Cerna® Microscope for Epi-Fluorescence and Trans-Illumination

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Side View of Cerna Microscope Kit 4
(Optical Table Not Included)

Features

• Six-Position Epi-Illuminator and Transmitted Illumination Modules
  • Epi-Illuminator Module Accepts Solis^® High-Powered LEDs, Chrolis™ High-Power LED Sources, or Ø3 mm Liquid Light Guides
  • Transmitted Light Module Accepts Mounted LEDs for Visible and/or IR Light
• Large and Open Working Space Underneath the Objective
  • Ideal for Sample Apparatuses, Recording Chambers, and Micromanipulators
• Compatible with Thorlabs and Major Manufacturers' Objectives, Scientific Cameras, Fluorescence Filters, and Illumination Sources
• Modular Design Allows User to Modify the Microscope's Optical Path

This Cerna^® microscope kit provides an optical path suited for experiments requiring either epi-fluorescence, reflected light, or brightfield imaging. The epi-illuminator module accepts up to six filter sets, ideal for targeting spectrally separated fluorophores, and the brightfield illumination module includes Thorlabs' Visible Illumination Kit to illuminate thin samples with visible light.

A quintuple-objective nosepiece, compatible with M25 x 0.75-threaded objectives, holds up to five objectives at once and lets you locate a region of interest using low-magnification objectives and then image using high-magnification objectives. Motorized objective and condenser focusing modules, each with 1" of travel, provide fine-tuned positioning along the optical axis.

Unlike competing microscopes with similar capabilities, the Cerna platform's modularity lets the user quickly install and remove the microscope modules as needed for each experiment, providing a high degree of access and control. For example, when the trans-illumination modules are installed, in vitro samples can be studied using epi-fluorescence, as well as with basic widefield and brightfield illumination. To free room underneath the objective for large sample holding apparatuses, the brightfield module can be removed, providing a path for in vivo studies.

To address a wide range of experimental parameters, Thorlabs offers eight Cerna microscope configurations, which are summarized in the table below. In addition, we can work with you to configure a microscope that meets your unique needs. To contact our team, please e-mail ImagingSales@thorlabs.com. We also offer Cerna components individually for custom modifications.

Cerna^® Microscope Kit 4

This Cerna microscope kit was designed from our line of modular components to provide several convenient features for imaging, highlighted below. We also offer a selection of microscope objectives, cameras, and illumination modules that can be used to complement this microscope configuration and customize it to your experiment. Details can be found on the Microscope Add-Ons tab. The Kit Components tab details the components used in this microscope configuration, as well as a link to each component's webpage, where additional information (such as mechanical drawings) is available. 

Epi-Illumination

Features

• Six-Position Epi-Illuminator Module (Filter Sets Sold Separately)
• Compatible Light Sources
  • Solis^® High-Power LEDs (Requires SM2A56 Adapter)
  • Chrolis™ High-Power LED Sources or Other Sources that Use Ø3 mm Liquid Light Guides (Requires LLG3A6 Adapter)

This microscope is able to target multiple fluorophores through the use of a six-position epi-illuminator module that couples light emitted by the illumination source into the imaging path, through the objective, and onto the sample. The epi-fluorescence generated by the sample passes through the module to the eyepieces and camera. A D3T female dovetail on the rear of the microscope accepts a wide range of white-light lamps. The illumination path includes AR-coated conditioning optics, a field stop diaphragm, and a shutter.

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This Cerna^® microscope kit features an epi-illuminator module with a 6-position filter turret. The filter position is labeled on the knurled wheel that rotates the turret.

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The rotating turret accommodates up to six filter sets (not included).

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The back of the epi-illuminator module has a female D3T dovetail that can be adapted to accept liquid light guides and LEDs.

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Transmitted Illumination Module with White Light LED

Trans-Illumination (Brightfield Imaging)

Features

• Supports Brightfield Illumination in the Visible and/or NIR
• Accepts Thorlabs' Illumination Kits (Visible LED Kit Included)
• Motorized Condenser Focusing Module with 1" Travel
• 0.78 NA Long-Working-Distance Condenser

This microscope kit includes a module for brightfield imaging, designed to direct visible and/or IR illumination generated by one of our Illumination Kits into the optical path of the Cerna Microscope. Please see the full web presentation for additional information.

Bright visible illumination is generated by the included illumination kit (Item # WFA1010), which uses one of Thorlabs' Mounted LEDs (Item # MWWHL3). The module features additional ports and a filter cube holder to allow for later expansion with IR or other wavelength LEDs. Please contact Technical Support with inquiries.

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The microscope body is based on a 95 mm optical rail.

Microscope Body

Features

• Large Working Volume: Optical Path is 7.74" (196.6 mm) Away from Edge of Rail
• Linear Dovetail Surface Allows Modules to be Added and Removed
• 400 mm Body Height to Accommodate Brightfield Illumination Module
• Motorized Objective Focusing Module with 1" Travel
• Mechanically Compatible with Thorlabs' 95 mm Rail Platforms

The backbone of this microscope is the 400 mm tall microscope body based on Thorlabs' 95 mm Precision Optical Rails, providing stable long-term support and excellent vibrational damping. Its linear dovetail mounting surface allows modules to be removed when they are not needed, freeing additional workspace and opening the door to user customization. For alternate rail heights, please see the full web presentation.

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This microscope includes trinoculars with a camera port for widefield viewing.

Widefield Viewing

Features

• Fixed Magnification Camera Port with C-Mount Accepts Most Industry-Standard Cameras
• Trinoculars with 10X Eyepiece Magnification and Adjustable Interpupil Distance

Widefield viewing is provided by trinoculars and a camera tube. The eyepieces feature an adjustable interpupil distance and rotate individually to allow the focus to be coarsely adjusted for each eye.

The included camera tube contains all of the optics needed to image the light from the objective onto a camera sensor. External C-mount (1.000-32") threads on the top of the camera tube accept Thorlabs' scientific cameras, as well as cameras from most major manufacturers. For additional viewing port and camera tube options, please see the full web presentation.

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This microscope kit has a nosepiece that can hold up to five objectives.

Objective Holders and Objectives

Features

• Use Low Magnification to Find the Region of Interest, then High Magnification to Image
• Compatible with M25 x 0.75-Threaded Objectives
• Hold Up to Five Objectives

The rotating quintuple-objective nosepiece offers direct compatibility with M25 x 0.75-threaded objectives. For other objective mounting options, please see the full web presentation. Microscope objectives are available for purchase separately from Thorlabs, and we can also order other objectives outside our catalog upon request. Keep in mind that the total system magnification will depend upon the objective chosen; see the Objective, Scan, and Tube Lens Tutorial for details.

This kit configuration is entirely constructed from our selection of modular Cerna^® components. See the comprehensive list below for each included item.

Item #	Qty.	Description	Photo (Click to Enlarge)
Microscope Body
CEA1400	1	Cerna Microscope Body with Epi-Illumination Arm, 400 mm Tall
Widefield Viewing
LAURE1	1	Trinoculars with Eyepieces
TC1X	1	1X Camera Tube with C-Mount
Epi-Illumination
CSE2100	1	Epi-Illuminator Module for Six Filter Sets (Filter Sets Not Included)
Condenser
CSC2001	1	LWD Condenser, 0.78 NA
Objective & Condenser Mounting
CSN1202	1	Dual-Objective Nosepiece
CSA1200	1	Mounting Arm for CSN1202 Nosepiece
CSA2000	1	Condenser Mounting Arm with ±2 mm Travel in X and Y
ZFM2020	1	Motorized Focusing Module with 1" Travel for Edge-Mounted Arms
ZFM2030	1	Motorized Focusing Module with 1" Travel for Middle-Mounted Arms
MCM3001	1	3-Axis Controller for Focus Control
Trans-Illumination
WFA1000	1	Brightfield Illumination / DIC Imaging Module
WFA0150	1	Transmitted Light Module Dovetail Clamp
Illumination Kit
WFA1010	1	Visible Illumination Kit
LEDD1B	1	T-Cube™ LED Driver, 1200 mA Max Drive Current (Power Supply Not Included)
KPS101	1	15 V Power Supply Unit for a Single K-Cube™ or T-Cube™

Application-Optimized Cerna Microscopes

Developed in collaboration with our colleagues in the field, the Cerna microscopy platform is uniquely modular and flexible, making it adaptable to a wide range of demanding experimental requirements. If you would like to work with our application specialists, engineers, and sales team to design your own microscope, please email ImagingSales@thorlabs.com.

Selected Accessories

In order to image with this microscope, it is necessary to add a scientific camera, an epi-illumination source, filter sets, objectives, and sample holders. It is often possible to improve the quality of your experimental data by carefully selecting accessories that complement your specific experiment. To that end, we have ensured that Cerna^® microscopes are compatible with a wide range of accessories. The information below compares the Cerna-compatible components that are manufactured or sold by Thorlabs. We have also indicated when it is possible to use equipment designed by other manufacturers.

Content

• Scientific Cameras for Widefield Viewing
• Illumination Sources for Epi-Illumination
• Filter Sets for Epi-Fluorescence
• Objectives
• Sample Holders

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The camera port provides a fixed magnification for visible light from the sample.

Scientific Cameras for Widefield Viewing

• Visualize the Field of View on a Computer
• Any C-Mount Camera is Compatible with a Cerna Microscope

Thorlabs offers scientific cameras optimized for a range of imaging needs. Cameras allow the field of view to be displayed on a computer screen and saved for later reference. Viewing your sample from a computer also enables remote sample positioning using our motion control accessories (see below), allowing samples to be moved in sensitive setups without introducing additional vibrations from your hands.

This Cerna microscope kit includes a camera tube, which provides a fixed magnification at the image plane.

Any camera with C-Mount (1.000"-32) threading is compatible with this microscope. The most popular cameras used with Cerna systems are given in the table below. Higher resolution options can be found in our complete range of scientific cameras.

Item #	DCU224M	340M-USB	1501M-USB
Product Photo (Click to Enlarge)
Primary Feature	Lightweight	Fast Frame Rate	High Resolution and Dynamic Range
Sensor Type	Sony ICX205AL	On Semi / Truesense KAI-0340 Monochrome CCD	Sony ICX285AL Monochrome CCD (Grade 0)
Sensor Format	1/2" (7.62 mm Diagonal)	1/3" Format (5.92 mm Diagonal)	2/3" Format (11 mm Diagonal)
Resolution	1280 x 1024 Pixels	640 x 480 Pixels	1392 x 1040 Pixels
Pixel Size	4.65 µm x 4.65 µm	7.4 μm x 7.4 μm	6.45 µm x 6.45 µm
Frame Rate (Max)	15 fps	200.7 fps	23 fps
Host PC Interface	USB 2.0 (Cable Included)	USB 3.0 (Cable Included)
Digital Output	8 Bits	14 Bits	14 Bits
	96 g (0.21 lbs)	750 g (1.65 lbs)

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Secure a Liquid Light Guide to the Six-Position Epi-Illuminator Module with a D3T Dovetail-to-LLG Adapter

Illumination Sources for Epi-Illumination

• White Light Sources Illuminate the Field of View Through the Objective
• Available Options Include Solis^® LEDs, Chrolis™ LED Sources, or Other Sources Coupled through Ø3 mm Liquid Light Guide
• Light is Tuned by Filter Sets for Specific Fluorophores (See Below)

The six-position epi-illuminator module that is included with this Cerna microscope kit requires a broadband white light source that emits across the visible region of the spectrum. Broadband emission makes it possible for the same microscope to stimulate fluorophores that have absorption wavelengths that are spectrally separated. Several filter sets aimed at common fluorophores are available below.

The Solis LED light sources have multiple wavelength emitting options, including broad sprectrum emission throughout the visible range. These LEDs are designed to be controlled by the DC20 or DC2200 drivers. The Solis LED is outfitted with collimating optics and can be mounted directly to the back of the epi-illuminator module using the SM2A56 dovetail adapter.

The Chrolis LED sources are user-configurable light engines that efficiently combine the output of six LEDs into a single liquid light guide (LLG). They are ideal for fluorescence imaging that requires up to six wavelengths of light. These sources are available in two pre-set configurations, as well as custom configurations; please see the full web presentation for more details. The Chrolis sources are compatible with the epi-illuminator module via our LLG3A6 adapter, which connects and collimates any Ø3 mm LLG to a female D3T dovetail; see image to the upper right.

Filter Transmission Spectraa
Item #	Target Fluorophore	Transmission Graph (Click for Plot)
MDF-BFP	BFP (Blue Fluorescent Protein)
MDF-GFP2	Alexa Fluor® 488
MDF-MCHAb	mCherry
MDF-MCHCb	mCherry
MDF-TOM	tdTomato

• Please see the full web presentation for a complete listing of fluorescence filter sets offered.
• While both filter sets target mCherry, the -MCHC excitation filter features a broader transmission band than the excitation filter in the -MCHC filter set.

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Thorlabs' MDF-GFP2 Filter Set

Filter Sets for Epi-Fluorescence

• Tune Epi-Illumination Source for the Excitation and Detection of Specific Fluorophores
• Up to Six Filter Sets can be Installed Simultaneously
• Thorlabs' Fluorescent Filter Sets Available
• Utilize Fluorescence Filters from Other Major Manufacturers

The epi-illumination module included with this microscope contains a turret that can hold up to six filter sets. The turret can be rotated by hand to switch between the filter sets. To learn more about the features of the CSE2100 Epi-Illuminator Module included with this microscope, please see its full web presentation.

The filter sets we offer, which consist of an excitation filter, an emission filter, and a dichroic mirror, come in the industry-standard sizes. For excitation and emission filters, the standard dimensions are Ø25 mm, and for dichroic mirrors, the standard dimensions are 25 mm x 36 mm. This allows Cerna microscopes to be compatible with filters from all major manufacturers.

Several popular filter sets are listed with their target fluorophores in the table to the right. Please see the full web presentation for the entire line of Thorlabs' filter sets.

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The RMSA1 Thread Adapter (not included) Converts RMS Threads to M25 x 0.75 Threads

Objectives

• Directly Accepts M25 x 0.75-Threaded Objectives (Nikon)
• Nikon Objectives Support DIC; Matching DIC Optics are Included (Polarizers, Prisms, and Analyzer)
• Compatible with RMS-Threaded Objectives (Olympus) using an RMSA1 Adapter

The nosepiece of this microscope contains M25 x 0.75 threads in two places, allowing it to hold two objectives simultaneously. M25 x 0.75 threads are typically used by Nikon objectives. For convenience, we stock several widefield Nikon objectives that are commonly used with Cerna microscopes, shown in the table below. Our in-stock selection is not exhaustive. If you would like to order a different objective, please contact us.

To use RMS-threaded objectives with this microscope, an RMSA1 thread adapter is needed. These adapters effectively convert the RMS threads to M25 x 0.75 threads, as shown in the photo to the right. RMS threads are most commonly used by Olympus objectives.

Item #	N4X-PF	N10X-PF	N20X-PF	N40X-PF	N60X-PF
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Magnification	4X	10X	20X	40X	60X
Numerical Aperture (NA)	0.13	0.3	0.50	0.75	0.85
Working Distance (WD)	17.2 mm	16 mm	2.1 mm	0.66 mm	0.31 - 0.4 mm
Threading	M25 x 0.75

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MP100-RCH2 Slide Holder in a
Cerna Microscope

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MLS203-1 Stage with MLS203P2 Slide Holder on CSA1000 Fixed Arm

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MP100-MLSH Rigid Stand with
MLS203P2 Slide/Petri Dish Holder

Sample Holders

• Rigid Stands Hold Samples Underneath and Around the Objective
  • Designed for Slides, Petri Dishes, Well Plates, Recording Chambers, Micromanipulators, and Custom Inserts
  • Translation Stages with 1" of X and Y Travel Available
• Fixed Arms Incorporate Fast XY Stage, Lens Tubes, and/or Cage Systems to be Placed Directly into Optical Path
  • CSA1000: For Our MLS203-1 Fast XY Scanning Stage
  • CSA1001: For Ø1" Lens Tubes and 30 mm Cage Systems
  • CSA1002: For Ø2" Lens Tubes and 60 mm Cage Systems

Thorlabs offers highly configurable solutions for mounting your sample beneath the objective of the Cerna microscope. Rigid stands are available with multiple platform styles that can accept slides, petri dishes, recording chambers, micromanipulators, and custom inserts. The included collar makes them lockable at a height and angle chosen by the user. We also manufacture translation stages for these rigid stands that provide motorized horizontal translation of the sample.

Our fixed arms attach directly to the dovetail that spans the height of the microscope body, allowing them to be positioned anywhere along the body height, putting the sample directly into the microscope's optical path, and taking advantage of the existing footprint of the scope. For a pre-configured sample holder solution, use the CSA1000 Fixed Arm with the MLS203-1 Fast XY Scanning Stage. This stage is compatible with our MZS500-E Piezo-Driven Insert, which adds high-resolution Z-axis adjustments. Alternatively, the CSA1001 and CSA1002 Fixed Arms are compatible with Thorlabs' extensive selection of optomechanical components, allowing custom sample holder configurations to be integrated into the microscope.

Several compatible options are outlined in the tables below. For our full range of rigid stand inserts and heights, please see their full web presentation.

Rigid Stands

Click to Enlarge MP150-RCH2 Slide Holder Designed for Standard 3" x 1" (76.2 mm x 25.4 mm) Microscope Slides Height Range: 198.1 - 309.3 mm Other Heights Available

Click to Enlarge MP150-MLSH Insert Holder Designed for Multiple Slides, Petri Dishes, Well Plates, Calibration Targets, Breadboards, Our MZS500-E Z-Axis Piezo Stage, and User-Designed Inserts Height Range: 198.1 - 309.3 mm Other Heights Available

Click to Enlarge MP150-RCH1 Recording Chamber Holder Circular Hole Designed for Recording Chambers Height Range: 198.1 - 309.3 mm Other Heights Available

Click to Enlarge MP150 Rigid Stand with Platform 24 M6 x 1.0 Tapped Holes for Holding Micromanipulators or Other Equipment Height Range: 198.1 - 309.3 mm Other Heights Available

Fixed Arms

Click to Enlarge CSA1000 Fixed Arm Accepts MLS203-1 Fast XY Scanning Stage

Click to Enlarge CSA1001 Fixed Arm Compatible with Ø1" Lens Tubes and 30 mm Cage Systems

Click to Enlarge CSA1002 Fixed Arm Compatible with Ø2" Lens Tubes and 60 mm Cage Systems

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Schematic of Hyperspectral Imaging

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A hyperspectral imaging system built using Thorlabs' Cerna Microscopy Platform, KURIOS-VB1 Tunable Bandpass Filter, and 1501M-GE 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.

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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.

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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.