Ocean Optics USB4000 User manual

USB4000 Fiber Optic Spectrometer
Installation and Operation Manual
Document Number 211-00000-000-02-0908
Offices: Ocean Optics, Inc. World Headquarters
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
E-mail: [email protected] (General sales inquiries)
[email protected] (Questions about orders)
[email protected] (Technical support)

Additional
Offices:
Ocean Optics Asia
666 Gubei Road, Kirin Tower, Suite 601B, Changning District,
Shanghai, PRC. 200336
Phone [phone]
Fax [phone]
E-Mail [email protected]
Ocean Optics Europe
Sales and Support Center
Geograaf 24, 6921 EW DUIVEN, The Netherlands
Phone [phone]
Fax [phone]
E-Mail [email protected]
Regional Headquarters
Maybachstrasse 11
73760 Ostfildern
Phone [phone]
Fax [phone]
E-Mail [email protected]
Copyright © 2008 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
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.

Table of Contents
About This Manual .......................................................................................................... iii
Document Purpose and Intended Audience.............................................................................. iii
What’s New in This Document .................................................................................................. iii
Document Summary.................................................................................................................. iii
Product-Related Documentation ............................................................................................... iii
Upgrades......................................................................................................................... iv
Chapter 1: Introduction ......................................................................1
Product Overview ............................................................................................................ 1
Features .......................................................................................................................... 2
System Requirements ..................................................................................................... 2
EEPROM Utilization .................................................................................................................. 3
About SpectraSuite.................................................................................................................... 3
Sampling System Overview....................................................................................................... 3
How Sampling Works............................................................................................................ 3
Modular Light Sources and Sampling Accessories .............................................................. 3
Interface Options ............................................................................................................. 4
Breakout Box ............................................................................................................................. 4
Shipment Components.................................................................................................... 4
Additional Equipment Needed......................................................................................... 5
Other Accessories Available ........................................................................................... 5
Chapter 2: Installing the USB4000.....................................................7
Overview ......................................................................................................................... 7
USB4000 Installation....................................................................................................... 7
USB Mode ................................................................................................................................. 7
Serial Port Mode........................................................................................................................ 8
Connect Spectroscopic Accessories ............................................................................... 8
External Triggering Options............................................................................................. 8
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Table of Contents
Chapter 3: Troubleshooting ...............................................................9
Overview ......................................................................................................................... 9
USB4000 Connected to Computer Prior to SpectraSuite Installation.............................. 9
Windows Operating Systems .................................................................................................... 9
Remove the Unknown Device from Windows Device Manager ........................................... 9
Remove Improperly Installed Files........................................................................................ 10
Mac Operating Systems ............................................................................................................ 10
Linux Operating Systems .......................................................................................................... 11
Appendix A: Calibrating the Wavelength of the USB4000...............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: External Triggering .......................................................17
Overview ......................................................................................................................... 17
Normal (Free Running).............................................................................................................. 17
External Software Trigger.......................................................................................................... 17
External Hardware Trigger ........................................................................................................ 17
External Hardware Trigger Delay.......................................................................................... 18
External Synchronization Trigger.......................................................................................... 18
Appendix C: Specifications................................................................21
Overview ......................................................................................................................... 21
How the USB4000 Works................................................................................................ 21
USB4000 Components Table.................................................................................................... 22
USB4000 Specifications.................................................................................................. 23
CCD Detector Specifications .....................................................................................................23
USB4000 Spectrometer............................................................................................................. 23
22-Pin Accessory Connector Pinout................................................................................ 25
22-Pin Accessory Connector Pinout Diagram........................................................................... 25
22-Pin Accessory Connector – Pin Definitions and Descriptions.............................................. 26
22-Pin Accessory Connector - Part Numbers ........................................................................... 27
Index.....................................................................................................29
ii 211-00000-000-02-0908

About This Manual
Document Purpose and Intended Audience
This document provides the users of USB4000 Spectrometers with instructions for setting up, calibrating
and performing experiments with their spectrometer.
What’s New in This Document
This version of the USB4000 Fiber Optic Spectrometer Installation and Operation Manual adds the
USB-ADP-BB adapter for the Breakout Box.
Document Summary
Chapter Description
Chapter 1: Introduction Contains descriptive information about the USB4000
Spectrometer and how sampling works. It also provides a list
of system requirements, interface options, and shipment
components.
Chapter 2: Installing the USB4000 Provides installation instructions.
Chapter 3: Troubleshooting Contains recommended steps to isolate and correct common
problems.
Appendix A: Calibrating the
Wavelength of the USB4000
Provides instructions for calibrating the USB4000
Spectrometer.
Appendix B: External Triggering Contains information about external triggering for the
USB4000.
Appendix C: Specifications Contains technical specifications and connector pinouts for the
USB4000 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 SpectraSuite Spectrometer Operating Software are located at:
http://www.oceanoptics.com/technical/SpectraSuite.pdf.
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About This Manual
•Detailed instructions for the Breakout Box are located at:
http://www.oceanoptics.com/technical/HR4_breakout.pdf.
•Detailed instructions for external triggering are located at:
http://www.oceanoptics.com/technical/External-Triggering.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.
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.
iv 211-00000-000-02-0908

Chapter 1
Introduction
Product Overview
The Ocean Optics USB4000 Spectrometer is our next generation, high-performance, miniature fiber-optic
spectrometer designed from our popular USB2000 model to include an advanced detector and powerful
high-speed electronics. New features consist of the 3648-element detector with shutter, high-speed
electronics, and interface capabilities to Linux, Macintosh and Windows operating systems. The
USB4000 is responsive from 200-1100 nm, but the specific range and resolution depends on your grating
and entrance slit selections.
The USB4000 is perfect for applications where enhanced electronics, high resolution and fast integration
times are required.
Data programmed into a memory chip on each USB4000 includes wavelength calibration coefficients,
linearity coefficients, and the serial number unique to each spectrometer. Our spectrometer operating
software simply reads these values from the spectrometer — a feature that enables hot swapping of
spectrometers among computers.
The USB4000 Spectrometer connects to a computer via the USB port or serial port. When connected
through a USB 2.0 or 1.1, the spectrometer draws power from the host computer, eliminating the need for
an external power supply. The USB4000, like all USB devices, can be controlled by our SpectraSuite
software, a completely modular, Java-based spectroscopy software platform that operates on Windows,
Macintosh and Linux operating systems.
Ocean Optics USB4000 Fiber Optic Spectrometer
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1: Introduction
Features
TCD1304AP Detector
Responsive from 200 to 1100 nm, specific range and resolution depends on your grating and
entrance slit choices
Sensitivity of up to 130 photons/count at 400 nm; 60 photons/count at 600 nm
An optical resolution of ~0.3 (FWHM)
A wide variety of optics available
•14 gratings
•6 slit widths
•3 detector coatings
•6 optical filters
Integration times from 3.8 ms to 10 seconds
Embedded microcontroller allows programmatic control of all operating parameters and
standalone operation
•USB 2.0 480Mbps (high speed) and 12Mbps (full speed)
•RS232 115K baud
•Multiple communication standards for digital accessories (SPI, I2C)
EEPROM storage for
•Wavelength Calibration Coefficients
•Linearity Correction Coefficients
•Absolute Irradiance Calibration (optional)
Low power consumption of only 250 mA @ 5 VDC
16 bit, 3MHz A/D Converter
5 triggering modes
2 programmable strobe signals for triggering other devices
22-pin connector for interfacing to external products
Programmable for Standalone Operation
CE Certification
System Requirements
You can use the USB4000’s USB connectivity with any computer that meets the following requirements:
•Operating system is one of the following:
•Windows – 98/Me/2000/XP
•Apple Macintosh – OS X version 10.0 or later
•Linux – Red Hat 9 or later, Fedora (any version), Debian 3.1 (Sarge), and SUSE (9.0 or
later)
•Ocean Optics’ SpectraSuite software application installed and configured for use with the
USB4000.
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1: Introduction
EEPROM Utilization
An EEPROM memory chip in each USB4000 contains wavelength calibration coefficients, linearity
coefficients, and a serial number unique to each individual spectrometer. The SpectraSuite 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 SpectraSuite
SpectraSuite 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,
as well as any other manufacturer’s USB instrumentation using the appropriate drivers.
SpectraSuite is a user-customizable, advanced acquisition and display program that provides a real-time
interface to a variety of signal-processing functions. With SpectraSuite, 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 SpectraSuite manual for hardware requirements when using SpectraSuite (see
Product-Related Documentation).
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 from the light source 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 SpectraSuite.
7. SpectraSuite compares the sample to the reference measurement and displays processed spectral
information.
Modular Light Sources and Sampling Accessories
Ocean Optics offers a complete line of spectroscopic accessories for use with the USB4000. 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. Available
accessories include the following:
•USB-ISS-UV-VIS Integrated Sampling System for Cuvettes (200–1100 nm)
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1: Introduction
•USB-ISS-VIS Integrated Sampling System for Cuvettes (390–900 nm)
•USB-LS-450 Pulsed Blue LED Module
•USB-DT Deuterium Tungsten Light Source (200–2000 nm)
•HR4-BREAKOUT Breakout Box for controlling devices (see Breakout Box) plus USB-ADP-BB
adapter
Interface Options
The USB4000 has both USB and serial port connectors (with the use of an adapter), enabling you to
connect the spectrometer to a computer via a USB or serial port. However, you must create custom
software if using the serial port. SpectraSuite software is available if you are connecting via the USB port.
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’ USB4000 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. An adapter (USB-ADP-BB) is required to connect
the 22-pin USB port connector on the USB4000 to the 30-pin connector on the Breakout Box.
Shipment Components
The following information and documentation ships with the USB4000 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.
USB Cable (USB-CBL-1)
Use this cable to connect your spectrometer to a computer running on a Windows, Mac or Linux
operating system.
Wavelength Calibration Data Sheet
Each spectrometer is shipped with a Wavelength Calibration Data Sheet that contains information
unique to your spectrometer. SpectraSuite Operating Software 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.
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1: Introduction
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.
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.
Additional Equipment Needed
SpectraSuite Operating Software
See About SpectraSuite for more information.
Other Accessories Available
Visit us at www.OceanOptics.com for a complete list of products available for all of your spectroscopy
needs.
Fibers
Light Sources
Integrated Sampling Systems
Cuvettes
Filter Holders
Lithium Ion Battery Pack
HR4-BREAKOUT Breakout Box
See Breakout Box for more information.
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1: Introduction
6 211-00000-000-02-0908

Chapter 2
Installing the USB4000
Overview
You must install the SpectraSuite software application prior to connecting the USB4000 Spectrometer to
the computer. The SpectraSuite software installation installs the drivers required for USB4000
installation. If you do not install SpectraSuite first, the system will not properly recognize the USB4000.
If you have already connected the USB4000 to a computer running on a Windows platform prior to
installing SpectraSuite, consult Chapter 3: Troubleshooting for information on correcting a corrupt
USB4000 installation.
Note the spectrometer(s) that you have installed are listed in the Data Sources pane.
USB4000 Installation
This section contains instructions for connecting the USB4000 via both USB and serial modes.
USB Mode
Note
The USB port on a computer can power up to five USB4000 spectrometer channels.
Systems with more than five channels require a powered USB hub.
►Procedure
Follow the steps below to connect the USB4000 to a computer via the USB port:
1. Install SpectraSuite on the destination computer.
2. Locate the USB cable (USB-CBL-1) provided with the USB4000.
3. Insert the square end of the cable into the side of the USB4000.
4. Insert the rectangular end of the cable into the USB port of the computer.
If you installed SpectraSuite prior to connecting the USB4000, the SpectrSuite installs the USB4000
drivers. If the drivers do not successfully install (or if you connected the USB4000 to the computer before
installing SpectraSuite), consult Chapter 3: Troubleshooting.
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2: Installing the USB4000
If you have followed the previous steps and started SpectraSuite, 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.
Note the spectrometer(s) that you have installed are listed in the Data Sources pane.
Once you install the software and hardware, and establish your sampling system, you are ready to take
measurements.
Serial Port Mode
To use the serial port capacity of the USB4000 Spectrometer, the computer must be running a 32-bit
version of the Windows operating system.
►Procedure
Follow the steps below to connect the USB4000 to the computer via serial port:
1. Connect the serial cable adapter block to the appropriate pins of the USB4000’s 22-Pin Accessory
Connector.
2. Connect one end of the 9-pin serial cable to the adapter block on the USB4000, and then connect
the other end to a serial port on the computer.
3. Note the number of the serial port (COM Port) to which you connected the USB4000 (some
computers may not have numbered ports; handheld computers typically have only one serial
port).
4. Plug the 5 VDC external power supply into an outlet and connect it to the USB4000.
Connect Spectroscopic Accessories
To find operating instructions for USB4000-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.
External Triggering Options
You can trigger the USB4000 using a variety of External Triggering options through the 22-pin
Accessory Connector on the spectrometer. See Appendix B: External Triggering for more information.
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Chapter 3
Troubleshooting
Overview
The following sections contain information on troubleshooting issues you may encounter when using the
USB4000 Spectrometer.
USB4000 Connected to Computer Prior to
SpectraSuite Installation
Windows Operating Systems
If you connected your Ocean Optics USB4000 device to the computer prior to installing your Ocean
Optics software application 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://www.oceanoptics.com/technical/engineering/correctingdevicedriverissues.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.
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3: Troubleshooting
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. 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 USB4000 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 USB4000 Spectrometer in a Mac operating system, you should not
encounter any problems if you installed the spectrometer before the SpectraSuite software.
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3: Troubleshooting
Linux Operating Systems
For Linux operating systems, all you need to do is install the SpectraSuite 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.
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3: Troubleshooting
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Appendix A
Calibrating the Wavelength of
the USB4000
Overview
This appendix describes how to calibrate the wavelength of your spectrometer. Though each spectrometer
is calibrated before it leaves Ocean Optics, the wavelength for all spectrometers will drift slightly as a
function of time and environmental conditions. Ocean Optics recommends periodically recalibrating the
USB4000.
About Wavelength Calibration
You are going to be solving the following equation, which shows that the relationship between pixel
number and wavelength is a third-order polynomial:
λ
p= I+ C1 p+ C2 p2+ C3 p3
Where:
λ = the wavelength of pixel p
I= the wavelength of pixel 0
C1= the first coefficient (nm/pixel)
C2= the second coefficient (nm/pixel2)
C3= the third coefficient (nm/pixel3)
Rλ= the reference intensity at wavelength λ
You will be calculating the value for Iand the three Cs.
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A: Calibrating the Wavelength of the USB4000
Calibrating the Spectrometer
Preparing for Calibration
To recalibrate the wavelength of your spectrometer, you need the following components:
•A light source capable of producing spectral lines
Note
Ocean Optics’ HG-1 Mercury-Argon lamp is ideal for recalibration. If you do not have an
HG-1, you need a light source that produces several (at least 4-6) spectral lines in the
wavelength region of your spectrometer.
•An USB4000 spectrometer
•An optical fiber (for spectrometers without a built-in slit, a 50-µm fiber works best)
•A spreadsheet program (Excel or Quattro Pro, for example) or a calculator that performs third-
order linear regressions
Note
If you are using Microsoft Excel, choose Tools | Add-Ins and check AnalysisToolPak
and AnalysisTookPak-VBA.
Calibrating the Wavelength of the Spectrometer
►Procedure
Perform the steps below to calibrate the wavelength of the spectrometer:
1. Place SpectraSuite into Scope mode and take a spectrum of your light source. Adjust the
integration time (or the A/D conversion frequency) until there are several peaks on the screen that
are not off-scale.
2. Move the cursor to one of the peaks and position the cursor so that it is at the point of maximum
intensity.
3. Record the pixel number that is displayed in the status bar or legend (located beneath the graph).
Repeat this step for all of the peaks in your spectrum.
4. Use the spreadsheet program or calculator to create a table like the one shown in the following
figure. In the first column, place the exact or true wavelength of the spectral lines that you used.
In the second column of this worksheet, place the observed pixel number. In the third column,
calculate the pixel number squared, and in the fourth column, calculate the pixel number cubed.
14 211-00000-000-02-0908