Ocean Optics Flame-S User manual

Flame Miniature Spectrometer
User Manual
Amy to r
For Products: FLAME-S, FLAME-T
Document: 225-00000-000-11-201604

AMERICAS & WORLD HEADQUARTERS
Phone: [phone]
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Orders: [email protected]
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www.oceanoptics.com
Copyright © 2015 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.
Trademarks
All products and services herein are the trademarks, service marks, registered trademarks or registered service marks of their
respective owners.
Limit of Liability
Every effort has been made to make this manual as complete and as accurate as possible, but no warranty or fitness is implied. The
information provided is on an “as is” basis. Ocean Optics, Inc. shall have neither liability nor responsibility to any person or entity
with respect to any loss or damages arising from the information contained in this manual.
Ocean Optics, Inc.
830 Douglas Ave.
Dunedin, FL 34698
USA
Manufacturing & Logistics
4301 Metric Dr.
Winter Park, FL 32792
USA
Ocean Optics Asia
666 Gubei Road
Kirin Tower Suite 601B
Changning District
Shanghai
PRC, 200336
Sales & Support
Geograaf 24
6921 EW Duiven
The Netherlands
Manufacturing & Logistics
Maybachstrasse 11
73760 Ostfildern
Germany

225-00000-000-11-201604 i
Table of Contents
About This Manual.........................................................................................................v
Document Purpose and Intended Audience..............................................................................v
Document Summary..................................................................................................................v
Product-Related Documentation ...............................................................................................vi
Document Version.....................................................................................................................vi
Patent Pending Notice...................................................................................................vi
Warranty........................................................................................................................vii
ISO Certification ............................................................................................................vii
Compliance ...................................................................................................................vii
Chapter 1: Introduction .....................................................................1
Product Introduction ......................................................................................................1
Product Features.......................................................................................................................2
Typical Applications...................................................................................................................3
Product Versions .......................................................................................................................6
Chapter 2: Installation and Setup.....................................................9
What’s In the Box ..........................................................................................................9
Flame Installation ..........................................................................................................9
Software Installation ..................................................................................................................10
About OceanView......................................................................................................................11
Hardware Setup.........................................................................................................................11
Hardware Features....................................................................................................................13
Flame LEDs ..........................................................................................................................13
Change the Slit......................................................................................................................13
Accessories...................................................................................................................14
Cables and Connectors.............................................................................................................14
DB15 Connector Cable (FLAME-CBL-DD4P-DB15P)..........................................................15
PAK50 Connector Cable (FLAME-CBL-DD4P-PAK50P) .....................................................16
Breakout Box (HR4-BREAKOUT) .............................................................................................16
Interchangeable Slits.................................................................................................................16
Light Sources, Cuvette Holders and Other Accessories...........................................................17
Measurement Techniques –Typical Set-ups.................................................................17
Absorbance ...............................................................................................................................17

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ii 225-00000-000-11-201604
Common UV-Vis Applications...............................................................................................18
Reflectance & Transmission......................................................................................................18
Common UV-Vis Reflectance Applications...........................................................................18
Common UV-Vis Transmission Applications ........................................................................18
Fluorescence.............................................................................................................................19
Common Fluorescence Applications ....................................................................................19
Irradiance...................................................................................................................................20
Common Irradiance Applications..........................................................................................21
Chapter 3: Flame Operation with OceanView..................................23
Overview .......................................................................................................................23
Launch OceanView .......................................................................................................23
OceanView Main Screen...............................................................................................24
Connect the Flame in OceanView.............................................................................................25
Set Acquisition Parameters.......................................................................................................25
Quick View and Device Response ............................................................................................26
Continuous and Single Acquisitions..........................................................................................26
Save Data..................................................................................................................................27
Saved Data Panel......................................................................................................................27
Projects and Methods................................................................................................................28
Spectroscopy Application Wizards............................................................................................29
Dark and Reference Measurements .........................................................................................29
Schematic View.........................................................................................................................30
Chapter 4: Troubleshooting..............................................................31
Overview .......................................................................................................................31
Microsoft Windows Operating Systems................................................................................32
Apple Mac OSX Operating Systems.....................................................................................33
Linux Operating Systems......................................................................................................33
Chapter 5: How the Flame Spectrometer Works .............................37
Overview .......................................................................................................................37
Chapter 6: Technical Specifications.................................................45
Mechanical Diagram......................................................................................................48
Electrical Pinout.............................................................................................................49
DD4 Accessory Connector Pinout Diagram ..............................................................................49
SPI.........................................................................................................................................52
I2C.........................................................................................................................................52

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CCD Overview...............................................................................................................52
CCD Detector ............................................................................................................................52
CCD Well Depth ........................................................................................................................53
Signal Averaging .......................................................................................................................53
Internal Operation......................................................................................................................54
Pixel Definition ......................................................................................................................54
CCD Detector Reset Operation.................................................................................................55
Timing Signals...............................................................................................................55
Strobe Signals ...........................................................................................................................55
Single Strobe.........................................................................................................................55
Continuous Strobe ................................................................................................................56
Synchronous Continuous Strobe ..........................................................................................56
External Triggering........................................................................................................56
Triggering Modes.......................................................................................................................57
Normal...................................................................................................................................57
External Synchronous Trigger Mode ....................................................................................57
External Hardware Level Trigger Mode ................................................................................57
External Hardware Edge Trigger Mode ................................................................................57
Chapter 7: Calibration .......................................................................59
Overview .......................................................................................................................59
Wavelength Calibration..................................................................................................59
About Wavelength Calibration...................................................................................................59
Calibrating the Spectrometer Wavelength.................................................................................60
Preparing for Calibration.......................................................................................................60
Calibrating the Wavelength of the Spectrometer..................................................................60
Irradiance Calibrations...................................................................................................63
Chapter 8: Firmware and Advanced Communications ...................65
FLAME-S Firmware.......................................................................................................65
Hardware Description................................................................................................................65
USB Information........................................................................................................................65
Instruction Set............................................................................................................................65
Command Syntax..................................................................................................................65
USB Command Summary.........................................................................................................66
USB Command Descriptions ................................................................................................67
Flame –S Serial Port Interface Communications and Control Information ...............................81
Hardware Description............................................................................................................81
Instruction Set .......................................................................................................................82
Command Descriptions.........................................................................................................84
FLAME-T Firmware.......................................................................................................91
Hardware Description................................................................................................................91

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Spectral Memory Storage .....................................................................................................91
USB Information........................................................................................................................91
Instruction Set............................................................................................................................91
Command Syntax..................................................................................................................91
USB Command Summary.........................................................................................................92
USB Command Descriptions ................................................................................................93
Flame –T Serial Port Interface Communications and Control Information................................106
Hardware Description............................................................................................................106
Spectral Memory Storage .....................................................................................................106
Instruction Set .......................................................................................................................106
Command Summary.............................................................................................................106
Command Descriptions.........................................................................................................108
Examples ..............................................................................................................................116
Index...................................................................................................117

225-00000-000-11-201604 v
About This Manual
Document Purpose and Intended Audience
Thank you for choosing Ocean Optics! We hope that you’ll be delighted with your decision. This
document provides the users of Flame Spectrometers with instructions for setting up,
calibrating and performing experiments with their spectrometer. It also contains detailed
technical specifications and information about firmware and hardware integration. If you can’t
find what you’re looking for in this document, please do not hesitate to contact us at
[e-mail] or via www.oceanoptics.com.
Document Summary
Chapter
Description
Chapter 1: Introduction
Introduces the product features. Contains descriptive
information about the Flame Spectrometer. It also provides a
list of system requirements, typical applications, and product
versions.
Chapter 2: Installation and Setup
Provides installation instructions, including how to set up the
Flame with OceanView. Also includes package contents and
typical set-ups for different measurement techniques.
Chapter 3: Flame Operation with
OceanView
Describes how to use the Flame with OceanView software,
including how to connect, acquire, save and other basic
features.
Chapter 4: Troubleshooting
Contains recommended steps to isolate and correct common
problems.
Chapter 5: How the Flame
Spectrometer Works
Describes how the Flame operates, illustrating the various
parts and functions.
Chapter 6: Technical
Specifications
Contains technical specifications and connector pinouts for the
Flame Spectrometer.
Chapter 7: Calibration
Provides instructions for calibrating the Flame Spectrometer.
Chapter 8: Firmware and
Advanced Communications
Contains a description of firmware commands.

About This Manual
vi 225-00000-000-11-201604
Product-Related Documentation
You can access documentation for Ocean Optics products by visiting our website at
http://www.oceanoptics.com. Select Support Technical Documents, then choose the
appropriate document from the available drop-down lists.
Document for…
Document Location
OceanView software
http://oceanoptics.com/wp-content/uploads/OceanViewIO.pdf
SpectraSuite software
http://oceanoptics.com///wp-content/uploads/SpectraSuite.pdf
HR-4 Breakout Box
http://oceanoptics.com/wp-content/uploads/HR-4-Breakout-Box.pdf
External triggering
http://oceanoptics.com/wp-content/uploads/External-Triggering-
Options_Firmware3.0andAbove.pdf
Replacing the slit
http://oceanoptics.com/wp-content/uploads/INTSMA-Slit.pdf
Device driver issues
http://oceanoptics.com///wp-content/uploads/Correcting-Device-Driver-Issues.pdf
Ocean Optics offers a Glossary of spectroscopy terms to help you further understand your
state-of-the-art products and how they function, located at: http://oceanoptics.com/glossary/.
Document Version
Document Number
Version
225-00000-000-11-201503
First release
225-00000-000-11-201503b
Updates technical specifications, troubleshooting instructions, and
other minor issues.
225-00000-000-11-201504
Updates the Electrical pinout information
225-00000-000-11-201505
Adds information for the Performance Charts.
225-00000-000-11-201505
Updates the specificaitons.
225-00000-000-11-201604
Updates the specifications and triggering information
Patent Pending Notice
The Flame spectrometer is covered by Patents Pending. Any violation of Ocean Optics
intellectual property will be prosecuted.

About This Manual
225-00000-000-11-201604 vii
Warranty
Our 3-Year Warranty covers Ocean Optics miniature fiber-optic spectrometers, spectral sensors,
light sources and sampling accessories –regardless of the application –from manufacturing
defects. It also covers fibers and probes for a full 12 months:
http://oceanoptics.com/services/exclusive-3-year-warranty/.
This comprehensive warranty ensures you of the highest level of craftsmanship and reliability
for years to come. No other manufacturer offers such a solid guarantee of quality and reliability.
The Ocean Optics 3-Year Warranty applies to Ocean Optics equipment (excluding OEM
configurations) purchased on or after July 1, 2010. The warranty covers parts and labor needed
to repair manufacturing defects that occur during the warranty period. We also will cover the
costs of shipping warranty-related repairs from our customers to Ocean Optics and from us to
our customers.
ISO Certification
Ocean Optics, the industry leader in miniature photonics, has been certified for ISO 9001:2008
certification applicable to the design and manufacture of electro-optical equipment since 2009.
Compliance
WARNING
This is a Class A product. In a domestic environment this product may
cause radio interference in which case the user may be required to take
adequate measures.

About This Manual
viii 225-00000-000-11-201604
FCC COMPLIANCE
This equipment has been tested and found to comply with the limits for
a Class A digital device, pursuant to Part 15 of the FCC Rules. These
limits are designed to provide reasonable protection against harmful
interference when the equipment is operated in a commercial
environment. This equipment generates uses and can radiate radio
frequency energy and, if not installed and used in accordance with the
instruction manual, may cause harmful interference to radio
communications. Operation of this equipment in a residential area is
likely to cause harmful interference in which the user will be required
to correct the interference at his own expense.
WARNING: The authority to operate this equipment is conditioned
by the requirement that no modifications will be made to the
equipment unless the changes or modifications are expressly approved
by the manufacturer.

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Chapter 1
Introduction
Product Introduction
The Flame Spectrometer is the latest generation of Ocean Optics’ ubiquitous Czerny-Turner
design. With the release of the world’s first miniature spectrometer in 1993, Ocean Optics
helped to make spectroscopy portable, inexpensive and flexible in a way that was never before
possible. Researchers, educators and OEM manufacturers embraced the technology and have
used it in ways we never thought possible.
Flame Spectrometer
Now, fueled by our passion for solving problems, and inspired by the feedback of our customers
we have reinvented our core miniature spectrometer platform to meet the most demanding
challenges of today’s applications. Flame combines our heritage, creativity and insight in a way
that delivers the power of miniature, modular spectroscopy without compromise.
Flame is built using industry leading manufacturing techniques that help deliver high thermal
stability and low unit to unit variation without compromising the flexibility and configurability
that are the hallmark of the design. New features such as interchangeable slits, indicator LEDs
and simpler device connectors deliver more freedom and less frustration.
Whether you are an educator looking for an instrument to teach students the basic principles of
spectroscopy, a research lab looking to make a breakthrough, a scientist working in the field to
study the world around us or an engineer working to integrate a spectrometer into an OEM
system, the Flame will provide you with the performance and features you need to make your
UV-Vis spectroscopy application successful.

1: Introduction
2 225-00000-000-11-201604
Product Features
Incredibly configurable, with over 1 billion possible off-the-shelf configurations across
the wavelength range 190-1100nm. Balanced throughput, resolution and range to
optimize the spectrometer for your application.
Works seamlessly with Ocean Optics’ large range of light sources, accessories and
software
Easy to use. Plug and play via the micro-USB connection.
User-interchangeable slit allows you to vary the resolution and throughput of the
spectrometer on demand. In seconds, go from high resolution to high throughput using
the same spectrometer.
Indicator LEDs show the power and data transfer status of the spectrometer at all times.
Compact and lightweight. The “go anywhere” spectrometer for the lab and in the field.
The introduction of new, high-tech manufacturing methods has dramatically improved
optical alignment accuracy resulting in improved unit-to-unit performance and
reproducibility.
High thermal stability allows for accurate and repeatable measurements in demanding
environments.
Choice of USB or RS-232 serial communications supported by drivers and software that
make it easy to integrate into almost any system.
8 GPIO pins and the ability to provide power to external devices through the 40-pin
connector.
Key Feature
Best For…
Example Applications
User-
Interchangeable
Slits
Users who wish to vary resolution and
throughput during measurements, or
switch from absorbance to
fluorescence in minutes
Life science and other labs using a wide
variety of biological samples
Indicator LEDs
Convenient visual reference for
spectrometer operation and status
Teaching and general lab use
Thermal Stability
Applications that require repeatable
results in industrial and other
environments with varying
temperatures and conditions
LED binning and light metrology,
process monitoring
Reduced Unit to
Unit Variation
OEM applications such as uncalibrated
sensitivity and other measurement
needs where users benefit from low
variance
OEM manufacturers of analytical
instrumentation

1: Introduction
225-00000-000-11-201604 3
Key Feature
Best For…
Example Applications
Configurability
Optimizing your spectrometer for
application-specific requirements;
adjusting range, throughput and
resolution and adding features such as
filters as required
Laser characterization, low signal
fluorescence and optimizing for specific
absorbance bands
Plug & Play
Operation
Users that want the convenience of
simple, fast operation via the micro
USB connection; lets users take the
measurement to the sample
Remote sensing measurements in the
field, including air and water quality
monitoring and solar irradiance
Ease of
Integration
OEMs and developers who need to
integrate a spectrometer as part of a
system via USB or RS-232
Engineering labs, developers, OEM
manufacturers; works with LabVIEW
and other design platforms
Typical Applications
Application Area
Examples
Light Laser LED
Laser Characterization
LED Measurement
Light Metrology Measurement
Research and Education
Applied Research
Basic Research
Teaching Labs for Physics, Chemistry, Biomed
Life Sciences
Biotechnology
Medical Diagnostics
Protein and Nucleic Acid Analysis
Materials Identification
Biomaterial Analysis
Metallurgical Analysis
Polymer Analysis
Semiconductor Materials Analysis

1: Introduction
4 225-00000-000-11-201604
Application Area
Examples
Semiconductors Processing and Thin Film
Metrology
Plasma Monitoring
Process Endpoint Detection
Thickness Measurement
Farm to Table Technologies
Agricultural Measurements and Monitoring
Food and Beverage Quality Control
Food Safety
Energy Technologies
Biofuels Analysis
Mining and Exploration
Oil and Petroleum Analysis
Photovoltaic Analysis
Solar Simulators
Anti-Counterfeit
Testing and Qualification
Product Identification and Authentication
Quality Control and Process Monitoring
Defect Identification
Raw Material Inspection
Verification Testing
Environmental Monitoring
Air and Water Quality Analysis
Remote Sensing
Volcanic Research
You can find more information about applications of UV-Vis spectroscopy and the Flame at
www.oceanoptics.com.

1: Introduction
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Specifications Summary
Specification
FLAME-S
FLAME-T
SPECTROSCOPIC
Optical resolution
~0.1-10.0 nm FWHM (configuration dependent)
Signal-to-noise ratio
250:1
300:1
Integration time
10 µs–65 seconds
3.8 ms –10 seconds
Corrected linearity
>99.8%
ELECTRONIC
A/D resolution
16 bit
Power requirement
(spectrometer functions)
250 mA @ +5 VDC
Inputs/Outputs
8 x digital user programmable GPIOs
Trigger modes
4 modes
Strobe functions
Yes
Gated delay feature
Yes
Connectors
Micro-USB and JAE DD4 40-pin connector
DETECTOR
Detector
Sony ILX511B linear silicon CCD
array
Toshiba TCD1304AP linear CCD array
Detector range
190–1100 nm
Pixels
2048 pixels
3648 pixels
PHYSICAL
Dimensions
88.9 mm x 63.5 mm x 31.9 mm
Weight
265 g

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6 225-00000-000-11-201604
Product Versions
Many variants of the Flame Spectrometer exist. Ocean Optics offers both preconfigured units as
well as custom-configured units, enabling you to order a customized spectrometer optimized for
your application. You can tell which kind of spectrometer you have by looking at the product
code, located on the bottom of your spectrometer.
You can find more information about the various components and possible configuration options
in Chapter 5: How the Flame Spectrometer Works.
Product Code Taxonomy
Spectrometer Family?
Detector Type?
Preconfigured or Custom?
FLAME-
S- (Sony ILX511B)
UV-VIS, VIS-NIR, XR
CUSTOM
T- (Toshiba TCD1304AP)
UV-VIS, VIS-NIR, XR
CUSTOM
F- (Hamamatsu S11639)
UV-VIS, VIS-NIR, XR
CUSTOM
Preconfigured Models
FLAME-S Preconfigured Models (Sony ILX511B Detector)
Model
Range
(nm)
Std
Slit
(μm)
Resolution
std slit
(nm)
Grating
#
Mirror
Type
Filters &
Detector
Options*
Lens
General
Purpose
FLAME-S-UV-VIS
200-
850
25
~1.5
1
Al
OSF
200-850
no
FLAME-S-UV-VIS-ES
L2
FLAME-S-VIS-NIR
350-
1000
25
~1.5
3
Al
OSF
350-1000
no
FLAME-S-VIS-NIR-ES
L2
Extended
Range
FLAME-S-XR1
200-
1025
25
~2
31
Al
OSF
200-1100
no
FLAME-S-XR1-ES
L2
Irradiance
FLAME-S-RAD
360-
1000
50
~3
2
Al
UV
Window
no

1: Introduction
225-00000-000-11-201604 7
FLAME-T Preconfigured Models (Toshiba TCD1304TP Detector)
Model
Range
(nm)
Std
Slit
(μm)
Resolution
std slit
(nm)
Grating
#
Mirror
Type
Filters &
Detector
Options*
Lens
General
Purpose
FLAME-T-UV-VIS
200-
850
25
~1.5
1
Al
OSF
200-850
no
FLAME-T-UV-VIS-ES
L2
FLAME-T-VIS-NIR
350-
1000
25
~1.5
3
Al
OSF
350-1000
no
FLAME-T-VIS-NIR-ES
L2
Extended
Range
FLAME-T-XR1
200-
1025
25
~2
31
Al
OSF
200-1100
no
FLAME-T-XR1-ES
L2
Irradiance
FLAME-T-RAD
360-
1000
50
~3
2
Al
UV
Window
no
For more information and specifications on preconfigured models, see www.oceanoptics.com.

1: Introduction
8 225-00000-000-11-201604

225-00000-000-11-201604 9
Chapter 2
Installation and Setup
What’s In the Box
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.
Flame Spectrometer
Your Flame spectrometer arrives pre-calibrated and ready to plug and play.
Micro USB Cable
Use this cable (CBL-MICROTOA-USB) 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. OceanView reads this calibration data from
your spectrometer when it interfaces to a computer via the USB port.
Note
Please save the Wavelength Calibration Data Sheet for future reference.
Flame Installation
The following procedure provides general instructions for getting your new Flame spectrometer
up and running.

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10 225-00000-000-11-201604
Caution
Be sure to install the software BEFORE connecting the spectrometer to your PC.
The software installs the drivers required for spectrometer installation. If you do
not install the software first, the system will not properly recognize the
spectrometer.
If you have already connected the Flame to a computer running on a Windows
platform prior to installing the operating software, consult Chapter 4:
Troubleshooting for information on correcting a corrupt Flame installation.
►Procedure
Use the following procedure to get your system up and running quickly. See Hardware
Setup for more detailed information.
1. Install your spectroscopy operating software by following the installation wizard
prompts. See Software Installation for more in-depth information.
2. Locate the micro USB cable provided with the spectrometer. Connect the spectrometer
to the USB port on your computer using this cable.
3. Take measurements. Refer to your spectrometer operating software manual for
information on the software user interface.
Software Installation
Use OceanView version 1.5 and above for Flame. Flame can be used with SpectraSuite, but will
appear as a USB2000+ Spectrometer in the software. You can use OceanView or SpectraSuite
on the following operating systems.
Caution
Be sure that you download the correct software package for your computer
version (32 or 64-bit). See the Frequently Asked Questions in Chapter 4:
Troubleshooting for more information on determining your computer version.