Halma Ocean Optics QE65 Pro User manual

000-00000-000-02-A
QE65 Pro Scientific-grade Spectrometer
Installation and Operation Manual
For Products: QE65Pro
Document: 220-12200-000-02-201603

AMERICAS & WORLD HEADQUARTERS
Phone: [phone]
Fax: [phone]
Sales: [email protected]
Orders: [email protected]
Support: [email protected]
EUROPE, MIDDLE EAST & AFRICA
Phone: [phone]
Fax: [phone]
Email: [email protected]
Germany : [phone]
UK : [phone]
France : [phone]
ASIA
Phone: [phone]
Fax: [phone]
Email: [email protected]
Japan & Korea: [phone]
www.oceanoptics.com
Copyright © 2012 Ocean Optics, Inc.
All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, by any means, electronic, mechanical,
photocopying, recording, or otherwise, without written permission from Ocean Optics, Inc.
This manual is part of an order and subject to the condition that it shall not, by way of trade or otherwise, be lent, re-sold, hired out or otherwise circulated
without the prior consent of Ocean Optics, Inc. in any form of binding or cover other than that in which it is published.
Trademarks
All products and services herein are the trademarks, service marks, registered trademarks or registered service marks of their respective owners.
Limit of Liability
Every effort has been made to make this manual as complete and as accurate as possible, but no warranty or fitness is implied. The information provided is
on an “as is” basis. Ocean Optics, Inc. shall have neither liability nor responsibility to any person or entity with respect to any loss or damages arising from
the information contained in this manual.
Ocean Optics, Inc.
830 Douglas Ave.
Dunedin, FL 34698
USA
Manufacturing & Logistics
4301 Metric Dr.
Winter Park, FL 32792
USA
Ocean Optics Asia
666 Gubei Road
Kirin Tower Suite 601B
Changning District
Shanghai
PRC, 200336
Sales & Support
Geograaf 24
6921 EW Duiven
The Netherlands
Manufacturing & Logistics
Maybachstrasse 11
73760 Ostfildern
Germany

220-12200-000-02-201603 i
Table of Contents
About This Manual.........................................................................................................iii
Document Purpose and Intended Audience..............................................................................iii
Document Summary..................................................................................................................iii
Product-Related Documentation ...............................................................................................iii
Upgrades.......................................................................................................................iv
Chapter 1: Introduction .....................................................................1
Product Overview..........................................................................................................1
Features........................................................................................................................2
System Requirements...................................................................................................3
EEPROM Utilization ..................................................................................................................3
How Sampling Works............................................................................................................4
Modular Sampling Accessories.............................................................................................4
Interface Options...........................................................................................................4
Shipment Components..................................................................................................5
Other Accessories Available..........................................................................................5
Breakout Box.............................................................................................................................5
Chapter 2: Installing the QE65 Pro...................................................7
Overview .......................................................................................................................7
QE65 Pro Installation.....................................................................................................7
USB Mode .................................................................................................................................7
Serial Port Mode........................................................................................................................8
QE65 Pro Configuration.................................................................................................8
Connect Spectroscopic Accessories..............................................................................8
External Triggering Options...........................................................................................8
Chapter 3: Troubleshooting..............................................................11
Overview .......................................................................................................................11
QE65 Pro Connected to Computer Prior to Software Installation...................................11
Windows Operating Systems ....................................................................................................11
Remove the Unknown Device from Windows Device Manager ...........................................11

Table of Contents
ii 220-12200-000-02-201603
Remove Improperly Installed Files........................................................................................12
Mac Operating Systems............................................................................................................12
Linux Operating Systems ..........................................................................................................12
Appendix A: Calibrating the Wavelength of the QE65 Pro .............13
Overview .......................................................................................................................13
About Wavelength Calibration .......................................................................................13
Calibrating the Spectrometer.........................................................................................14
Preparing for Calibration............................................................................................................14
Calibrating the Wavelength of the Spectrometer ......................................................................14
Saving the New Calibration Coefficients: USB Mode.....................................................16
Appendix B: Specifications...............................................................17
Overview .......................................................................................................................17
How the QE65 Pro Works..............................................................................................17
QE65 Pro Components Table ...................................................................................................18
QE65 Pro Specifications................................................................................................19
CCD Detector Specifications.....................................................................................................19
QE65 Pro Spectrometer Specifications.....................................................................................19
System Compatibility.....................................................................................................20
30-Pin Accessory Connector Pinout ..............................................................................20
30-Pin Accessory Connector Pinout Diagram...........................................................................21
30-Pin Accessory Connector –Pin Definitions and Descriptions..............................................21
30-Pin J2 Accessory Connector - Part Numbers.......................................................................23
QE65 Pro 15-Pin Accessory Cable Pinout.....................................................................24
Index...................................................................................................25

220-12200-000-02-201603 iii
About This Manual
Document Purpose and Intended Audience
This document provides the user of the QE65 Pro Spectrometer with instructions for setting up,
calibrating and performing experiments with their spectrometer.
What’s New in this Document
This version of the QE65 Pro Scientific-grade Spectrometer Installation and Operation Manual updates
the specifications.
Document Summary
Chapter
Description
Chapter 1: Introduction
Contains descriptive information about the QE65 Pro
Spectrometer and how sampling works. It also provides a list of
system requirements, interface options, and shipment
components.
Chapter 2: Installing the QE65 Pro
Provides installation and configuration instructions.
Chapter 3: Troubleshooting
Contains recommended steps to isolate and correct common
problems.
Appendix A: Calibrating the
Wavelength of the QE65 Pro
Provides instructions for calibrating the QE65 Pro Spectrometer.
Appendix B: Specifications
Contains technical specifications and connector pinouts for the
QE65 Pro Spectrometer.
Product-Related Documentation
You can access documentation for Ocean Optics products by visiting our website at
http://www.oceanoptics.com. Select Technical Operating Instructions, then choose the appropriate
document from the available drop-down lists.
Document for…
Document Location
OceanView software
http://oceanoptics.com///wp-content/uploads/OceanViewIO.pdf

About This Manual
iv 220-12200-000-02-201603
Document for…
Document Location
SpectraSuite software
http://oceanoptics.com///wp-content/uploads/SpectraSuite.pdf
HR-4 Breakout Box
http://oceanoptics.com///wp-content/uploads/HR-4-Breakout-Box.pdf
External triggering for
firmware versions
below 3.0
http://oceanoptics.com///wp-content/uploads/External-Triggering-Options.pdf
External triggering for
firmware versions 3.0
and above
http://oceanoptics.com///wp-content/uploads/External-Triggering-
Options_Firmware3.0andAbove.pdf
Ocean Optics offers a Glossary of spectroscopy terms to help you further understand your state-of-the-art
products and how they function, located at: http://oceanoptics.com/glossary/.
Upgrades
Occasionally, you may find that you need Ocean Optics to make a change or an upgrade to your system.
To facilitate these changes, you must first contact Customer Support and obtain a Return Merchandise
Authorization (RMA) number. Please contact Ocean Optics for specific instructions when returning a
product.
Warranty
Our 3-Year Warranty covers Ocean Optics miniature fiber optic spectrometers, light sources and
sampling accessories –regardless of the application –from manufacturing defects. It also covers fibers
and probes for a full 12 months: http://oceanoptics.com/services/exclusive-3-year-warranty/.
This comprehensive warranty ensures you of the highest level of craftsmanship and reliability for years to
come. No other manufacturer offers such a solid guarantee of quality and reliability.
The Ocean Optics 3-Year Warranty applies to Ocean Optics equipment (excluding OEM configurations)
purchased on or after July 1, 2010. The warranty covers parts and labor needed to repair manufacturing
defects that occur during the warranty period. We also will cover the costs of shipping warranty-related
repairs from our customers to Ocean Optics and from us to our customers.
ISO Certification
Ocean Optics, the industry leader in miniature photonics, has been certified for ISO 9001:2008
certification applicable to the design and manufacture of electro-optical equipment since 2009.

3: Troubleshooting
220-12200-000-02-201603 v
WARNING
This is a Class A product. In a domestic environment this product may cause radio
interference in which case the user may be required to take adequate measures.
FCC COMPLIANCE
This equipment has been tested and found to comply with the limits for a Class A
digital device, pursuant to Part 15 of the FCC Rules. These limits are designed to
provide reasonable protection against harmful interference when the equipment is
operated in a commercial environment. This equipment generates, uses and can
radiate radio frequency energy and, if not installed and used in accordance with the
instruction manual, may cause harmful interference to radio communications.
Operation of this equipment in a residential area is likely to cause harmful
interference in which the user will be required to correct the interference at his own
expense.
WARNING: The authority to operate this equipment is conditioned by the
requirement that no modifications will be made to the equipment unless the changes
or modifications are expressly approved by the manufacturer.

About This Manual
vi 220-12200-000-02-201603

220-12200-000-02-201603 1
Chapter 1
Introduction
Product Overview
Ocean Optics has taken its best scientific-grade spectrometer, the QE65000, and enhanced its optical
bench to provide unmatched performance to improve response in the UV and shortwave NIR regions. The
Ocean Optics QE65 Pro Spectrometer produces lower stray light and provides superior dynamic range
and high sensitivity for low-light level applications such as fluorescence, Raman analysis and DNA
sequencing.
Ocean Optics QE65 Pro High-Sensitivity Fiber Optic Spectrometer
The QE65 Pro features a Hamamatsu low-etaloning, back-thinned FFT-CCD detector with a 2-D
arrangement of pixels (1044 horizontal x 64 vertical) that is responsive from 200-1100 nm and has a peak
quantum efficiency of ~90% (with a QE of 65% at 250 nm). The detector’s columns are binned, or
summed, inside the detector prior to the readout process, thereby minimizing readout noise. Additionally,
the detector can be cooled down to –15 ºC with the onboard TE-Cooler to reduce dark noise. The
reduction of noise and dark signal allows integration times of the spectrometer (analogous to the shutter
speed of a camera) of up to 15 minutes, which greatly enhances the detection limit in low-light level
applications. The back-illuminated detector has great response in the UV. The inherent UV response
eliminates the need for UV-sensitive detector coatings that can be difficult to apply consistently from
batch to batch.
The combination of the spectrometer’s low-noise detector and 16-bit A/D Converter delivers a dynamic
range of 25000:1 (for a single acquisition) and a signal-to-noise ratio of 1000:1 (at full signal).
Replaceable slits are offered for added convenience.

1: Introduction
2220-12200-000-02-201603
The QE65 Pro’s onboard module has 10 user-programmable digital I/O lines for interfacing to other
equipment; and a pulse generator for triggering other devices. You can use the I/Os to flash a lamp,
stop/start a process, and send a message/alarm during the spectrometer’s integration period. The
spectrometer’s operating parameters can be controlled through software. In fact, wavelength calibration
coefficients unique to each spectrometer are programmed into a memory chip right on the spectrometer.
TheQE65 Pro’s high-speed electronics have been designed for considerable flexibility in connecting to
various modules and external interfaces, including PCs, PLCs and other embedded controllers, through
USB 2.0 or RS-232 communications. Its USB 2.0 interface enables full spectral scans into memory every
7 milliseconds.
The QE65 Pro operates via USB interface. A +5 VDC external power supply is required for the TE
Cooler (TEC) and to operate the spectrometer via an RS-232 interface. This power supply is included
with your spectrometer.
Features
Hamamatsu S7031-1006S Detector
Peak QE: 90% at peak; 65% at @ 250 nm
Back-thinned for good UV sensitivity
MPP operation for low noise
TE Cooled
Spectrometer Design
Symmetrical Crossed Czerny Turner
101mm focal length
14 gratings across UV-NIR; HC-1 composite grating for broad wavelength coverage
6 slit widths ranging from 50 to 200 µm
Electrical Performance
16 bit, 500KHz A/D converter
Integration times from 8ms to ~15min
Embedded microcontroller allows programmatic control of all operating parameters and
standalone operation
USB 2.0 480Mbps (high-speed) & 12Mbps (full speed)
RS232 115Kbaud
Multiple communication standards for digital accessories (SPI, I2C)
Onboard Pulse Generator
2 programmable strobe signals for triggering other devices
Software control of nearly all pulse parameters
Onboard GPIO
10 user-programmable digital I/Os

1: Introduction
220-12200-000-02-201603 3
EEPROM storage for
Wavelength Calibration Coefficients
Linearity Correction Coefficients
Absolute Irradiance Calibration (optional)
Plug-n-play interface for PC applications
30-pin connector for interfacing to external products
System Requirements
You can use the QE65 Pro’s USB connectivity with any PC that meets the following requirements:
Microsoft Windows –Windows 2000/XP/7; 32-bit and 64-bit and Windows Vista (32-bit only)
Apple Macintosh –version 10.5 Intel or later
Linux –Any version released for an x86 or amd64 platform since 2010
Alternately, the QE65 Pro has a serial port for connecting to PCs, PLCs, and other devices with a
Windows 32-bit operating system that support the RS-232 communication protocol. However, this
connection method requires an external power supply to power the QE65 Pro, the Breakout Box, and a
serial cable.
EEPROM Utilization
An EEPROM memory chip in each QE65 Pro contains wavelength calibration coefficients, linearity
coefficients, and a serial number unique to each individual spectrometer. The OOI software application
reads these values directly from the spectrometer, enabling the ability to “hot-swap” spectrometers
between computers without entering the spectrometer coefficients manually on each computer.
About OceanView Software
OceanView is the latest generation of operating software for all Ocean Optics spectrometers. It is a
completely modular, Java-based spectroscopy software platform that operates on Windows, Macintosh
and Linux operating systems. The software can control any Ocean Optics USB spectrometer and device.
OceanView is a user-customizable, advanced acquisition and display program that provides a real-time
interface to a variety of signal-processing functions. With OceanView, you have the ability to perform
spectroscopic measurements (such as absorbance, reflectance, and emission), control all system
parameters, collect and display data in real time, and perform reference monitoring and time acquisition
experiments. Consult the OceanView manual for hardware requirements when using OceanView (see
Product-Related Documentation).

1: Introduction
4220-12200-000-02-201603
Sampling System Overview
How Sampling Works
Ocean Optics components function in a sampling system as follows:
1. The user stores reference and dark measurements to correct for instrument response variables.
2. The light transmits through an optical fiber to the sample.
3. The light interacts with the sample.
4. Another optical fiber collects and transmits the result of the interaction to the spectrometer.
5. The spectrometer measures the amount of light and transforms the data collected by the
spectrometer into digital information.
6. The spectrometer passes the sample information to the spectrometer operating software.
7. The software compares the sample to the reference measurement and displays processed spectral
information.
Modular Sampling Accessories
Ocean Optics offers a complete line of spectroscopic accessories for use with the QE65 Pro. Most of our
spectroscopic accessories have SMA connectors for application flexibility. Accordingly, changing the
sampling system components is as easy as unscrewing a connector and replacing an accessory.
Interface Options
The QE65 Pro has both USB and serial port connectors (with the use of an adapter), enabling you to
connect the spectrometer to a desktop or notebook computer via a USB port or serial port. However, you
must create custom software if using the serial port. OceanViewsoftware is available if you are
connecting via the USB port.
Computer
Interface
Operating System Requirements
Part Needed
Description of Part
Computer via
USB Port
OceanView: Microsoft Windows –
Windows 2000/XP/7; 32-bit and 64-
bit and Windows Vista (32-bit only)
Apple Macintosh –version 10.5
Intel or later
Linux –Any version released for an
x86 or amd64 platform since 2010
USB-CBL-1
(included)
Cable that connects from USB port on
QE65 Pro to USB port on desktop or
notebook PC
Desktop or
Notebook PC
via Serial
Port
Any 32-bit or 64-bit Windows
operating system
HR4-
BREAKOUT
(not included)
Adapter block that enables connection
from serial port on QE65 Pro to serial
port on desktop or notebook PC; comes
with 5 VDC power supply (required
when connecting to serial port)

1: Introduction
220-12200-000-02-201603 5
Shipment Components
QE65 Pro Spectrometer
+ 5VDC power supply
The following information and documentation also ships with the QE65 Pro Spectrometer:
Packing List
The packing list is inside a plastic bag attached to the outside of the shipment box (the invoice
arrives separately). It lists all items in the order, including customized components in the
spectrometer (such as the grating, detector collection lens, and slit). The packing list also includes
the shipping and billing addresses, as well as any items on back order.
Wavelength Calibration Data Sheet
Each spectrometer is shipped with a Wavelength Calibration Data Sheet that contains information
unique to your spectrometer. OceanView reads this calibration data from your spectrometer when
it interfaces to a computer via the USB port.
Note
Please save the Wavelength Calibration Data Sheet for future reference.
Other Accessories Available
Visit us at www.OceanOptics.com for a complete list of products available for all of your spectroscopy
needs.
Slits
Fibers
Light Sources
Integrated Sampling Systems
Cuvettes
Filter Holders
Lithium Ion Battery Pack
HR4-BREAKOUT Breakout Box
Breakout Box
Ocean Optics also offers the Breakout Box (HR4-BREAKOUT), a passive module that separates the
signals from their 22-pin port to an array of standard connectors and headers, enabling easy access to a
variety of features found in Ocean Optics’ QE65 Pro Spectrometer. In addition to the accessory
connector, the breakout box features a circuit board based on a neutral breadboard pattern that allows
custom circuitry to be prototyped on the board itself.

1: Introduction
6220-12200-000-02-201603

220-12200-000-02-201603 7
Chapter 2
Installing the QE65 Pro
Overview
You must install the operating software application prior to connecting the QE65 Pro Spectrometer to the
computer. The Ocean Optics spectrometer operating software installs the drivers required for the QE65
Pro spectrometer installation. If you do not install the software first, the system will not properly
recognize the QE65 Pro.
If you have already connected the QE65 Pro to the computer prior to installing the operating software,
consult Chapter 3: Troubleshooting for information on correcting a corrupt QE65 Pro installation.
QE65 Pro Installation
This section contains instructions for connecting the QE65 Pro via both USB and serial modes.
Caution
Ensure that TEC power is always applied (using OceanView software) before USB
power.
USB Mode
This section contains instructions for connecting the QE65 Pro in USB mode. To connect the QE65 Pro to
a computer via the USB port, the computer must be running a Windows 2000/XP/7 or Vista (32-bit), Mac
OS X or Linux operating system.
►Procedure
Follow the steps below to connect the QE65 Pro to a computer via the USB port:
1. Install the spectrometer operating software on the destination computer.
2. If you intend to run the TE Cooler, plug the +5 VDC power supply into the QE65 Pro.
3. Locate the USB cable (USB-CBL-1) provided with the QE65 Pro.
4. Insert the square end of the cable into the side of the QE65 Pro.
5. Insert the rectangular end of the cable into the USB port of the PC.

2: Installing the QE65 Pro
8220-12200-000-02-201603
If you installed the spectrometer operating software prior to connecting the QE65 Pro, the software
installs the QE65 Pro drivers. If the drivers do not successfully install (or if you connected the QE65 Pro
to the computer before installing the software), consult Chapter 3: Troubleshooting.
Serial Port Mode
To use the serial port capacity of the QE65 Pro Spectrometer, the PC must be running a 32-bit version of
the Windows operating system (or Windows CE 2.11 or higher for handheld PCs).
►Procedure
Follow the steps below to connect the QE65 Pro to the PC via serial port:
1. Plug the 5 VDC external power supply into an outlet and connect it to the QE65 Pro.
2. Connect the serial cable adapter block to the appropriate pins of the QE65 Pro’s 30-Pin
Accessory Connector.
3. Connect one end of the 9-pin serial cable to the adapter block on the QE65 Pro, and then connect
the other end to a serial port on the PC.
4. Note the number of the serial port (COM Port) to which you connected the QE65 Pro (some PCs
may not have numbered ports; handheld PCs typically have only one serial port).
QE65 Pro Configuration
The QE65 Pro can be used with OceanView software when connected to the USB port.
If you have followed the previous steps and started OceanView, the spectrometer is already acquiring
data. Even with no light in the spectrometer, there should be a dynamic trace displayed in the bottom of
the graph. If you allow light into the spectrometer, the graph trace should rise with increasing light
intensity. This means the software and hardware are correctly installed.
Connect Spectroscopic Accessories
To find operating instructions for QE65 Pro-compatible products (such as light sources, sampling
chambers, and probes), consult the Ocean Optics website at http://oceanoptics.com/support/technical-
documents/.
External Triggering Options
You can trigger the QE65 Pro using a variety of External Triggering options through the 30-pin
Accessory Connector on the spectrometer.
For QE65 Pro firmware versions below 3.0, see the External Triggering Options document located at
http://oceanoptics.com///wp-content/uploads/External-Triggering-Options.pdf.

2: Installing the QE65 Pro
220-12200-000-02-201603 9
For QE65 Pro firmware version 3.0 and above, see the External Triggering Options document located at
http://oceanoptics.com///wp-content/uploads/External-Triggering-Options_Firmware3.0andAbove.pdf.
The triggering document contains instructions for configuring External Triggering options for the QE65
Pro.
Note
Only the external software triggering option is available when using a handheld
computer.

2: Installing the QE65 Pro
10 220-12200-000-02-201603

220-12200-000-02-201603 11
Chapter 3
Troubleshooting
Overview
The following sections contain information on troubleshooting issues you may encounter when using the
QE65 Pro Spectrometer.
QE65 Pro Connected to Computer Prior to
Software Installation
Windows Operating Systems
If you connected your Ocean Optics QE65 Pro device to the computer prior to installing your
spectrometer operating software application (OceanView) on a Windows platform, you may encounter
installation issues that you must correct before your Ocean Optics device will operate properly.
Follow the applicable steps below to remove the incorrectly installed device, device driver, and
installation files.
Note
If these procedures do not correct your device driver problem, you must obtain the
Correcting Device Driver Issues document from the Ocean Optics website:
http://oceanoptics.com///wp-content/uploads/Correcting-Device-Driver-Issues.pdf.
Remove the Unknown Device from Windows Device Manager
►Procedure
1. Open Windows Device Manager. Consult the Windows operating instructions for your computer
for directions, if needed.
2. Locate the Other Devices option and expand the Other Devices selection by clicking on the "+"
sign to the immediate left.
Note
Improperly installed USB devices can also appear under the Universal Serial Bus
Controller option. Be sure to check this location if you cannot locate the unknown device.

3: Troubleshooting
12 220-12200-000-02-201603
3. Locate the unknown device (marked with a large question mark). Right-click on the Unknown
Device listing and select the Uninstall or Remove option.
4. Click the OK button to continue. A warning box appears confirming the removal of the Unknown
Device. Click the OK button to confirm the device removal.
5. Disconnect the QE65 Pro from your computer.
6. Locate the section in this chapter that is appropriate to your operating system and perform the
steps in the following Remove Improperly Installed Files section.
Remove Improperly Installed Files
►Procedure
1. Open Windows Explorer.
2. Navigate to the Windows | INF directory.
Note
If the INF directory is not visible, you must disable the Hide System Files and Folders
and Hide File Extensions for Known File Types options in Windows Folder Options.
Access Windows Folder Options from Windows Explorer, under the Tools | Folder
Options menu selection.
3. Delete the OOI_USB.INF in the INF directory. If your computer is running either the Windows
2000 or XP operating system, you must also delete the OOI_USB.PNF file in the INF directory.
4. Navigate to the Windows | System32 | Drivers directory.
5. Delete the EZUSB.SYS file.
6. Reinstall your Ocean Optics application and reboot the system when prompted.
7. Plug in the USB device.
The system is now able to locate and install the correct drivers for the USB device.
Mac Operating Systems
Since there are no device files for the QE65 Pro Spectrometer in a Mac operating system, you should not
encounter any problems if you installed the spectrometer before the operating software.
Linux Operating Systems
For Linux operating systems, all you need to do is install the software, then unplug and replug in the
spectrometer. Technically, the driver files for Linux simply give nonprivileged users permission to use
newly connected hardware. There isn’t any long-term harm to plugging in the device before installing the
software.