Halma Ocean Optics QE65000 User manual

1.
QE65000 Spectrometer
Installation and Operation Manual
Document Number 220-00000-000-02-0605
Offices: Ocean Optics, Inc.
830 Douglas Ave., Dunedin, FL, USA 34698
Phone [phone]
Fax [phone]
8 a.m.– 8 p.m. (Mon-Thu), 8 a.m.– 6 p.m. (Fri) EST
Ocean Optics B.V. (Europe)
Geograaf 24, 6921 EW DUIVEN, The Netherlands
Phone [phone]
F
ax 31-(0)26-3190505
E-mail: [email protected]m (General sales inquiries)
[email protected] (European sales inquiries)
[email protected] (Questions about orders)
[email protected] (Technical support)

Copyright © 2001-2005 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 sold as 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
Microsoft, Windows, Windows 95, Windows 98, Windows Me, Windows NT, Windows 2000, Windows XP and Excel are either registered
trademarks or trademarks of Microsoft Corporation.
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.

Table of Contents
About This Manual .......................................................................................................... v
Document Purpose and Intended Audience.............................................................................. v
Document Summary.................................................................................................................. v
Product-Related Documentation ............................................................................................... v
Upgrades......................................................................................................................... vi
Chapter 1: Introduction ......................................................................1
Product Overview ............................................................................................................ 1
Features .......................................................................................................................... 2
System Requirements ..................................................................................................... 3
EEPROM Utilization .................................................................................................................. 3
About OOIBase32 ..................................................................................................................... 3
Sampling System Overview....................................................................................................... 4
How Sampling Works............................................................................................................ 4
Modular Sampling Accessories............................................................................................. 4
Interface Options ............................................................................................................. 4
Shipment Components.................................................................................................... 5
Chapter 2: Installing the QE65000.....................................................7
Overview ......................................................................................................................... 7
QE65000 Installation ....................................................................................................... 7
Configuring the QE65000 in OOIBase32 ........................................................................ 7
Operator and Serial Number Dialog Box................................................................................... 8
Default Spectrometer Configuration File ................................................................................... 8
Configure Hardware Screen ...................................................................................................... 8
Spectrometer Configuration Screen .......................................................................................... 9
QE65000 Controls ..................................................................................................................... 10
Connect Spectroscopic Accessories ............................................................................... 11
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Chapter 3:Troubleshooting ...............................................................13
Overview ......................................................................................................................... 13
QE65000 Connected to PC Prior to OOIBase32 Installation .......................................... 13
Remove the Unknown Device from Windows Device Manager................................................ 14
Remove Improperly Installed Files ............................................................................................ 14
Older Version of OOIBase32 Installed ............................................................................ 15
Chapter 4: Sample Experiments........................................................17
Overview ......................................................................................................................... 17
Preparing for Experiments............................................................................................... 17
Taking Measurements..................................................................................................... 18
Application Tips ......................................................................................................................... 18
Absorbance Experiments ..........................................................................................................18
Transmission Experiments ........................................................................................................20
Reflection Experiments.............................................................................................................. 22
Relative Irradiance Experiments ............................................................................................... 24
Time Acquisition Experiments ......................................................................................... 26
Configuring the Time Acquisition Channel Configuration Screen ............................................. 27
Configuring for a Combination of Two Time Channels ......................................................... 28
Configuring the Time Acquisition Configuration Screen............................................................ 28
Appendix A: Calibrating the Wavelength of the QE65000...............31
Overview ......................................................................................................................... 31
About Wavelength Calibration......................................................................................... 31
Calibrating the Spectrometer........................................................................................... 32
Preparing for Calibration............................................................................................................ 32
Calibrating the Wavelength of the Spectrometer ...................................................................... 32
Saving the New Calibration Coefficients: USB Mode ...................................................... 34
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Table of Contents
Appendix B: Specifications................................................................35
Overview ......................................................................................................................... 35
How the QE65000 Works................................................................................................ 35
QE65000 Components Table .................................................................................................... 36
QE65000 Specifications .................................................................................................. 37
CCD Detector Specifications .....................................................................................................37
QE65000 Spectrometer Specifications ..................................................................................... 38
System Compatibility....................................................................................................... 39
Compatibility for Desktop or Notebook PCs .............................................................................. 39
30-Pin Accessory Connector Pinout................................................................................ 39
30-Pin Accessory Connector Pinout Diagram........................................................................... 40
30-Pin Accessory Connector – Pin Definitions and Descriptions.............................................. 40
30-Pin J2 Accessory Connector - Part Numbers ...................................................................... 42
QE65000 15-Pin Accessory Cable Pinout....................................................................... 43
Index.....................................................................................................45
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About This Manual
Document Purpose and Intended Audience
This document provides the user of the QE65000 Spectrometer with instructions for setting up,
calibrating and performing experiments with their spectrometer.
Document Summary
Chapter Description
Chapter 1: Introduction Contains descriptive information about the QE65000 Spectrometer
and how sampling works. It also provides a list of system
requirements, interface options, and shipment components.
Chapter 2: Installing the QE65000 Provides installation and configuration instructions.
Chapter 3: Troubleshooting Contains recommended steps to isolate and correct common
problems.
Chapter 4: Sample Experiments Offers instructions for preparing for and taking measurements with
the QE65000 Spectrometer.
Appendix A: Calibrating the
Wavelength of the QE65000
Provides instructions for calibrating the QE65000 Spectrometer.
Appendix B: Specifications Contains technical specifications and connector pinouts for the
QE65000 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. Or, use the Search by Model Number field at the bottom
of the web page.
•Detailed instructions for the OOIBase32 Spectrometer Operating Software are located at:
http://www.oceanoptics.com/technical/ooibase32bit.pdf.
Engineering-level documentation is located on our website at Technical →Engineering Docs.
You can also access operating instructions for Ocean Optics products from the Software and Technical
Resources CD that ships with the product.
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About This Manual
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.
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Chapter 1
Introduction
Product Overview
The Ocean Optics QE65000 Spectrometer is a novel combination of detector, optical bench and
electronics technologies that provide you with a remarkably sensitive system for demanding, low-light
level applications such as fluorescence, DNA sequencing and Raman spectroscopy. The QE65000 is
Ocean Optics’ most sensitive spectrometer, achieving up to 90% quantum efficiency with high signal-to-
noise and improved signal processing speed.
Ocean Optics QE65000 High-Sensitivity Fiber Optic Spectrometer
The QE65000 features a Hamamatsu back-thinned detector with a 2-D arrangement of pixels (1044
horizontal x 64 vertical) that is responsive from 200-1100 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 combination of the spectrometer’s low-noise detector and 16-bit A/D Converter delivers a dynamic
range of 25000:1 and a signal-to-noise ratio of 1000:1.
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1: Introduction
The QE65000’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.
TheQE65000’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 QE65000 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 S7031-1006 Detector
•Peak QE: 90%
•Back-thinned for good UV sensitivity
•MPP operation for low noise
•TE Cooled
•Spectrometer Design
•Symmetrical Crossed Czerny Turner
•101mm focal length
•14 gratings
•6 slit widths
•Electrical Performance
•16 bit, 500KHz A/D converter
•Integration times from 7ms 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
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1: Introduction
•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
•CE certification
System Requirements
You can use the QE65000’s USB connectivity with any PC that meets the following requirements:
•Windows 98/Me/2000/XP operating system (or Windows CE 2.11 or later for handheld PCs)
•Ocean Optics OOIBase32 software application installed and configured for use with the QE65000
(OOIPS2000 software if using a handheld PC). See the Configuring the QE65000 in OOIBase32
section of Chapter 2: Installing the QE65000 for specific configuration instructions.
Alternately, the QE65000 has a serial port for connecting to PCs, PLCs, and other devices that support the
RS-232 communication protocol. However, this connection method requires an external power supply to
power the QE65000, the HR4000 Breakout Box, and a serial cable.
EEPROM Utilization
An EEPROM memory chip in each QE65000 contains wavelength calibration coefficients, linearity
coefficients, and a serial number unique to each individual spectrometer. The OOIBase32 software
application reads these values directly from the spectrometer, enabling the ability to “hot-swap”
spectrometers between PCs without entering the spectrometer coefficients manually on each PC.
About OOIBase32
OOIBase32 is the latest generation of operating software for all Ocean Optics spectrometers and is
available free to all customers. OOIBase32 is a user-customizable, advanced acquisition and display
program that provides a real-time interface to a variety of signal-processing functions. With OOIBase32,
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.
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1: Introduction
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 OOIBase32.
7. OOIBase32 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 QE65000. 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 QE65000 has both USB and serial port connectors (with the use of an adapter), enabling you to
connect the spectrometer to a desktop or notebook PC via a USB port or serial port.
Computer
Interface Operating System Requirements Part Needed Description of Part
Desktop or
Notebook PC
via USB Port
Windows 98/Me/
2000/XP
USB-CBL-1
(included)
Cable that connects from USB port on QE65000 to
USB port on desktop or notebook PC
Desktop or
Notebook PC
via Serial Port
Any 32-bit
Windows
operating system
HR4-
BREAKOUT
(not included)
Adapter block that enables connection from serial port
on QE65000 to serial port on desktop or notebook PC;
comes with 5 VDC power supply (required when
connecting to serial port)
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1: Introduction
Shipment Components
QE65000 Spectrometer
+ 5VDC power supply
The following information and documentation also ships with the QE65000 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. OOIBase32 Operating Software reads this calibration data from
your spectrometer when it interfaces to a PC via the USB port. Any other interface requires that
you manually enter the calibration data in OOIBase32 (select Spectrometer | Configure |
Wavelength Calibration tab). See the OOIBase32 documentation for more information (refer to
Product-Related Documentation for instructions on accessing OOIBase32 documentation).
Note
Please save the Wavelength Calibration Data Sheet for future reference.
Software and Technical Resources CD
Each order ships with the Ocean Optics Software and Resources CD. This disc contains software,
operating instructions, and product information for all Ocean Optics software, spectrometers, and
spectroscopic accessories. You need Adobe Acrobat Reader version 6.0 or higher to view these
files. Ocean Optics includes the Adobe Acrobat Reader on the Software and Technical Resources
CD.
With the exception of OOIBase32 Spectrometer Operating Software, all Ocean Optics software
requires a password during the installation process. You can locate passwords for the other
software applications on the back of the Software and Technical Resources CD package.
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1: Introduction
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Chapter 2
Installing the QE65000
Overview
You must install the OOIBase32 software application prior to connecting the QE65000 Spectrometer to
the PC. The OOIBase32 software installation installs the drivers required for QE65000 installation. If you
do not install OOIBase32 first, the system will not properly recognize the QE65000.
If you have already connected the QE65000 to the PC prior to installing OOIBase32, consult Chapter 3:
Troubleshooting for information on correcting a corrupt QE65000 installation.
QE65000 Installation
This section contains instructions for connecting the QE65000 in USB mode. To connect the QE65000 to
a PC via the USB port, the PC must be running the Windows 98/ME/2000/XP operating system.
►Procedure
Follow the steps below to connect the QE65000 to a PC via the USB port:
1. Install OOIBase32 on the destination PC.
2. Locate the USB cable (USB-CBL-1) provided with the QE65000.
3. Insert the square end of the cable into the side of the QE65000.
4. Insert the rectangular end of the cable into the USB port of the PC.
5. If you intend to run the TE Cooler, plug the +5 VDC power supply into the QE65000.
If you installed OOIBase32 prior to connecting the QE65000, the Add New Hardware Wizard appears
and installs the QE65000 drivers. If the drivers do not successfully install (or if you connected the
QE65000 to the PC before installing OOIBase32), consult Chapter 3: Troubleshooting.
Configuring the QE65000 in OOIBase32
Once you install the QE65000, you must configure OOIBase32’s Configure Spectrometer options so
that OOIBase32 recognizes the QE65000 Spectrometer. Consult the OOIBase32 Spectrometer Operating
Software Operating Instructions for detailed instructions on configuring the spectrometer in OOIBase32
(see Product-Related Documentation).
The following sections contain instructions on initially configuring the QE65000 the first time you start
OOIBase32.
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2: Installing the QE65000
Operator and Serial Number Dialog Box
The Operator and Serial Number screen prompts you to enter a user name and software serial number
into OOIBase32. Some data files created by OOIBase32 during sampling procedures use this information
in the file headers.
Default Spectrometer Configuration File
The Default Spectrometer Configuration File screen prompts you to select a spectrometer configuration
(.SPEC) file for use with the QE65000. The unique serial number of the QE65000 precedes the file
extension (for example, DEFAULT.SPEC).
Navigate to the OOIBase32 installation directory and select the spectrometer configuration file.
Configure Hardware Screen
The Configure Hardware screen prompts you to enter spectrometer-specific information into
OOIBase32 the first time you run the program. Typically, you need only enter this information the first
time you run OOIBase32. However, you can alter the hardware configuration at any time using the
Spectrometer Configuration screen. Select Spectrometer | Configure from the OOIBase32 menu bar
to access the Spectrometer Configuration screen.
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2: Installing the QE65000
►Procedure
To configure hardware in USB mode,
1. Specify QE65000 in the Spectrometer Type drop-down menu.
2. Specify QE65000 in the A/D Converter Type drop-down menu.
3. Specify the serial number of the QE65000 under the USB Serial Number drop-down menu.
Note
The system pre-fills this drop-down menu with the serial numbers of all discovered
QE65000 Spectrometers.
4. Click the OK button to accept the selected options.
5. The spectrometer should now be able to acquire data and respond to light. Exit and restart
OOIBase32 to save configuration data to disk.
Spectrometer Configuration Screen
The Spectrometer Configuration screen prompts you to configure specific channel-level spectrometer
information, if necessary.
►Procedure
1. Select Spectrometer | Configure from the menu and set system parameters.
2. Select the Wavelength Calibration tab. OOIBase32 pre-fills the coefficients for the QE65000
from information on a memory chip in the spectrometer.
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2: Installing the QE65000
3. Verify that the calibration coefficients match the coefficients from the Wavelength Calibration
Data Sheet that accompanied the spectrometer. If necessary, modify these values using the USB
Programmer utility.
4. Additionally, ensure that you select both the Master and Channel Enabled boxes.
5. In the A/D Interface tab, enter the same values as in the Configure Hardware screen.
OOIBase32 stores this information for future use once you close the program.
QE65000 Controls
The QE65000 toolbar in OOIBase32 allows you to control a variety of options on the QE65000
Spectrometer. Click your right mouse button while in the OOIBase32 toolbar to display the QE65000
toolbar.
Note
If your version of OOIBase32 does not have the options listed below, you should upgrade
your version of OOIBase32 to the latest release.
Visit http://www.oceanoptics.com/technical/softwaredownloads.asp to obtain the
latest software version.
Control Description
TEC On Check this box to enable (recommended setting for laboratory conditions) or
uncheck to disable the thermoelectric cooler.
Det. Temp. Set Point Enter the target temperature of the spectrometer detector as follows:
•Minimum is –15 ºC,
•Recommended is –5 ºC
The TEC and fans will operate until the detector reaches this temperature.
Apply Click this button to apply the changes made in this toolbar to the QE65000
Spectrometer.
Current Det. Temp. Displays the current temperature of the detector in the spectrometer.
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Connect Spectroscopic Accessories
To find operating instructions for QE65000-compatible products (such as light sources, sampling
chambers, and probes), consult the Software and Technical Resources CD or the Ocean Optics website at
http://www.oceanoptics.com/technical/operatinginstructions.asp.
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