Ocean Insight NanoQuest User manual

NanoQuest
MEMS-Based FT-IR Sensor
Installation and Operation Manual
For Product: NANOQ-2.5

Table of Contents
About This Manual .................................................... ii
Cautions...................................................................................................... ii
Warranty..................................................................................................... iii
Certifications and Compliance................................................................. iii
Product Overview ...................................................... 5
NanoQuest Technology .............................................................................5
Working principle........................................................................................5
Measurement Steps...................................................................................7
Interfaces....................................................................................................8
System Requirements................................................................................8
Environmental Conditions .........................................................................9
Warm-up......................................................................................................9
Mechanical Drawing.................................................................................10
Performance Optimization ....................................... 11
Measurement Parameters.......................................................................11
Advanced Settings ...................................................................................12
NanoQuest Software ................................................15
Installation ................................................................................................15
Description of the GUI..............................................................................16
Recommended Setups .............................................19
Transmission/Absorbance Measurements ...........................................19
Diffuse Reflection Measurements ..........................................................21
Advanced Settings ...................................................................................24
Troubleshooting ......................................................30
System Performance ...............................................................................30
Software....................................................................................................31
References ..............................................................32
Specifications..........................................................33
Copyright © 2020 Ocean Insight
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 Insight.
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 Insight, 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 Insight 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

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About This Manual
Cautions
Caution: Do not let contaminants get into the bench. Keep the protective cap on the slit aperture when not connected to an
accessory, probe or fiber.
Caution: Do not immerse the device in any fluid, place fluids on top of or attempt to clean with liquid detergents or cleaning
agents. This may cause an electrical hazard. Do not use if accidental wetting occurs.
Caution: Consult local codes and ordinances for proper disposal of equipment and other consumable goods.
Caution: Do not use if device is dropped and/or damaged. Have an authorized service representative check the device before
using again.
Caution: Be sure to install any software BEFORE connecting the spectrometer to your PC or host system. The software installs
the drivers required for spectrometer installation. If you do not install the software first, the system may not properly
recognize the spectrometer.
Caution: The user of this spectrometer shall have the sole responsibility for any malfunction which results from improper use,
faulty maintenance, improper repair, damage or alteration by anyone other than Ocean Insight or their authorized
service personnel.

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Caution: Do not apply excessive vibration or shock to the device. Although vibration rejection mode is supported, excessive
vibrations may damage the unit.
Caution: Do not use organic solvents in cleaning. Wipe with a dry and clean tissue.
Caution: When attempting to connect the fiber, do not apply excessive force to the optical connector. Excessive force may
damage the connector and will affect measurement results.
Warranty
For the most current warranty information, please visit OceanInsight.com.
Certifications and Compliance
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.
Warning

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This device has been tested and complies with the following standards:
EMC Directive 2014/30/EU
EN 61326-1:2013
ISO Certification
Ocean Insight, the industry leader in miniature photonics, has been certified for ISO 9001:2015 certification applicable to the
design and manufacture of electro-optical equipment.
The WEEE symbol on the product indicates that the product must not be disposed of with normal household waste. Instead,
such marked waste equipment must be disposed of by arranging to return to a designated collection point for the recycling of
waste electrical and electronic equipment. Separating and recycling this waste equipment at the time of disposal will help to
conserve natural resources and ensure that the equipment is recycled in a manner that protects human health and the
environment
WEEE Compliance

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Product Overview
NanoQuest is a spectral sensing module whose working principle is based on the standard Fourier Transform Infrared (FT-IR)
spectroscopy technique commonly used in conventional spectrometers. The core engine of FT-IR spectrometers is a Michelson
interferometer. In NanoQuest, the whole Michelson interferometer is integrated on a single silicon chip.
NanoQuest Technology
NanoQuest determines the spectral content of the input light in the NIR wavelength range from 1350 –2500 nm (7400 –4000 cm-1).
The input light is either transmitted through a sample material or reflected from it using external sampling accessories. Post-analysis
of the output spectra delivers the same functionality as standard benchtop FT-IR spectrometers: quantification, qualification, or
identification of materials.
Working principle
NOTE
Post-analysis of the measured spectra can be done using an advanced analysis software like Analyze IQ Chemistry Software or
by working with our Ocean Intelligence Machine Learning Software Team. Post-analysis software is not provided with the
NanoQuest package.

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Fourier Transform Infrared (FT-IR) Spectroscopy
The core of any FT-IR spectrometer is a two-beam optical interferometer named the Michelson interferometer. The basic block
diagram of a Michelson interferometer’s discrete components is shown below.
A beamsplitter splits the incident beam into two paths: one of the beams is reflected by a moving mirror, and the other is used as a
reference when reflected by a fixed mirror. The moving mirror controls the Optical Path Difference (OPD) between the two reflected
beams, which interfere to produce a pattern that corresponds to the spectral content of the input light. The latter is captured by the
single photodetector generating an interferogram. The spectrum of the input light is directly generated by applying a Fourier
Transform to the interferogram.

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Measurement Steps
The spectrum (S) of a sample is given by the ratio of the spectrum of the beam transmitted or reflected from the sample (I)to the
spectrum of the beam at the front face of the sample (Io) over the spectral range of interest
󰇛󰇜󰇛󰇜

To measure the sample’s spectrum (S), the background spectrum should be measured (Io)(background measurement), as well as the
light transmitted or reflected from the sample (I)(sample measurement). The NanoQuest software enables the acquisition of the
background measurement and stores it to be used as a reference spectrum in further sample measurements.
It is recommended that the background spectrum be measured as frequently as possible, and ideally before each sample
measurement. This ensures the most accurate results from the device.
Transmission Measurements
The background measurement Iois obtained by measuring the spectrum of the transmitted beam without placing any material in the
light path (e.g. an empty cuvette), under the same conditions at which the measurement of the sample will be conducted. Once the
background measurement has been made, the sample measurement Iis made by placing the sample in the sample holder.
Reflection Measurements
The background measurement (Io) is obtained by measuring the spectrum of the reflected beam from an appropriate reflection
reference standard with nearly flat spectral response across the spectral range of interest under the same conditions at which the
measurement of the sample will be conducted. The sample spectrum (I)is then obtained by measuring the beam reflected from the
sample.

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Interfaces
•Optical interface: light can be coupled to NanoQuest via an optical fiber with standard FC-PC connector
•Data and power interface: communication with NanoQuest is established through USB 2.0 interface. NanoQuest has a Mini-B
receptacle USB connector for the interface with other devices. The USB connector is also used to supply NanoQuest with its
required power for operation.
System Requirements
Parameter
Requirements
Operating systems
Microsoft Windows 7 (both x86 and x64)
Microsoft Windows 8 (both x86 and x64)
Microsoft Windows 10 (both x86 and x64)
Ubuntu 12.04 (both x86 and x64)
Debian 32 bit (ARM architecture)
CPU Specs
Processor: Core 2 Duo, 2 GHz or higher
RAM: 2 GB or higher

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Environmental Conditions
The NanoQuest should be kept in environments that maintain the temperature conditions listed below.
Parameter
Value
Units
Operating temperature
-5 –+40
o C
Storage temperature
- 20 - +85
o C
Warm-up
Upon connecting the NanoQuest to the PC via USB, the system takes 15 to 20 minutes to become thermally stabilized. The module is
operational during warm-up. However, repetitive measurements of the same sample while the unit is warming up may lead to slightly
different spectra. If measurements are to be taken during warm-up time, it is recommended to make a background measurement
right before each sample measurement.

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Mechanical Drawing

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Performance Optimization
The performance of spectral sensors is commonly characterized by different parameters that are usually interdependent. The
software enables optimization of performance by allowing a set of values for some parameters to be changed and certain hardware
settings to be adjusted.
This chapter describes the effect of the different parameters on the Signal to Noise Ratio (SNR), as well as some advanced settings
that can be used to optimize the overall performance of the system.
Measurement Parameters
NanoQuest is based on FT-IR, so the dependencies between the different performance parameters are governed by the same
relationships as conventional FT-IR systems. Scan time and resolution are two parameters than can be set with the software to
optimize the performance of the system depending on target requirements. In this section, we summarize the main elements that
need to be considered when adjusting these two parameters.
Scan Time
Scan time is defined as the time taken by the interferometer to scan the input light signal. Higher scan time implies higher number of
scan cycles to be averaged, hence higher SNR.
The scan time can be adjusted by setting a value higher than 10 ms.
The Signal to Noise Ratio (SNR) of the system is directly proportional to the square root of the scan time (ts) [  ] [1].

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Resolution
There are several definitions for resolution. In FT-IR, nominal resolution is often defined as the reciprocal of the maximum OPD.
Practically, resolution is defined as the minimum spacing between two consecutive wavelength (Δλ) / wavenumber (Δν) points that
can be fully resolved. Two neighboring spectral features of equal height and width are said to be resolved if there is a dip of at least
20% between the two maxima.
The Signal to Noise Ratio (SNR) of the system is directly proportional to resolution (Δν) [  ] [1].
Advanced Settings
Gain Settings
The NanoQuest module has an internal Analog to Digital Converter (ADC) that converts the interferogram data (analog current
detected by the photodetector) to a digital signal.
NanoQuest has two main gain settings:
•Transmission: optimum gain setting corresponding to the coupled power in a typical transmission setup.
•Reflection: optimum gain setting corresponding to the coupled power equivalent of 1/32 of the coupled power in a typical
transmission setup.
The conversion ratio can be adjusted to:
1. Avoid saturation of the amplifiers: saturation leads to signal clipping and attenuation.
2. Enhance the SNR: using the Transmission gain option for diffuse Reflection measurements degrades the optimum SNR by a
factor between 3-5 depending on the optical power coupled from the reflection setup.
Apodization
The interferogram can be multiplied by one of several different apodization functions to make a gradual decay to zero values at both
sides of the interferogram, and hence to smooth the spectrum.

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The process of apodization affects both the resolution and the noise level of FT-IR spectra:
•Resolution: the information near the interferogram’s centerburst determines the shape of the single-beam spectrum, and this
low-resolution spectrum is largely unchanged when the interferogram is multiplied by an apodization function. Conversely, the
sinusoids of narrow spectral features take much longer to decay and are therefore far more attenuated when the spectral
data are apodized, leading to degradation of resolution.
•Noise: lowspatial-frequency noise and very broad bands are also largely unaffected by apodization. Highspatial-frequency
noise is attenuated on apodization. On the average, the root mean square (rms) noise on the spectrum is decreased on
apodization and the SNR increases.
The specific apodization function that should be used for a certain application is chosen by experimentation [1].
Zero Padding
Spectra being measured on FT-IR spectrometers consist of intensity values at equally spaced intervals. The discrete nature of the
data makes it highly unlikely that the maximum absorption of any band will correspond exactly with one of these data points. In
addition, the slope of the spectrum can appear to change markedly from one point to the next. To eliminate these problems, some
form of interpolation or alternative data processing is necessary. One of the most useful of these is zero padding (also known as
Zero Filling).
Considering complex Fourier transformation of an interferogram that consists of N data points, the real and imaginary spectra each
contain N/2 data points. Increasing the number of points by N (adding N/2 zeros to each end of the double-sided interferogram)
increases the number of data points per resolution element to two. This process may be continued until the data point spacing in the
calculated spectrum is so small that no information is lost visually [2].
Available options of zero padding are: 0,1,3,7 corresponding to
•0: No zero padding is applied
•1: N zeros are added to the interferogram
•3: 3N zeros are added to the interferogram
•7: 7N zeros are added to the interferogram

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Wavenumber Correction
The wavelength/wavenumber axis of the measured spectrum can drift with aging. Two correction techniques are available:
1. Self-Correction: system is auto-corrected with a smart built-in algorithm. The auto-correction is done after measuring the
background reference white light -- i.e., no sample in the light path.
2. Correction using Reference Material: the user can use a standard reference material to correct wavenumber drifts in
NanoQuest. The user enters the reference absorption peak positions that correspond to the selected resolution (8 nm or 16
nm at wavelength 1,550 nm).
Wavelength/wavenumber correction should be applied regularly to maintain NanoQuest performance. Depending on the
environment, wavelength/wavenumber correction can be performed every day, week, month or year. Details on how to perform
wavenumber correction using the NanoQuest software is explained in the Advanced Settings section.

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NanoQuest Software
NanoQuest Software enables plotting, saving, and loading measured spectra, as well as setting acquisition and data processing
parameters for the NanoQuest.
Installation
1. Run the installation wizard.
2. The NanoQuest software is only available in English.
3. When the welcome screen appears, make sure that all other applications are closed, then click Next.
4. After the terms and conditions are read, click Next to proceed.
5. Browse to the installation directory then click Next.
6. Select the Start Menu folder in which the NanoQuest software shortcuts shall be created then click Next.
7. Check preferences to Create a desktop icon then click Next.
8. When the wizard is ready to install, click Install to proceed.
9. The installation wizard will detect if the appropriate JRE Version is already installed on the computer:
a. If it exists, installation wizard will proceed to Step 10.
b. If it does not already exist, a JRE installer will be launched automatically.
10. The installation wizard will start preparation of the installation process of the NanoQuest hardware drivers. A pop-up screen
will give guidance for the remaining steps required to finish the installation procedure. This may require user permission for
Windows Security. If the warning message “Windows can’t verify the publisher of this driver software” appears, select the
option “Install this driver software anyway” on Windows Vista, Windows 7 or Windows 10. Select “Yes” on Windows XP to
proceed.
11. The software installation is complete.

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Description of the GUI
1. Tabs selection:
•“Spectrum” tab: This tab is used to set acquisition parameters and display spectral data.
•“Interferogram & PSD” tab: This tab displays the measured interferogram and its
corresponding Power Spectral Density (PSD)
2. Measurements Parameters area:
•Scan Time: User can specify the Scan Time for the measurements.
•Resolution: User can select between different pre-set resolution values.
•Optical Gain Settings: User can select the optical gain for different measurement types
(Absorbance/Transmission or Reflection). The X button allows deleting a gain setting
selected in the dropdown menu.
•Run Mode:
i. Single: Display the data for a single measurement at the specified scan time.
ii. Cont.: Take continuous consecutive measurements at the specified scan time.
•Command buttons:
i. Spectrum tab:
1. Background: Initiate the background measurement. No material should be present in the light path
during this measurement. For the best measurement results, background measurements should be
taken as frequently as possible. A new background measurement must be taken when any
measurement parameter is changed (e.g., Resolution, Optical Gain Settings, etc.).
2. Run: Initiates the spectrum measurement for the sample placed in the light path. The background-
corrected spectrum is automatically calculated and displayed.
3. Stop: Cancels the current measurement in progress.

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ii. Interferogram and PSD tab:
1. Run: Initiates measurement of the interferogram and the corresponding
PSD.
2. Stop: Cancels the current measurement in progress.
3. Plots Graph Manipulation area:
•Save: Save all data sets (X- and Y-axis values of plotted graphs) shown in the display area.
Files collected in the Spectrum tab will be saved with *.Spectrum extension. Data collected
in the Interferogram & PSD tab will be saved with *.InterPSD and *.Interferogram
extensions. This command allows the user to select a folder where all data sets are saved
and specify a prefix which will be used with the measurement number, shown in the
legend below the display area, to save the file.
•Load: User can load previously saved data in *.Spectrum, *.InterPSD or *.Interferogram
formats.
•Clear: Clears all displayed data sets in the display area.
•Capture: Useful only in continuous run mode. Keeps the last plotted graph so it is not
replaced by the next measurement.
•Auto Save check box: When enabled, automatically saves measured data.
i. Single run mode: Saves each plotted graph.
ii. Continuous run mode: Saves only the captured and the last plotted graphs.
4. Data Display area:
•Spectrum tab: Select units for the Y-axis of displayed data (either absorbance or percentage
transmittance/reflectance). Select units for the X-axis of displayed data (either nm or cm-1).
•Interferogram & PSD tab: Select units for the X-axis of displayed data (either nm or cm-1).
5. Advanced Settings area:
Advanced settings are accessed by clicking Spectrometer | Advanced/FFT Settings from the top toolbar. Advanced Settings
and FFT Settings menus will display below the Spectrum window.

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•Add Optical Gain Settings: Opens a wizard that enables the
creation of new gain settings optimized for the optical power
coupled into the NanoQuest. The gain settings are stored on
the PC on which the measurement is being performed. The
gain settings will not be transported when the module is used
on another host unless the settings are burned into the
NanoQuest.
•Wavelength/Wavenumber Correction: Opens a wizard that allows correction of wavelength/wavenumber errors
caused by long term drift.
•Burn Settings: Opens a wizard that enables burning the advanced setting changes to the NanoQuest.
•Restore Default Settings: Reloads the default settings with which the module was delivered.
6. FFT Settings:
•Apodization: Select one of several filter techniques to apply to the displayed spectrum.
•Zero Padding: Select one of the zero padding options to smooth the displayed spectrum.
•Update Results: Apply the selected FFT Settings to the displayed spectrum.