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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