filters and other optical elements at the correct orientations for microscopy. For example, filter cubes are essential for fluorescence microscopy and reflected light microscopy.

Köhler Illumination: A method of illumination that utilizes various optical elements to defocus and flatten the intensity of light across the field of view in the sample plane. A condenser and light collimator are necessary for this technique.

Nosepiece: A type of arm used to hold the microscope objective in the optical path of the microscope.

Optical Path: The path light follows through the microscope.

Rail Height: The height of the support rail of the microscope body.

Throat Depth: The distance from the vertical portion of the optical path to the edge of the support rail of the microscope body. The size of the throat depth, along with the working height, determine the working space available for microscopy.

Trans-Illumination: Illumination on the opposite side of the sample as the viewing apparatus. Brightfield, differential interference contrast (DIC), Dodt gradient contrast, and darkfield microscopy are some examples of imaging modalities that utilize trans-illumination.

Working Height: The height of the support rail of the microscope body plus the height of the base. The size of the working height, along with the throat depth, determine the working space available for microscopy.

 

microscope bodyClick to Enlarge
Cerna Microscope Body
Body Height Comparison
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Body Details

Microscope Body

The microscope body provides the foundation of any Cerna microscope. The support rail utilizes 95 mm rails machined to a high angular tolerance to ensure an aligned optical path and perpendicularity with the optical table. The support rail height chosen (350 - 600 mm) determines the vertical range available for experiments and microscopy components. The 7.74" throat depth, or distance from the optical path to the support rail, provides a large working space for experiments. Components attach to the body by way of either a linear dovetail on the support rail, or a circular dovetail on the epi-illumination arm (on certain models). Please see the Microscope Dovetails tab or here for further details.

Microscope Bodies Microscope Translator

 

microscope bodyClick to Enlarge
Illumination with a Cerna microscope can come from above (yellow) or below (orange). Illumination sources (green) attach to either.

Illumination

Using the Cerna microscope body, a sample can be illuminated in two directions: from above (epi-illumination, see yellow components to the right) or from below (trans-illumination, see orange components to the right).

Epi-illumination illuminates on the same side of the sample as the viewing apparatus; therefore, the light from the illumination source (green) and the light from the sample plane share a portion of the optical path. It is used in fluorescence, confocal, and reflected light microscopy. Epi-illumination modules, which direct and condition light along the optical path, are attached to the epi-illumination arm of the microscope body via a circular D1N dovetail (see the Microscope Dovetails tab or here for details). Multiple epi-illumination modules are available, as well as breadboard tops, which have regularly spaced tapped holes for custom designs.

Trans-illumination illuminates from the opposite side of the sample as the viewing apparatus. Example imaging modalities include brightfield, differential interference contrast (DIC), Dodt gradient contrast, oblique, and darkfield microscopy. Trans-illumination modules, which condition light (on certain models) and direct it along the optical path, are attached to the support rail of the microscope body via a linear dovetail (see Microscope Dovetails tab or here). Please note that certain imaging modalities will require additional optics to alter the properties of the beam; these optics may be easily incorporated in the optical path via lens tubes and cage systems. In addition, Thorlabs offers condensers, which reshape input collimated light to help create optimal Köhler illumination. These attach to a mounting arm, which holds the condenser at the throat depth, or the distance from the optical path to the support rail. The arm attaches to a focusing module, used for aligning the condenser with respect to the sample and trans-illumination module.

Epi-Illumination Body Attachments Brightfield Illumination DIC Dodt Condensers Condenser Mounting Light Sources
Epi-Illumination Modules Breadboards
& Body Attachments		 Brightfield DIC Dodt Condensers Condenser Mounting Light Sources

 

microscope bodyClick to Enlarge
Light from the sample plane is collected through an objective (blue) and viewed using trinocs or other optical ports (pink).

Sample Viewing/Recording

Once illuminated, examining a sample with a microscope requires both focusing on the sample plane (see blue components to the right) and visualizing the resulting image (see pink components).

A microscope objective collects and magnifies light from the sample plane for imaging. On the Cerna microscope, the objective is threaded onto a nosepiece, which holds the objective at the throat depth, or the distance from the optical path to the support rail of the microscope body. This nosepiece is secured to a motorized focusing module, used for focusing the objective as well as for moving it out of the way for sample handling. To ensure a light-tight path from the objective, the microscope body comes with a bellows (not pictured).

Various modules are available for sample viewing and data collection. Trinoculars have three points of vision to view the sample directly as well as with a camera. Double camera ports redirect or split the optical path among two viewing channels. Camera tubes increase or decrease the image magnification. For data collection, Thorlabs offers both cameras and photomultiplier tubes (PMTs), the latter being necessary to detect fluorescence signals for confocal microscopy. Breadboard tops provide functionality for custom-designed data collection setups. Modules are attached to the microscope body via a circular dovetail (see the Microscope Dovetails tab or here for details).

Objectives & Accessories Objective Mounting
Body Attachments
Sample Viewing Cameras PMTs Breadboards & Body Attachments

 

microscope bodyClick to Enlarge
The rigid stand (purple) pictured is one of various sample mounting options available.

Sample/Experiment Mounting

Various sample and equipment mounting options are available to take advantage of the large working space of this microscope system. Large samples and ancillary equipment can be mounted via mounting platforms, which fit around the microscope body and utilize a breadboard design with regularly spaced tapped through holes. Small samples can be mounted on rigid stands (for example, see the purple component to the right), which have holders for different methods of sample preparation and data collection, such as slides, well plates, and petri dishes. For more traditional sample mounting, slides can also be mounted directly onto the microscope body via a manual XY stage. The rigid stands can translate by way of motorized stages (sold separately), while the mounting platforms contain built-in mechanics for motorized or manual translation. Rigid stands can also be mounted on top of the mounting platforms for independent and synchronized movement of multiple instruments, if you are interested in performing experiments simultaneously during microscopy.

Translating Platforms Rigid Stands Translation Stages for Rigid Stands Motorized XY Stage Manual XY Stage
Translating Platforms Rigid Stands Translation Stages for Rigid Stands Motorized XY Stages Manual XY Stage

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For sample viewing, Thorlabs offers trinoculars, double camera ports, and camera tubes. Light from the sample plane can be collected via cameras, photomultiplier tubes (PMTs), or custom setups using breadboard tops. Click here for additional information about viewing samples with a Cerna microscope.

Product Families & Web Presentations
Sample Viewing Breadboards
& Body Attachments		 Cameras PMTs

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Microscope objectives are held in the optical path of the microscope via a nosepiece. Click here for additional information about viewing a sample with a Cerna microscope.

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Large and small experiment mounting options are available to take advantage of the large working space of this microscope. Click here for additional information about mounting a sample for microscopy.

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Thorlabs offers various light sources for epi- and trans-illumination. Please see the full web presentation of each to determine its functionality within the Cerna microscopy platform.

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Epi-illumination illuminates the sample on the same side as the viewing apparatus. Example imaging modalities include fluorescence, confocal, and reflected light microscopy. Click here for additional information on epi-illumination with Cerna.

Product Families & Web Presentations
Epi-Illumination Web Presentation Body Attachments Light Sources
Epi-Illumination Body Attachments Light Sources

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Trans-illumination illuminates from the opposite side of the sample as the viewing apparatus. Example imaging modalities include brightfield, differential interference contrast (DIC), Dodt gradient contrast, oblique, and darkfield microscopy. Click here for additional information on trans-illumination with Cerna.

Product Families & Web Presentations
Brightfield Web Presentation DIC Web Presentation Dodt Web Presentation Condensers Web Presentation Condenser Mounting Web Presentation Illumination Kits Web Presentation Other Light Sources
Brightfield DIC Dodt Condensers Condenser Mounting Illumination Kits Other Light Sources

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The microscope body provides the foundation of any Cerna microscope. The 7.74" throat depth provides a large working space for experiments. Click here for additional information about the Cerna microscope body.

Product Families & Web Presentations
Microscope Body Web Presentation Microscope Body Translator
Microscope Bodies Microscope Translator
Additional Cerna® Modular Microscopy Platform
  • Cerna Series Overview

  • Cerna-Based Single-Channel Confocal Systems

  • Cerna-Based Four-Channel Confocal Systems

  • Cerna Microscopes: Preconfigured Optical Paths

  • DIY Cerna Components: Imaging for Home Builders