THORLABS EDU-OMC1 User manual

Rev C, October 1, 2020
Optical Microscopy Course
EDU-OMC1
EDU-OMC1/M
User Guide

Optical Microscopy Course Kit
Table of Contents
Chapter 1 Warning Symbol Definitions .........................................................................................1
Chapter 2 Safety...............................................................................................................................2
Chapter 3 Brief Description ............................................................................................................3
Introduction ............................................................................................................. 3
Setup Overview ........................................................................................................ 5
Lab Notes and Course Notes Overview...................................................................... 7
Supplementary Documentation ................................................................................ 9
Getting started......................................................................................................... 9
Chapter 4 Kit Components............................................................................................................10
Chapter 5 Setup and Adjustment.................................................................................................21
Breadboard and Rail Assembly ............................................................................... 21
Optics Subassemblies ............................................................................................. 22
5.2.1 Halogen Lamp Assembly 23
5.2.2 Collector Lens Assembly 25
5.2.3 Field Stop 26
5.2.4 Filter Wheel Assembly 26
5.2.5 Flip Mount Assembly 28
5.2.6 Condenser Assembly 29
5.2.7 Sample Stage Assembly 30
5.2.8 PCX Objective Assembly 32
5.2.9 Achromatic Objective Assembly 33
5.2.10 Back Focal Plane (BFP) Beamsplitter Assembly 34
5.2.11 Microscope Objective (Nikon) 35
5.2.12 Filter Holder Assembly 35
5.2.13 Polarization Mount Assembly 36
5.2.14 Fluorescence Filter Assembly 37
5.2.15 Diffuser Assembly 37
5.2.16 LED and Multi-Purpose Mount Assembly 38
5.2.17 Sample Camera Assembly 39
5.2.18 Back Focal Plane (BFP) Camera Assembly 41
5.2.19 780 nm Longpass Filter Assembly 42
5.2.20 Multi-Purpose Mount Assembly 43
5.2.21 Optical Fiber Mount 43
5.2.22 Zero Order Blocking Mask 44
Thin Slip-On Post Collars ......................................................................................... 45
Strain Relief............................................................................................................ 45
Overhead Lamp and LED Flashlight......................................................................... 46
Plastic Bin and Spare Parts ..................................................................................... 47
Chapter 6 Samples.........................................................................................................................48
Chapter 7 Software Installation and Digital Materials................................................................50
Software Installation .............................................................................................. 50
7.1.1 ThorCam Camera Software 50
7.1.2 Thorlabs OSA Spectrometer Software 50
7.1.3 Additional Software 51
Supplied Digital Materials ...................................................................................... 52
Chapter 8 Regulatory.....................................................................................................................53
Chapter 9 Thorlabs Worldwide Contacts ....................................................................................54

Optical Microscopy Course Kit Chapter 1: Warning Symbol Definitions
Rev C, October 1, 2020 Page 1
Chapter 1 Warning Symbol Definitions
Below is a list of warning symbols you may encounter in this manual or on your device.
Symbol
Description
Direct Current
Alternating Current
Both Direct and Alternating Current
Earth Ground Terminal
Protective Conductor Terminal
Frame or Chassis Terminal
Equipotentiality
On (Supply)
Off (Supply)
In Position of a Bi-Stable Push Control
Out Position of a Bi-Stable Push Control
Caution: Risk of Electric Shock
Caution: Hot Surface
Caution: Risk of Danger
Warning: Laser Radiation

Optical Microscopy Course Kit Chapter 2: Safety
Page 2 MTN015225-D02
Chapter 2 Safety
CAUTION
After the QTH10 lamp warms up, the housing will reach a temperature of up to 55 °C. Be careful not to touch the
lamp housing during operation.
CAUTION
The kit includes an IR LED (LED940E), which does not emit in the visible range. The LED emission can be
checked with most cameras (camera chips are often IR sensitive). Do not look into IR LEDs in general for a
prolonged time.

Optical Microscopy Course Kit Chapter 3: Brief Description
Rev C, October 1, 2020 Page 3
Chapter 3 Brief Description
Introduction
This experimental setup is a teaching-oriented kit covering the content of a whole quarter- or semester-long optics
and microscopy course. It is structured in 10 units, each covering a different topic. Each unit is accompanied by
extensive teaching materials: The Course Notes cover theory, the Lab Notes cover lab procedures, and the
Instructor Notes include tips for running the course. Additional video content is provided online on the product
website www.thorlabs.com/OMC. During the course, students build working light microscopes using
optomechanical parts, then use them to investigate imaging and contrast methods (including darkfield and phase
contrast, as well as fluorescence), theory (including aberrations, the Abbe theory of image formation, and
fluorescence filter use), and proper microscope set-ups (including Kohler illumination and camera use).
This User Guide provides a starting point for working with this kit. An overview of the documentation for this course
is provided in Section 3.2, followed by the component assembly in Chapter 5. This lab course and materials were
developed by Neil Switz and Daniel Fletcher at the University of California, Berkeley, and have been used in the
teaching curriculum there for many years. They have been substantially updated and revised as part of a multiyear
collaboration with Thorlabs in order to make the material more widely available; in the process, substantial new
hardware has been developed to improve and/or simplify offering of the material.
Figure 1 Overview of the optical microscopy setup. The kit contains an open rail with all optical
components to go through the teaching steps. Furthermore, the kit contains a research grade
spectrometer, various samples and tools to experiment, learn and evaluate.

Optical Microscopy Course Kit Chapter 3: Brief Description
Page 4 MTN015225-D02
User Guide
Lab Notes
Course Notes
Instructor Notes
Figure 2 Overview of the included documentation. A total amount of about 500 pages gives the physical
background, step-by-step instructions of the assembly and lab procedure, as well as tips for tutoring
the course.
The Course Notes cover the theory for each lab's material. The Lab Notes provide instructions and tasks for the
students (intended for 3-hour lab sections) and provide the basis for each lab report. The Instructor Notes are for
instructors and teaching assistants overseeing the lab sections and include suggestions for pre lab quizzes and
tips for supporting the labs. Note: These notes are not intended to replace lectures or to provide complete
documentation for those lectures. The suggested workflow of using this kit is shown in Figure 3.

Optical Microscopy Course Kit Chapter 3: Brief Description
Rev C, October 1, 2020 Page 5
Figure 3 Graphical representation of the workflow during a lecture week and distribution of the
documentation. The # stands for one of the 10 labs provided.
This kit is intended for use in a course-based teaching environment, and may be difficult to use outside of one
because of the in-depth teaching materials fitted to this concept. The kit targets optics faculty who want to expand
their teaching beyond theoretical explanations; in the United States this material would typically underlie a quarter-
or semester-long lab class, at the upper-division level. The benefit of this kit is an all-in-one solution with tested
samples and supporting materials covering most important aspects of microscopy and optical imaging. Students
will usually work on one rail setup in small groups, with preferably not more than two students per setup.
Additionally, a lab instructor should be available to support students during the lab work.
The documentation is not intended to be cook-book; questions for students are regularly raised without answers
necessarily being provided, and students are led to figure out for themselves how to accomplish various tasks.
Images in the documentation are purposefully limited in order to get students to think for themselves about their
results rather than merely replicating steps in a lab manual. During this course, students build their knowledge in a
systematic manner –the lab material is carefully sequenced –providing the opportunity both to learn and then to
apply that new knowledge in a hands-on manner. The intent is to provide students with skills that enable them to
confidently develop their own applications of imaging and microscopy for future projects and work.
Setup Overview
The central focus of the kit is to learn how to set up an optical microscope and explore different microscope
properties and configurations.
Starting in Labs 1 and 2, the students learn how to handle the optical rail system and lenses, and how to set up
camera imaging in an infinity-corrected system. Acquiring their first images using the rail system concludes the first
two labs.
In Labs 3 and 4, students learn about optical resolution, illumination coherence, and chromatic aberrations by
manipulating the numerical aperture of their objective, adjusting their light source, and using a diffusor. At the end
of Lab 4, students will have their microscope in the most commonly used configuration, set up for Kohler
illumination as shown in Figure 4.
In Labs 5 and 6, students explore manipulation of image information in the objective back focal plane, and different
imaging and contrast methods (e.g. darkfield) are introduced. Students explore the Abbe theory of image formation,
and learn how image formation results from interference of diffracted beams, as shown in Figure 4 and Figure 5.
Labs 7 and 8 delve further into resolution and contrast, introducing the Modulation Transfer Function (MTF).
Students also learn about –and set up themselves –phase contrast, and explore its imaging properties.
In Labs 9 and 10, fluorescence microscopy is introduced, and students set it up on the rail using excitation and
emission filters. There is an extensive problem set / worked exercise, where students optimize filter selection for a
given fluorophore and illumination source.
Lecturer
•Lectures on Lab #
•Provides (well in advance):
Course Notes and Lab Notes
for entire course
Students
•Attend Lecture on Lab #
•Read Course Notes for Lab #
•Read Lab Notes for Lab #
Do experiments in Lab #
•Refer to Lab Notes # for
procedures and support
during lab
Lab
Instructor
•Reviews Instructor Notes #
•Checks all necessary parts
available for upcoming Lab #
•Practices with equipment
•
•Gives reading quiz on Lab #
•Provides support and
instruction, aided by
Instructor Notes for Lab #

Optical Microscopy Course Kit Chapter 3: Brief Description
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Each experiment includes multiple evaluation tasks for students to perform, giving them experience with both
qualitative observation and quantitative comparison of data with theory.
Figure 4 Overview of the components on the optical rail: 1) Camera, 2) Objective, 3) Sample, 4) Condenser
and Aperture Stop, 5) Neutral Density Filter Wheel, 6) Green Filter, 7) Field Stop, 8) Collector Lens,
and 9) Lamp with IR Filter
Figure 5 Photo of a second camera imaging the back focal plane of the objective to teach image
formation: 10) Beamsplitter and 11) Back Focal Plane Camera.
1
2
3
4
7
8
9
10
11
5
6

Optical Microscopy Course Kit Chapter 3: Brief Description
Rev C, October 1, 2020 Page 7
Lab Notes and Course Notes Overview
This section provides a quick run through of the content of each lab with graphical illustrations of the key features.
Lab
Lab Content
1
Introduction to Optical Imaging (I)
-Handling Cameras and Using
Camera Software Controls
-Imaging and Lenses; Lens
Focal Length
-Cameras (Color and
Monochrome)
-Light Spectra
2
Introduction to Optical Imaging (II)
-Imaging with a Camera and
Focusing at Infinity
-Setting Up the Rail System
-Imaging and Resolution
Measurement
3
Aberrations and Illumination
-Lens Orientation
-Illumination Spatial Coherence
-Color (Chromatic Aberration);
Achromatic Lenses
4
Köhler Illumination
-Collection Optics
-Condensing Optics
-Kohler Illumination
-Numerical Aperture (NA)
oResolution
oImage Brightness
5
Example of a Brightfield and Darkfield Image
Köhler, Conjugate Planes, and
Darkfield Imaging
-Point-Spread Function (PSF)
-Darkfield and Oblique
Illumination
-Image Manipulation in the
Objective Back Focal Plane
(BFP):
oDarkfield I: Image
Subtraction
oConvolution and the PSF
oDarkfield II: Convolution
and Subtraction

Optical Microscopy Course Kit Chapter 3: Brief Description
Page 8 MTN015225-D02
6
The Abbe Theory of Image
Formation (I)
-Imaging the BFP: Setting Up a
BFP-Imaging Camera
-Diffraction and the BFP
-Spatial Filtering in the BFP
7
The Abbe Theory of Image
Formation (II)
-The Modulation Transfer
Function (MTF)
oIncoherent MTF
oCoherent MTF
-The Edge-Spread Function
(ESF) and the MTF
8
Contrast Methods and Abbe
Theory
-Brightfield
-Darkfield and Signal-to-
Background
-MTF and Contrast
-Phase Contrast
9
Fluorescence Microscopy
-Fluorescence and
Fluorescence Imaging on the
Following Samples:
oAutofluorescent Slides
oLens Tissue with
Fluorescent Markers
oH&E (Fluorescent Eosin)
Stained Tissue Samples
10
Spectra and Filters
-Light Spectra
-Filter Transmission and
Behavior
-Spreadsheet-Based Problem
Set on Quantitative Filter
Selection
Oscillation
Corresponding Out
of Focus Area

Optical Microscopy Course Kit Chapter 3: Brief Description
Rev C, October 1, 2020 Page 9
Supplementary Documentation
This kit references various additional resources (beyond those in the course documentation) useful for teaching
aspects of microscopy, including videos, webpages, and scientific literature. All webpages referenced in the notes
have a link to the kit’s product page, which has a central references tab with the current web links. Particular
emphasis is placed on video material, specifically a beautiful microscopy tutorial by Dr. Peter Evennett that covers
the Abbe theory of image formation, as well as extended video material for working with optomechanical hardware.
A USB stick is also provided with the kit and includes all documentation (Course Notes, Lab Notes, and Instructor
Notes), as well as the Evennett Abbe videos and assembly videos. Secondary references to the optics literature
include some papers, which may require access to technical journals either via a typical university library or
subscription.
Getting started
Chapter 4 of this document shows all parts included in the kit. The following chapter, Chapter 5, provides
instructions on assembling the optical components. After assembly of the optics, you should prepare the
computer(s) and install the camera and spectrometer software. You will find helpful information in the Appendices
of the Lab Notes, Course Notes, and (particularly) the Instructor Notes. The primary course instructor should go
through all labs with the lab instructor(s) and schedule the weeks for the different labs. Unless this is the first
offering of the course, be sure to check that consumable materials like gloves, cover slides and lens tissues have
been replenished. Consumables can also be found on the Thorlabs web page
1
.
After setting up the rail and assembly of the components, you can read the Course Notes and (especially) the Lab
Notes and plan how you wish to use the materials / approach the course. The Instructor Notes are particularly
helpful for refreshing your memory of labs from year-to-year, and for helping prepare teaching staff. For instructors,
especially those using the materials for the first time, we strongly recommend using the Assembly, Kohler, and
Back Focal Plane videos at the www.thorlabs.com/OMC video tab both for a quick rundown of the assembly steps
and to assist in setting up the system for the first time. Be aware that using these videos will skip most of the
learning experience; we recommend that students approach the course via the Lab Notes and working it out
themselves, in class, instead.
1
Optics Lab Supplies: https://www.thorlabs.com/navigation.cfm?guide_id=2007

Optical Microscopy Course Kit Chapter 4: Kit Components
Page 10 MTN015225-D02
Chapter 4 Kit Components
All kit components are shown below, broken out by subassembly for convenience as you set up. Unless otherwise
noted, in cases where the metric and imperial kits contain parts with different item numbers, metric part numbers
and measurements are indicated by parentheses.
Rail System
1 x Aluminum Breadboard
8" x 36" x 1/2"
(20 cm x 90 cm x 1.27 cm),
Single Density Taps
2 x RDF1
Rubber Damping Feet, Set of 4
1 x XT34-100
1 x XT34-900
34 mm Construction Rails,
100 mm and 900 mm Long
4 x RS2P (RS2P/M)
Ø1" Pedestal Post,
1/4"-20 (M6) Taps, 2" Long
4 x CF175C (CF175C/M)
Clamping Fork, 1.75" (44.8 mm),
1/4"-20 (M6) Captive Screw
6 x XT34HP (XT34HP/M)
Dovetail Mounting Clamp for
34 mm Rails
12 x XT34TR1 (XT34TR1/M)
1/2" (12.5 mm) Rail Carrier
1 x XT34TR2 (XT34TR2/M)
1" (25 mm) Rail Carrier
1 x Right Angle Rail Adapter
for XT34HP (XT34HP/M) Dovetail
Mounting Clamp

Optical Microscopy Course Kit Chapter 4: Kit Components
Rev C, October 1, 2020 Page 11
General Tools and Optomechanics
1 x CCS200 (CCS200/M)
Compact Spectrometer, 200 nm - 1000 nm, Software and Fiber Patch
Cable Included
2 x R2T
Thin Slip-On Post Collar for
Ø1/2" Posts, 5 Pack
(10 Post Collars Total)
1 x TR2 (TR50/M)
Ø1/2" (Ø12.7 mm) Optical Post,
Stainless Steel, 2" (50 mm) Long
16 x TR3 (TR75/M)
Ø1/2" (Ø12.7 mm) Optical Post,
Stainless Steel, 3" (75 mm) Long
6 x TR4 (TR100/M)
Ø1/2" (Ø12.7 mm) Optical Post,
Stainless Steel, 4" (100 mm) Long
1 x LA1765
Ø30.0 mm N-BK7 Plano-Convex
Lens, f = 75.0 mm, Uncoated
1 x LA1031
Ø30.0 mm N-BK7 Plano-Convex
Lens, f = 100 mm, Uncoated
1 x MC-5
Lens Tissues, 25 Sheets per
Booklet, 5 Booklets
1 x SPW602
SM1 Spanner Wrench,
Graduated, Length = 3.88"
1 x SPW603
SM05 Spanner Wrench,
Length = 1"
1 x BD-KIT (BD-KIT/M)
Balldriver Kit
BD-KIT
BD-KIT/M

Optical Microscopy Course Kit Chapter 4: Kit Components
Page 12 MTN015225-D02
1 x HKTS-3/16 (HKTS-5M)
3/16" (5 mm) Hex Key
Thumbscrews, Pack of 4
1 x MS10UW2
Microscope Slides, 1 mm Thick,
White Marking Region, Pack of 200
1 x CG00C2
Cover Glasses, #0 Thickness,
22 x 22 mm, Pack of 200
1 x SM1EC2B
Snap-On Plastic Dust Cap for
SM1 Lens Tubes, 5 Pack
4 x SM1RC (SM1RC/M)
Slip Ring for SM1 Lens Tubes
5 x LMR1 (LMR1/M)
Lens Mount with Retaining Ring for
Ø1" Optics 8-32 (M4) Tap
1 x BA1 (BA1/M)
Mounting Base, 1" x 3" x 3/8"
1 x FH2
Filter Holder
1 x FGL780M
780 -1800 nm Colored Glass Filter,
SM1-Threaded Mount
1 x SM1SMA
SMA Fiber Adapter Plate with
External SM1 Thread
1 x Zero Order Blocking Mask
NBK7 Glass Substrate with
1.25 mm Central Spot
1 x SM1L03
Ø1" Lens Tube, 0.30" Long
1 x SMR1(/M)
Lens Mount with No Retaining Lip
for Ø1" Optics, 8-32 (M4) Tap
1 x USB-C-72
72" USB 2.0 Type-A High-Speed
Extension Cable, Black

Optical Microscopy Course Kit Chapter 4: Kit Components
Rev C, October 1, 2020 Page 13
Lamp
1 x QTH10 (QTH10/M)
Quartz Tungsten-Halogen Lamp
1 x SM2A6
Adapter with External SM2
Threads and Internal SM1
Threads
1 x FGB37M
Mounted Ø25 mm BG40 Colored
Glass Bandpass Filter,
335 - 610 nm
1 x HSLT2
Passive-Heat-Sink SM1 Lens
Tube with External SM2 Threads
1 x SM1CP2
End Cap, External SM1 Threads
Collector and Field Stop
1 X LA1027
Ø1" N-BK7 Plano-Convex Lens,
f = 35 mm, Uncoated
1 x ID25 (ID25/M)
Mounted Iris Diaphragm,
Ø25.0 mm Max Aperture
Neutral Density Filter Wheel
1 x CFW6 (CFW6/M)
30 mm Cage Filter Wheel
1 Each of ND05B, ND10B ND13B,
ND20B, ND30B
Neutral Density Filters: OD 0.5,
1.0, 1.3, 2.0, 3.0

Optical Microscopy Course Kit Chapter 4: Kit Components
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Spectral Filtering
2 x TRF90 (TRF90/M)
90° Flip Mount for Ø1" Filters and
Optics
1 x ER1
Ø6 mm Cage Assembly Rod,
1" Long
1 x Colored Glass
Bandpass Filter
Ø25 mm VG9, 3 mm Thick
1 x FBH520-40
Ø25 mm Premium Bandpass
Filter, 520 nm CWL, 40 nm FWHM
(Fluorescence Excitation Filter)
Condenser Optic
1 x SM1V10
Ø1" Adjustable Lens Tube,
0.81" Travel
1 x AC254-050-A
Ø1" Achromatic Doublet,
f = 50.0 mm, 400 - 700 nm
1 x SM1M10
SM1 Lens Tube, 1" Long,
Two Retaining Rings Included
1 x SM2D25
SM2 Lever-Actuated Iris
Diaphragm (Ø0.8 - Ø25 mm)
1 x SM1A2
Adapter with External SM1
Threads and Internal SM2
Threads

Optical Microscopy Course Kit Chapter 4: Kit Components
Rev C, October 1, 2020 Page 15
Sample Stage
1 x MS1S + Metric Micrometer
(MS1S/M)
6.5 mm Travel Single-Axis
Translation Stage with Side-
Mounted Metric Micrometer
1 x XYF1 (XYF1/M)
XY Mount for 1" - 3" Rectangular
Optics
1 x Sample Stage Adapter
Connects MS1S (MS1S/M) to
XYF1 (XYF1/M)
Plano-Convex (PCX) Objective
1 x LA1951
Ø1" N-BK7 Plano-Convex Lens,
f = 25.4 mm, Uncoated
1 x SM1RRC
Extra-Thick SM1 (1.035"-40)
Threaded Retaining Ring
Achromatic Objective
1 x SM05V05
Ø1/2" Adjustable-Length Lens
Tube, Rotating, 0.3" Travel
1 x SM05M05
SM05 Lens Tube, 1/2" Long,
Two Retaining Rings Included
1 x SM05RC (SM05RC/M)
Slip Ring for SM05 Lens Tube
1 x SM1A1
Adapter with External SM05
Threads and Internal SM1
Threads
1 x SM1D12C
Calibrated Ring-Activated SM1 Iris
Diaphragm
1 x AC127-025-A
Ø1/2" Achromatic Doublet,
f = 25.0 mm, 400 - 700 nm

Optical Microscopy Course Kit Chapter 4: Kit Components
Page 16 MTN015225-D02
Nikon Objective
1 x N10X-PHE
10X Nikon Phase Contrast
Objective, Apodized Dark Low
Phase Type, 0.25 NA, 6.2 mm WD
1 x SM1A12
External SM1 to Internal M25
Thread Adapter
(for Nikon Objective)
Beamsplitter
1 x LMR2 (LMR2/M)
2" Fixed Lens Mount
1 x EBP2
Ø2" 30:70 Beamsplitter
Sample Camera
1 x CS165MU (CS165MU/M)
Zelux™ 1.6 MP Monochrome
CMOS Camera
1 x SM1V10
Ø1" Adjustable Lens Tube,
0.81" Travel
3 x SM1L10
Ø1” Lens Tube, 1" Long
1 x SM1L30
Ø1” Lens Tube, 3" Long
1 x SM1L05
Ø1" Lens Tube, 0.5" Long
1 x AC254-150-A
Ø1" Achromatic Doublet,
f = 150.0 mm, 400 - 700 nm