Ocean Optics CHEM2000 User Manual

OOICHEM Software
User's Guide

Document Number 105-00000-CHM-02-0405

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Offices: Ocean Optics, Inc.

830 Douglas Ave., Dunedin, FL, USA 34698

Phone [phone]
Fax [phone]

8:30 a.m.–6 p.m. EST

Ocean Optics B.V. (Europe)

Nieuwgraaf 108 G, 6921 RK DUIVEN, The Netherlands

Phone [phone]
Fax [phone]

E-mail: [e-mail] (General sales inquiries)

[e-mail] (European sales inquiries)
[e-mail] (Questions about orders)
[e-mail] (Technical support)

Copyright © 2000-2005 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 ......................................................................................................... iii

Document Purpose and Intended Audience ............................................................................. iii

Document Summary.................................................................................................................. iii

Product-Related Documentation ............................................................................................... iii

Upgrades......................................................................................................................... iv

Chapter 1: ......................................................................1Introduction

Company History............................................................................................................. 1

OOIChem Spectrometer Operating Software.................................................................. 1

OOIBase32 Spectrometer Operating Software ............................................................... 2

Packing List ..................................................................................................................... 2

Quick Start....................................................................................................................... 2

Step 1: Install OOIChem Software ............................................................................................ 2

Step 2: Configure OOIChem Software...................................................................................... 3

Step 3: Receive Data................................................................................................................. 4

Chapter 2: Using OOIChem Software................................................5

Display Functions ............................................................................................................ 6

Spectrometer Channel Selection............................................................................................... 6

Mode of Operation..................................................................................................................... 6

Cursor Function Bar ..................................................................................................................8

Text Box..................................................................................................................................... 9

Acquisition Parameters ............................................................................................................. 9

Reference Scan......................................................................................................................... 9

Dark Scan..................................................................................................................................10

Subtract Dark............................................................................................................................. 10

Acquire Data Modes.................................................................................................................. 10

Scaling the Graph...................................................................................................................... 11

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Table of Contents

File Menu Functions ........................................................................................................ 11

Save Spectral Values ................................................................................................................ 11

Save Kinetics Values................................................................................................................. 11

Open Spectrum Overlay............................................................................................................ 11

Open Kinetics Values ................................................................................................................ 11

Printer Setup.............................................................................................................................. 11

Print Spectra and Kinetics ......................................................................................................... 11

Exit............................................................................................................................................. 12

Edit Menu Functions........................................................................................................ 12

Clear Spectrum Overlays .......................................................................................................... 12

Clear Kinetics Values ................................................................................................................12

Autoscale X ............................................................................................................................... 12

Autoscale Y ............................................................................................................................... 12

Show Kinetics Values ................................................................................................................ 12

Show Legends........................................................................................................................... 13

Spectrometer Menu Functions ........................................................................................ 13

Scan........................................................................................................................................... 13

Select Concentration Wavelength ............................................................................................. 13

Calculate Calibration Curve....................................................................................................... 13

Enable Strobe............................................................................................................................14

Kinetics Configuration ............................................................................................................... 15

CHAPTER 3: Experiment Tutorial......................................................17

Overview.......................................................................................................................... 17

Absorbance Experiments ................................................................................................ 17

Transmission Experiments .............................................................................................. 18

Relative Irradiance Experiments...................................................................................... 20

Concentration Experiments ............................................................................................. 21

Kinetics Experiments....................................................................................................... 24

Index.....................................................................................................27

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About This Manual

Document Purpose and Intended Audience

This document provides information for installing and operating OOIChem software with the Maxwell
system.

Document Summary

Chapter Description

Chapter 1: Introduction Contains descriptive information about OOIChem software

and a quick start procedure.

Chapter 2: Using OOIChem

Software

Chapter 3: Experiment Tutorial Contains procedures for taking measurements in Absorbance,

Provides installation and configuration instructions for
OOIChem software.

Transmission, Relative Irradiance, Concentration, and Kinetics
experiments.

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.

• Instructions for the OOIPS2000 Operating Software for the handheld PC are located at:

http://www.oceanoptics.com/products/ooips2000.asp.

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.

OOIChem software will be updated and improved continuously. To obtain free upgrades, visit out web
site at www.oceanoptics.com/products/Software.asp. To download free upgrades, you will need the
following password: hG59mP236I

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Chapter 1

Introduction

Company History

Ocean Optics miniature fiber optic spectrometers and accessories have revolutionized the analytical
instrumentation market by dramatically reducing the size and cost of optical sensing systems. More than
10,000 Ocean Optics spectrometers have been sold worldwide -- striking evidence of the far-reaching
impact of low-cost, miniature components for fiber optic spectroscopy. Diverse fields such as research
and development, industrial process control, medical diagnostics, environmental monitoring and of
course, education have benefited from access to Ocean Optics technology.

In fact, Ocean Optics has its roots in education. It formed in 1989 when Florida university researchers
developed a fiber optic pH sensor as part of an instrument designed to study the role of the oceans in
global warming. The researchers soon formed Ocean Optics, Inc. and their ingenious work earned a Small
Business Innovation Research grant from the U.S. Department of Energy. While designing the pH­monitoring instrument, the researchers wanted to incorporate with their sensor a spectrometer small
enough to fit onto a buoy and were surprised to discover none existed. So, they built their own.

In 1992, the founders of Ocean Optics filled a substantial need in the research community and changed
the science of spectroscopy forever by introducing a breakthrough technology: the S1000 Miniature Fiber
Optic Spectrometer, nearly a thousand times smaller and ten times less expensive than previous systems.
Due to this dramatic reduction in size and cost of optical sensing systems, applications once deemed too
costly or impractical using conventional spectrometers were now feasible.

OOIChem Spectrometer Operating Software

OOIChem is a basic acquisition and display software that provides a real-time interface to a variety of
spectral-processing functions. OOIChem allows users to perform basic spectroscopic measurements such
as absorbance, transmission, relative irradiance, and concentration. OOIChem operates with Windows
95/98/Me/XP and Windows NT/2000. Visit our website at

www.OceanOptics.com/products/software.asp to download free OOIChem upgrades.

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1: Introduction

OOIBase32 Spectrometer Operating Software

OOIBase32 is our standard spectrometer operating software that we provide free of charge to all
customers. While OOIChem is a basic acquisition and display program, OOIBase32 is user-customizable
and a much more advanced acquisition and display program. With OOIBase32 you have the ability to
control all system parameters; collect data from up to 8 spectrometer channels simultaneously and display
the results in a single spectral window; perform reference monitoring and time acquisition experiments;
and use numerous editing, viewing and spectral processing functions. At any time, users can receive free
OOIBase32 updates from our web site at

Ocean Optics also offers a complete line of light sources, sampling holders, in-line filter holders, flow
cells, and other sampling devices; an extensive line of optical fibers and probes; and collimating lenses,
attenuators, diffuse reflectance standards and integrating spheres. All components have SMA terminations
so that changing the sampling system is as easy as unscrewing a connector and adding a new component
or accessory.

This modular approach -- components are easily mixed and matched -- offers remarkable applications
flexibility. Users pick and choose from hundreds of products to create distinctive systems for an almost
endless variety of optical-sensing applications

www.OceanOptics.com/products/software.asp.

Packing List

A packing list comes with each order. It is located inside a plastic bag attached to the outside of the
shipment box. The invoice is mailed separately. The items listed on your packing slip include all of the
components in your order. However, some items on your packing list are actually items installed into
your spectrometer, such as the grating and slit. The packing list also includes important information such
as the shipping address, billing address, and components on back order.

Quick Start

Step 1: Install OOIChem Software

► Procedure

Before installing OOIChem, make sure that no other applications are running.

1. Insert the software CD into your floppy drive. Execute Setup.exe.

2. At the Welcome dialog box, click Next.

3. At the Destination Location dialog box, select a destination directory. Click Next.

4. At the Backup Replaced Files dialog box, select either Yes or No. Selecting Yes is
recommended and enables you to choose a destination directory. Click Next.

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1: Introduction

5. Select a Program Manager Group. Click Next. At the Start Installation dialog box, click
Next.

6. At the Installation Complete dialog box, choose Finish.

7. When prompted to do so, restart your computer when the installation is complete.

Step 2: Configure OOIChem Software

After you restart your computer, navigate to the OOIChem icon and select it. The first time you run
OOIChem after installation, you must follow several prompts to configure your system before taking
measurements.

Hardware Configuration

The Configure Hardware dialog box opens when you first run OOIChem. The parameters in this dialog
box are usually set only once – when OOIChem is first installed and the software first opens.

Procedure

►

1. Under Spectrometer Type, choose S4000.

2. Under A/D Converter Type, choose HR4000.

3. In the USB Serial Number field, select the serial number of the HR4000 spectrometer in
your Maxwell system from the drop-down list.

4. For your setup, only these parameters apply to your system. Click OK. You can always
change these settings once OOIChem is fully operational by selecting Spectrometer |
Hardware Configuration.

Spectrometer Configuration

At this point, OOIChem should be acquiring data from your spectrometer. There should be a dynamic
trace responding to light near the bottom of the displayed graph. Now that OOIChem is running, you need
to configure your system. Select Spectrometer | Spectrometer Configuration from the menu.

• Coefficients. Loaded automatically from the spectrometer.

• Trigger mode. Select No External Trigger, unless you have wired an external triggering device

to the spectrometer for synchronizing data with an external event.

• Graph and chart display mode. Choose Spectrum Only to only view live spectra from one
spectrometer channel. Choose Spectrum & Kinetics to view both real-time live spectra in the top
half of the graph and to view a chart displaying your kinetics experiment in the bottom half of the
graph.

• Flash Delay. This function is for use with a strobe light source. The Maxwell system does not
come with a strobe light source.

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1: Introduction

• Color Temperature. Enter the color temperature of your reference light source used in relative
irradiance measurements.

Acquisition Parameters

Set data acquisition parameters by choosing an integration period and selecting averaging and boxcar
smoothing values.

Text Box

Enter the operator name, or any other identifying text here. This text appears in your data files. You can
edit this text at any time.

Step 3: Receive Data

Run OOIChem in Scope Mode and take a reference spectrum and a dark spectrum (see Experiment

Tutorial

sample measurements.

for details). Choose the absorbance, transmission, or relative irradiance mode to take your

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Chapter 2

Using OOIChem Software

OOIChem software provides users with five different modes of operation: Scope, Absorbance,
Transmission, Relative Irradiance, and Concentration. In addition, the software allows users to control
data acquisition features such as integration period, averaging, and boxcar smoothing -- directly from the
spectral graph display. Users can acquire data by taking manual single scans or by running continuous
scans, and add into the spectral window as many as 8 previously saved overlay spectra.

Users can also perform kinetics
experiments, which allows users to
monitor and report up to 4 single
wavelengths or up to 2 calculated
values from a combination of
wavelengths – for example, an
absorbance value of 400 minus an
absorbance value of 700. A kinetics
chart displays the time series. When
the experiment is complete, the data
can be exported to an ASCII file for
additional processing.

Another exciting feature of
OOIChem is that users can control
the parameters for all system
functions such as acquiring data,
designing the graph display, and
configuring the cursor. Additional
features of OOIChem include the
ability to save data as ASCII files
and to store and retrieve sample
spectra.

If you find that you need more
advanced spectrometer operating
software, we have included, free of charge, OOIBase32, a sophisticated, 32-bit, user-customizable
advanced acquisition program. See the included OOIBase32 manual for a list of functions and features.

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