focal point review

ROHIT BHARGAVA
DEPARTMENTS OF BIOENGINEERING
MECHANICAL SCIENCE AND ENGINEERING
ELECTRICAL AND COMPUTER ENGINEERING
BECKMAN INSTITUTE FOR ADVANCED SCIENCE AND TECHNOLOGY
UNIVERSITY OF ILLINOIS CANCER CENTER
UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
URBANA, IL 61801

Infrared Spectroscopic Imaging:

The Next Generation
Infrared (IR) spectroscopic imaging seemingly
matured as a technology in the mid-2000s, with
commercially successful instrumentation and
reports in numerous applications. Recent de-
velopments, however, have transformed our
understanding of the recorded data, provided
capability for new instrumentation, and greatly
enhanced the ability to extract more useful
information in less time. These developments
are summarized here in three broad areas—
data recording, interpretation of recorded data,
and information extraction—and their critical
review is employed to project emerging trends.
Overall, the convergence of selected compo-
nents from hardware, theory, algorithms, and
sight, which will present new opportunities for
the applied spectroscopist.
Index Headings: Infrared spectroscopic imag-
ing; Fourier transform infrared spectroscopy;
FT-IR imaging; Infrared microspectroscopy;
Mapping; Focal plane arrays; FPA; Discrete
frequency IR imaging; Quantum cascade la-
sers; QCL; Synchrotron; Chemical imaging;
Scalar wave theory; Electromagnetic theory;
Compressive sensing; Reconstruction; Noise
reduction.
INTRODUCTION
propagating light such that data can be
recorded and interpreted and informa-
tion extracted from the targeted area.
These three areas of spectrometry—data
recording, interpretation, and informa-
tion retrieval—form the core of the
science of IR microspectroscopy. Appli-
cations to particular problems, using a
combination of specific techniques in
the three areas, are covered in other
recent reviews.10–16 Here, we focus on
the science of IR microspectrometry,
especially on recent developments that
can potentially transform imaging spec-

applications is one trend. Instead of similar,
general-purpose instrumentation, another
trend is likely to be diverse and application-
targeted designs of instrumentation driven by
emerging component technologies. The recent
renaissance in both fundamental science and
instrumentation will likely spur investigations
at the confluence of conventional spectroscopic
analyses and optical physics for improved data
interpretation. While chemometrics has domi-
nated data processing, a trend will likely lie in
the development of signal processing algo-
rithms to optimally extract spectral and spatial
information prior to conventional chemometric
analyses. Finally, the sum of these recent
advances is likely to provide unprecedented
capability in measurement and scientific in-
Received 24 July 2012; accepted 25 July 2012.
E-mail: rxb@illinois.edu.
DOI: 10.1366/12-06801
T
he combination of infrared (IR)
vibrational spectroscopy and op-
tical microscopy has been the
subject of many studies and the analyt-
ical approach has been employed in
thousands of applications for many
decades. The recent evolution of the
field can be found in periodic reviews1–3
and compilations.4–7 While there are
approaches in which optical microscopy
can provide structural detail and point
measurements of spectra provide chem-
ical information,8 the two measurements
are commonly performed today such
that IR absorption provides the contrast
mechanism for the entire field of view of
the optical image.9 The underlying
concept for obtaining spatially resolved
spectroscopic data is to localize the
interacting volume of a sample with
troscopy in the future.
A segmentation of IR microscopy
systems for the purposes of study can
be along the length scale of measure-
ments. The spectral bandwidth of most
mid-IR measurements (2–14 lm) pro-
vides a convenient reference length
scale. Macroscopic or bulk measure-
ments can be understood to be from
configurations in which the spatial
localization is approximately ten-fold
larger than the longest wavelength of
this bandpass (.100 lm), microscopic
measurements from configurations in
which the spatial localization is on the
order of the wavelengths of interest (~1
lm), and nanoscopic measurements
from configurations in which the local-
ization is ten-fold smaller than the
shortest wavelength (,0.1 lm). The

APPLIED SPECTROSCOPY 1091

focal point review
measurement of bulk samples is now a combines an interferometer, IR micro- aging attempts,35 and the use of filter-
mature topic that is well-described in scope, and array detector (Fig. 1).33 Data based imaging.36,37 From the initial,
classic texts.17 Nanoscale measurements is recorded by spectral multiplexing in relatively crude, step-scan systems with
are less common than those in other time using the interferometer and simul- attendant issues of sub-optimal data
spectral regions 18 though they are taneously by a large number of detectors recording,38,39 instrumentation has now
strongly emerging in many configura- (multichannel advantage). The genesis evolved into rapid-scan systems40,41
tions19–23 and are discussed in a recent of this instrumentation can be traced to with improved detector electronics and
compilation.24 We focus here on micro- the availability of focal plane array fast signal processing. Step-scan imag-
scale measurements. Though an older (FPA) detectors with extended wave- ing, similar to bulk step-scan spectros-
field of study, the past few years have length sensitivity,34 non-microscopy im- copy, would still be useful for time-
seen a renaissance driven by new
concepts, theory, hardware, and algo-
rithms. A review of the developments
and their likely impact in the future are
the subject of this manuscript. Micro-
scale measurements can be conducted in
two configurations that depend on the
type of detector used.25 Point microsco-
py typically refers to the use of a single
element detector. Spatial localization is
not aided by the detector architecture in
this case but rather achieved using
selective illumination (using apertures)
or local sensing (using probes). Aper-
tures have been employed for decades
and the technology26,27 has been essen-
tially unaltered since the advent of
Fourier transform infrared (FT-IR) mi-
croscopy. While scanning probes have
received considerably more attention for
nanoscale spectroscopic mapping, their
use for microscale measurements28–31 is
generally useful only to localize signal
from specific regions or samples32 and
not for large area mapping. IR imaging
typically refers to the use of multichan-
nel detectors to achieve spatial local-
ization, which enables recording a
reasonably sized image in short times.
IR imaging is now the standard for
microscopy due to the exceptionally
large multichannel detection advantage
(typically .16 000) and robust detec-
tors. New applications, hardware, and
theory may well present situations in
which point measurements are the better
option for IR microscopy in the future.
Hence, this review will focus primarily
on imaging and discuss point microsco- FIG. 1. (A) Typical layout of a Fourier transform infrared (FT-IR) spectrometer.
Instrumentation is usually general purpose, with transmission and reflection sampling
py only when new ideas are introduced configurations in the same system (only the transmission path is shown here), dual
that may lead to competitive technolo- detectors enabling both point mapping and imaging technology, as well as external
gies in the future. interferometer and computer to acquire and process data [figure by Kevin Yeh]. (B)
Conceptually, the optical path proceeds from a source to a spectrometer, microscope,
sample, and to the detector. The computer serves to operate the spectrometer and process
DATA RECORDING: signals from the detector into information. (C) The ongoing evolution of technology will
INSTRUMENTATION make computing and control central to imaging. The source/spectrometer combination will
essentially function as a known and controlled light source. Information about the sample
Fourier transform infrared spectro- and microscope configuration will be fed to the computer and used to process signals from
scopic imaging, which is most common- the detector via new theory and algorithms as described in this article. The quality of
ly referred to as FT-IR imaging, information extracted, as a consequence, will be considerably improved.

1092 Volume 66, Number 10, 2012

resolved FT-IR imaging42 but has only
been reported in a few studies.43–45
Though imaging instrumentation is
commercially available, no major con-
ceptual innovations have occurred over
the past 8 to 10 years in the available
systems. To some extent, this is a sign of
mature component technology. While
some advances can be foreseen, such as
detectors with improved speed and
larger formats, the approach to imaging
is largely the same as a decade ago. As
argued later in this article, this stagna-
tion is also a product of a lack of
theoretical and fundamental understand-
ing that can guide further development.
The stagnation has also spurred a look
elsewhere for competing technologies
and alternate approaches that address
specific shortcomings of present-day
instrumentation.
In a competing approach, which we
term discrete frequency IR (DF-IR)
imaging, data may be recorded at single
frequencies of limited bandwidths with-
out extensive spectral multiplexing in
time. A frequency sweep, as for example
with gratings, has long been out of favor
for spectrometry due to the Fellgett and
Jacquinot advantages offered by inter-
ferometry. Filters and gratings, never-
theless, have been used sporadically.
While these attempts were useful for
sampling a single frequency or a few
bandwidth regions, they did not gain
much favor for spectroscopy over ap-
preciable spectral bandwidths. As op-
posed to bulk measurements, however,
spatially resolved measurements are
actually more favorable for these alter-
nate forms of spectral recording. The
throughput and multiplexing advantage
can be recovered somewhat by relaxing
slit width as lower spectral resolutions
are typically required in imaging con-
densed matter while simultaneous re-
cording with a multichannel focal plane
array (FPA) detector alleviates the
multiplexing advantage to some extent.
While the use of gratings permits the
recording of smaller bandwidths of data,
instrumentation in other spectral re-
gions46 has typically focused on specific
applications requiring compact size,
robust performance, and speed. These
advantages are typically not the driving
requirements for mid-IR microscopy
systems, though they can potentially be
used in this spectral region as well. The
reduction in bandwidth can be continued
to the level of recoding a single spectral
resolution element at a time. Towards
this end, there are two major emerging
trends. In the first, lasers are becoming
more available and practical for the mid-
IR region. Quantum cascade laser
(QCL) technology,47 in particular, is
maturing and transitioning from aca-
demic to commercial success. The
second trend is the increasing integration
of powerful computers in spectroscopy.
This trend will enable the extraction of
significantly higher quality information,
even from poorer quality recorded data.
Spatial deconvolution, noise rejection,
and other signal-processing approaches
can potentially provide solutions that
displace the need for sophisticated
hardware. We examine these trends next
and discuss progress in the context of
recent advances.
Interferometers with Extended
Frequency Sources. The globar has
long been the source of choice for both
IR spectrometry and imaging due to its
broadband emission, sufficiency of light
for most conventional applications, sim-
plicity, robustness, and low cost. The
output of a globar is matched well to the
detector characteristics of modern sin-
gle-element detectors and electronics
such that photon flux is not a limitation
for the vast majority of bulk measure-
ments. For imaging, due to the need for
focusing and uniform distribution of
light over a large area, the flux per
detector element is significantly smaller
and requires longer observation times.
At the same time, the miniaturized
detector and electronics in an FPA are
noisier. Hence, imaging data are inher-
ently noisier than their corresponding
single-point measurements.48 Interest-
ingly, quantitative analyses of the ex-
pected signal-to-noise ratio (SNR)
indicate that an increased SNR can be
realized with miniaturized detectors—if
the same flux can be maintained.49
Hence, a higher flux source is likely to
prove beneficial for imaging.
Compared to thermal sources, a
synchrotron provides high-brightness
radiation that is particularly relevant
for microscopy and imaging.50–54 A
summary of the properties of synchro-
trons and their applications for micros-
APPLIED SPECTROSCOPY
copy is available,55 and hence, we only
focus on the features relevant for
imaging. Details of recent developments
and description of a major improvement
in performance are available in a recent
review.56 The emitted beam from a
synchrotron is of high brightness, colli-
mated, and of a small size. While this
property was excellent for point micros-
copy in which light from a larger
diameter would anyway be rejected, it
was not very effective for wide-field
imaging. There were reports of coupling
a focal plane array to synchrotrons57,58
and the notion of improved data quality
was proposed. A major recent advance
was the combination of multiple beams
to provide a bright, wide beam source
that could be coupled into an interfer-
ometer.59 While SNR improvement was
a major outcome, the work has changed
IR imaging in a more fundamental
manner. The resolution of any IR
imaging system is limited by the dif-
fraction limit and the numerical aperture
(NA) of the objective. As demonstrated
in the above study and shown theoret-
ically (discussed further in this article in
the Microscopy section),60 the sample
size imaged per pixel was not optimized.
Commercial instruments typically image
~5 lm per pixel in order to ensure a
sufficient SNR from the weak thermal
source. Using a synchrotron source with
the same setup alleviates the lack of
throughput and enables smaller pixel
sizes at the sample plane to be recorded.
The resulting image quality clearly
demonstrated the utility of the synchro-
tron source in providing diffraction-
limited images for the first time. The
quality of images was so dramatically
different that these are dubbed ‘‘high-
definition’’ (HD) images to distinguish
them from the previous state-of-the-art.
The study also highlighted the need to
develop new sources and detectors and
exposed the lack of rigorous consider-
ations in the design of most instruments.
A new set of synchrotron-based high-
performing microscopes will probably
result given the development of new
beamlines that is currently underway
and the convincing demonstration of HD
imaging. The obvious drawback of this
approach for applied spectroscopists is
that synchrotron sources for IR imaging
have limited availability due to their
1093
focal point review
cost, size, and accessibility. Free elec-
tron lasers, 61 another source using
accelerated particles but using an undu-
lator to achieve optical amplification,
can generate an output with a much
higher spectral brightness and coherence
than a synchrotron. Used sporadically
for microscopy of practical systems,62
their application for IR microscopy is
even more limited than that of synchro-
trons. These are perhaps better suited for
fundamental spectroscopic studies,63
therapeutic use,64 or near-field nano-
scopy65,66 approaches. In summary, no
major advances in the technology of
sources are anticipated but changes are
likely forthcoming in the manner in
which these sources are used, for
example, for HD imaging.
Hybrid Spatial–Spectral Microsco-
py. A new approach to spectrometry was
described involving an FPA detector in
which a conventional grating arrange-
ment was used to disperse light and
individual pixels in the array were
employed to record a single resolution
element region (Fig. 2, left).67 The
spectrometer is termed planar array
infrared (PA-IR) spectrograph. While
the genesis of the PA-IR approach is
both in the use of gratings and single-
element detectors that preceded FT-IR
spectroscopy as well as in the use of
multichannel detection68 in ultrafast
spectroscopy or nanoscale mapping,69
the approach has significant additional
implications for microscopy and imag-
ing. The approach is flexible as different
bandwidths can be selected depending
on the optical and array arrangements70
as well as very high fidelity in terms of
speed71 and sensitivity.72 The spectrom-
eter inherently involves multiplexing
due to the multi-channel detection, and
elimination of a narrow slit results in
improved SNR. The flux is very effi-
ciently utilized, enabling measurements
even in aqueous solutions.73 Since there
are no moving parts for recording a
specific (though, limited) bandwidth,
data acquisition can be rapid and is
limited only by the integration times
(~10 ls) of the detector. The frame rate
of the detector determines the temporal
interval between spectral acquisitions (~
1 ms), making the rate of spectral
acquisition quite comparable to the
fastest FT-IR imaging systems. With
1094 Volume 66, Number 10, 2012
the inevitable future availability of FPA
detectors with faster electronics and
larger sizes, ~100 ls spectral acquisi-
tion is likely going to become possible
and larger bandwidths may be accessi-
ble. The limited bandwidth problem of
this approach can be overcome by using
multiple pixel rows available in the
FPA. Configurations have been pro-
posed to illuminate the FPA with two
or more separate and independent spec-
tral bandwidths. Perhaps the greatest
advantage of this technology lies in its
ability to perform real-time background
corrections by obtaining sample and
background single beams from the same
FPA image, virtually eliminating the
effects of water vapor or source fluctu-
ations. Despite these advantages, how-
ever, the use of this approach for
imaging has not been actively pursued.
In principle, using an aperture and
systematically translating the sample to
collect spectra permits mapping of the
sample in a manner comparable to point
mapping. A similar concept has been
implemented, though using prisms,74 for
point-mapping measurements.75 The
spatial area-defining aperture of the
microscope at the sample plane also
served as the entrance slit to the
spectrograph and light is dispersed both
along the column (spatial information)
as well as across the row (spectral
information) of the detector array (Fig.
2, middle). Prisms require a more
complicated setup to provide the higher
resolution typically afforded by grating-
based systems but, for a particular array,
the spectral coverage can be higher.
Since FPA detectors are two dimension-
al, it also is possible to spectroscopically
and spatially map the sample at the same
time. A hybrid imaging approach has
been proposed76,77 in which one dimen-
sion of the FPA is used for spectral
recording while the other is used for
spatial resolution. The line-scan ap-
proach to mapping, however, has not
yet been extended to raster the sample.
This could prove to be an exciting
development for some applications.
Recorded spectra compared very favor-
ably with those from an FT-IR spec-
trometer (Fig. 2, right) and can be seen
to depend strongly on the optical setup
(slit width). Because the slit width
would also be coupled to the spatial
resolution, spectral and spatial resolu-
tion would be correlated in any mapping
system using this architecture. Hence,
considerable thought and optimization
may be needed to design a flexible
system that can provide both excellent
spectral and spatial resolution. Given the
ability to perform high fidelity spectros-
copy, real-time corrections, and other
advantages enumerated above, it should
be possible to obtain data of very high
quality using an appropriately designed
instrument. Given the coupling between
spectral and spatial domains as well as
challenges in accessing vibrational
modes over large bandwidths, hybrid
mapping or point microscopy systems
would likely only be useful for moderate
performance applications where cost,
robustness, and simplicity are significant
considerations.
A practical benefit of a microscope
based on PA-IR spectrometers would be
in the rapid examination of small
regions of exceptionally small signals,
e.g., mapping of monolayers, an ability
that is not easily available in FT-IR
microscopes. The most exciting result,
however, is probably the ability to
provide exceptionally low levels of
noise. The peak-to-peak noise level of
the baseline in absorption spectra ac-
quired in tens of minutes was reported to
be of the level of 10-5. Combined with
the spatial localization of microscopy,
the SNR could potentially provide the
capability to image domains, inclusions,
or impurities at the sub-picogram level
or lower in minutes. The sensitivity,
speed, and robustness of such a micro-
scope could potentially be useful for
real-time quality control or forensics, for
example, but no applications have been
reported in those directions. While not
explicitly stated or analyzed theoretical-
ly in the above works, there is a
fundamental concept of significant value
in using the PA-IR system for imaging.
Interferometry has been so ingrained
into the body of knowledge for decades
that it has become synonymous with
multiplexing. Multiplexing can also
occur in the spatial domain. In the non-
imaging version of the PA-IR setup,
spectra from different spatial regions
were simply averaged to provide an
average ‘‘bulk’’ spectrum while a multi-
channel detection advantage was ob-
FIG. 2. Hybrid spatial–spectral data recording is possible using a grating or a prism-based spectrograph coupled to a microscope. (Left)
Experimental arrangement of components in the PA-IR spectrograph. (Middle) Spectra acquired (across a row) using a prism-based
spectrograph. The detector image of Parylene can be used to extract spectra (right) that change with the optical parameters of the system.
Spectra recorded at slit width settings of (a) 46, (b) 64, (c) 108, and (d) 153 lm with the sodium chloride single-pass prism spectrograph. (e)
The CH stretching and fingerprint regions of the FT-IR spectrum were acquired at 22 and 14 cm-1 resolution, respectively. [Figure at left
reproduced with permission from Ref. 67, copyright Society for Applied Spectroscopy. Figures in the center and to the right reproduced with
permission from Ref. 75, copyright Society for Applied Spectroscopy.]

tained using different pixels to record
data. Thus, the spectral acquisition was
multiplexed in both the spatial regions
of the sample as well as the spatial
extent of the detector. While Fellgett’s
advantage78 in temporal/spectral multi-
plexing is often cited as a major
competitive advantage of interferometry,
this spatial multiplexing confers an
advantage of similar magnitude, though
arising from different considerations.
Hence, we argue that the long-accepted
belief in the general utility of the Fellgett
advantage for spectroscopy should be
re-examined in the context of imaging,
as discussed in the next section.
Discrete Frequency Infrared (DF-
IR) Spectroscopic Imaging. The mul-
tiplex advantage has played a central
role in the evolution of instrumentation
in the mid-IR. Briefly, in an interferom-
eter, all frequencies in the bandpass of
the optical system are acquired all the
time. Hence, as opposed to sequentially
measuring each spectral resolution ele-
ment individually, an N-fold higher
signal is measured N times. Compari-
sons of interferometric methods with
other methods often rely on the assump-
tion that the entire spectrum of large
bandwidth has to be measured, that the
finite dynamic range of the detector does
not play into the theoretical advantage,
and that a high spectral resolution is
required. A complete discussion of the
relative merits of interferometric versus
other approaches is in preparation;79
here, the most important considerations
are summarized. The first pertinent
aspect is the sheer size of the data. As
opposed to N spectral data points in a
single spectrum, there are Nx and Ny
spatial resolution elements as well.
Hence, the total data points that are to
be measured is N 3 Nx 3 Ny in an
imaging experiment. For the purposes of
acquisition, which is limited by detector
readout speed, and for recording and
analyzing the fewest data needed, in the
interest of conserving time and resourc-
es, it may not be necessary to record the
entire spectrum. For many applications,
such as imaging biological tissues,80 it
may be beneficial to record only specific
spectral bands of interest. A second
pertinent issue is the one of limited
performance of available array detectors,
mainly their electronics and dynamic
range. Interferometry encodes the inten-
sity of the source such that that there is a
massive signal recorded around zero
optical retardation. The spectral SNR
of the single beam is approximately
equal to thepffiffiffiffi SNR of the centerburst
divided by N . In a conventional spec-
trometer, the speed of the interferometer
can be increased for large signals and
signal averaging can be extensive,
thereby reducing detector noise contri-
butions in a given acquisition time. With
FPA systems, the readout time of the
detector is fixed, whereas the integration
time for signal acquisition can be
tailored to best fit the centerburst signal
into the dynamic range of the ADC.
Methods such as gain ranging,81 stag-
gered step-scan,82 rapid scanning, inter-
ferometer modulation,83 and detector
aperture matching84 have been proposed
around this limitation but have not been
able to address the limited dynamic
range problem. Further, the full range
is not utilized for fear of saturating the
detector and some range is lost to
thermal background. Since the globar
bandwidth used in interferometry is
large, N is typically 512–2048 points
and the SNR for one scan at each pixel
is no more than 250:1. Typically, studies
report 100:185 and uncooled detectors86
would report SNR of 10:1. While small
detectors provide impressive SNRs,5
spatial coverage suffers dramatically.
Practitioners today have to tolerate the
reduced multichannel advantage to gain
high SNR, for example, for biomedical
applications, or sacrifice SNR to gain
imaging speed, for example, for kinetics
experiments.87
An alternative approach to overcome
these difficulties encountered with FT-
IR imaging has been recently pro-

APPLIED SPECTROSCOPY 1095

focal point review
posed.88 In this approach, a spectrally
narrow-band beam is provided to the
microscope and a spectral image at a
specific frequency is recorded directly.
Hence, high SNR can be achieved
rapidly by averaging a small spectral
range instead of spectrally scanning a
large bandwidth. Since the recording of
spectral elements is decoupled from
recording the entire bandwidth (the FT-
IR case), this approach is termed DF-IR
spectroscopy (Fig. 3). The approach
would ideally, first, greatly simplify
instrumentation while providing perfor-
mance at least comparable to an FT-IR
spectrometer in terms of recording
spectral elements of interest, resolution,
and data recording speed. Second, it
would make instrumentation more ro-
bust by replacing the sensitive interfer-
ometer with a simple moving part or
solid-state lasers. The ability to selec-
tively acquire data at a few or all
wavelengths and to do so in random
access is the obvious advantage of this
approach. The same advantages are
available using lasers. There are differ-
ent approaches to lasers that are now
becoming more prominent for the mid-
IR spectral region. We divide spectros-
copy candidates into two major groups
based on the components and output of
the laser system. The first group includes
lasers in which mid-IR radiation is
directly generated and available, includ-
ing QCLs and lead-salt or CO2 lasers.
The second group is based on frequency
conversion, using well-established
sources from other spectral regions, for
example, using optical parametric gen-
eration in nonlinear crystals. While the
DF-IR term was first introduced with
respect to filters, the idea is essentially
the same using lasers. Hence, we use the
term to imply the general embodiment
of imaging where selective and individ-
ually addressable wavelengths can be
employed for imaging. In general,
throughput in a laser system will be
higher than filter-based systems, as will
be cost and complexity.
A second advantage of DF-IR ap-
proaches addresses the dynamic range
problem directly. In DF-IR measure-
ments, the dynamic range is simply
filled by a narrowband signal and the
single-beam SNR can be 1000:1 (cooled
FPA) or 100:1 (uncooled FPA). The
1096 Volume 66, Number 10, 2012
ability to use uncooled arrays is perhaps
the most exciting aspect of DF-IR
approaches. Uncooled FPAs are cheaper
and have much larger formats than
cooled arrays. Hence, coverage can be
enhanced and more time can be spent
averaging signal to improve SNR.
Uncooled FPAs are also becoming
increasingly available in larger formats,
though only at near-video-rate readouts
due to technological and market limita-
tions, and are likely to be used for
spectroscopy only in this format. Fur-
ther, the ADC can be filled by integrat-
ing the signal for varying times for each
spectral element. Hence, we can obtain
uniform SNR (or by design, enhanced
SNR at any frequency) simply by
software control. This potential, though
not implemented in any reports thus far,
will also mean that the conventional
notions of SNR will need to be recon-
sidered. In DF-IR spectroscopic imag-
ing, SNR can be tailored for different
elements of the spectrum such that SNR
in absorbance, rather than baseline noise
as obtained in interferometry, is constant
across the spectrum. In summary, the
DF-IR approach has the potential to be
simpler, robust, and cheaper, as well as
being superior to FT-IR imaging in
some cases. We emphasize that these
analyses do not imply that DF-IR is
superior to FT-IR imaging in all cases. If
the entire spectrum is required at high
resolution, the detector is of large
dynamic range and low noise, the source
is exceptionally weak (emission spec-
tra), or there are noise frequencies that
can be filtered, then FT-IR imaging will
be distinctly superior. DF-IR imaging
will likely evolve for very specific uses,
also providing additional opportunity to
optimize performance and lower costs.
In particular, its use is likely to be
popular where a few spectral features
provide all the information of interest,89
for example, in tissue typing.90
The possibility raised above points to
a trend in which the source, spectrom-
eter, and analysis need to be controlled
and to be in sync with one another. This
is not only required but can potentially
provide improved performance. Efforts
to maximize performance, however, also
usually restrict the range of studies that
one particular implementation can ad-
dress. To become more generally appli-
cable, optical arrangements for DF-IR
systems would have to be flexible and
configurable; implying again the use of
software for optimization and control
significantly more than presently imple-
mented.
The critical technology for DF-IR
imaging is obviously the ‘‘source’’,
which integrates a source of light at
different wavelengths as well as a means
to separate multiple frequencies into
individual narrowband ones. The dis-
tinction from interferometric methods is
that the source–spectrometer combina-
tion provides the opportunity to select a
single narrowband illumination at one
time, while the distinction from grating
based methods is that the intensity at
frequencies is unrelated to a single
grating frequency that has been opti-
mized. Three major classes of such
sources are available and are worth
following as the DF-IR approach be-
comes more prevalent. Technology for
sources and software approaches are
discussed in the next section.
Spectrometer Components for DF-
IR Imaging: Filters. In IR imaging, a
microscope is coupled to a spectrometer.
Hence, for both DF-IR and FT-IR
imaging, the microscope, sample mount-
ing, and beam steering components are
the same. The source of light and the
spectrometer are the only differences.
The effects of microscopy optics and
sample are discussed in subsequent
sections; here we examine the source–
spectrometer component. The use of
filters allows recording of spectral data
directly using narrow linewidths. There
are two major impediments to this ideal.
The first is conceptual in that it is not
simple to design narrowband filters of
multiple bandpass (resolution) appropri-
ate for spectroscopy. The second is
practical in that conventional processes
such as mechanical ruling used to
manufacture gratings are far too slow
and, consequently, too expensive to
mass produce sets of filters. There are
other minor concerns such as how an
optical design would incorporate tens to
hundreds of filters that may be needed.
Recent renaissance in optical sciences
provides technology that is capable of
providing filters with characteristics
sufficient for use in spectroscopy in the
form of so-called guided-mode reso-
FIG. 3. (A) Essentials of the FT-IR and (B) DF-IR Setup. A broadband source (C) is encoded and decoded by FT-acquisition using (D)
interferograms. (E) A small number of filters are used in DF mode to measure the informative spectral sections.
nance filters (GMRF).91 Mass produc-
tion of the filters is enabled by recent
advances in nanofabrication technology,
optical modeling, and use of unconven-
tional materials for manufacture. For
effective application in IR spectroscopy,
the set of filters should provide high
reflection efficiency over a narrow
wavelength range for all spectral reso-
lution elements. The resolution achieved
must be the same as common FT-IR
settings (4 to 16 cm-1). A set of filters
should also be capable of spanning a
large wavelength range (e.g., 3950
cm-1, the sampling cut-off for under-
sampled FT-IR spectroscopy to 950
cm-1, the FPA cut-off). The materials
and fabrication challenges to achieve
these conditions are quite significant
and, until recently, only wide (~100
cm-1) band filters had been reported in
the mid-IR. The efficient production of
these filters and design of ones with
tailored characteristics are likely to
remain topics for research. Hence, we
examine the concept behind these filters,
their testing, and review the state of the
art in the next few paragraphs.
Since their discovery more than a
century ago92 and as described in recent
analyses,93–96 anomalies in periodically
modulated structures have attracted much
attention for spectral selectivity. Reso-
nant anomalies,97,98 termed guided-mode
resonance (GMR), in waveguide-gratings
result from structures with a sub-wave-
length modulation in refractive index
along one dimension. Designed struc-
APPLIED SPECTROSCOPY
tures can be used to function as filters that
produce complete exchange of energy
between forward- and backward-propa-
gating diffracted waves. More important-
ly, for spectroscopy applications, it was
shown that smooth line shapes and
arbitrarily narrow linewidths could be
obtained.99 GMR arises from the intro-
duced periodicity that allows phase-
matching of externally incident radiation
into modes that can be re-radiated into
free-space. They are often referred to as
‘‘leaky eigenmodes’’ of the structures as
these modes possess finite lifetimes
within such structures. GMRFs store
energy at the resonance wavelength,
which is manifested in optical near fields
that interact with the device itself as well
as with the external environment. For
1097
focal point review
normal incidence illumination, the re-
sponse of the GMRF is coupled to the
second-order Bragg condition and there-
fore the spectral location of peak reflec-
tion can be given by:
k ¼ neff K ð1Þ
where k is the resonant wavelength, neff
is the effective index, and K is the
modulation period.100
The effective index is a weighted
average of the refractive indices of the
materials in which the standing wave
generated at resonance is supported.
Hence, structures to provide large num-
bers of resonant wavelengths needed for
spectroscopy can be readily tailored by
changing geometric parameters (modu-
lation period). There were successful
examples101 of making such structures
for ultraviolet (UV), visible, and near-
infrared (NIR) wavelengths and the first
example for mid-IR wavelengths was
also recently reported.91 Although mod-
eling and simulation of these structures
required additional details and account-
ing for dispersion in the materials used,
actual fabrication and unproven manu-
facturing in the mid-IR were impedi-
ments that needed to be overcome. The
primary challenge is that materials of the
structure need to have little or no
absorption at the resonant wavelength
in order to maintain near 100% reflec-
tion efficiency. We have selected plas-
ma-enhanced chemical vapor deposited
(PE-CVD) silicon nitride (SiN) and
fumed silica dielectrics specifically for
their low mid-IR absorption and have
produced highly efficient reflectance
spectra. Since there are a large number
of frequencies, a secondary challenge is
to ensure both an efficient fabrication
and use of these filters. A ‘‘filter wheel’’
has been developed using a single wafer
to address both needs. One positive
aspect of fabricating filters for mid-IR
wavelengths is that the device period,
which must be less than one-half the
resonant wavelength, increases as wave-
length increases according to Eq. 1. A
device designed to measure the CH
stretching mode, for example, is reso-
nant at k ~ 3.45 lm and requires a
period of K = 2.1 lm, which dictates
that the size of etched features will be
1.1 lm. Features of this size are well
within the dimensions of routine contact
1098 Volume 66, Number 10, 2012
photolithography using conventional
photoresists and chrome exposure
masks. Hence, mass fabrication is pos-
sible and can be very cost effective. We
have obtained filter parameters that can
provide narrow linewidths at usual FT-
IR resolutions. Filters with these char-
acteristics were fabricated and demon-
strate performance as per theory. These
filters can be demonstrated in principle
but have not been used for imaging
spectroscopy due to fabrication and
interfacing challenges at this time. This
technology is in its earliest stages but the
economic argument is compelling. Ad-
vances in modern fabrication and the
wide availability of electronics manu-
facturing can be leveraged to provide
fairly inexpensive spectrally resolved
sources for microscopy. This aspect is
likely to sustain interest in developing
low-cost filters.
A typical GMRF and its use for mid-
IR imaging is shown in Fig. 4. The filter
(Fig. 4A) is conceptualized to comprise
a low refractive index substrate (soda
lime glass, n = 1.5) upon which a thin
film of high refractive dielectric material
(silicon nitride, n = 1.975) is deposited.
A one-dimensional linear grating pattern
upon the dielectric material is realized
by photolithography and a reactive ion
etch process is used to etch grooves
partially into its surface (Fig. 4B). With
theory-guided selection of the material
refractive index parameters, dielectric
layer thickness, and grating depth, the
device structure performs the function of
a highly efficient reflectance filter. At
the resonant wavelength, the structure
achieves high reflection efficiency for a
narrow bandpass and other wavelengths
are transmitted. They are eventually
absorbed by the thick soda glass. A
rigorous coupled wave analysis 102
(RCWA) computer code was written
for simulations of these structures and
used to predict the reflection efficiency
as a function of wavelength, that were
subsequently validated in individual
filters (Fig. 4C), though important dif-
ferences between the predicted and
observed performance could be seen. A
number of filters could be co-housed on
the same substrate (Fig. 4D), which is
incorporated into an optical arrangement
for both testing against an FT-IR
spectrometer as well as for use in a
microscopy system (Fig. 4E). A narrow-
band absorbance image obtained using
the filters demonstrates that imaging is
possible (Fig. 4F). Any frequency can,
hence, be addressed rapidly and ran-
domly by turning the wheel from
software control.
While the DF-IR approach enabled by
GMRFs is an exciting avenue, many
challenges remain. Filters have been
designed and tested and important
insights obtained into their design.
However, the filter–optical setup is not
optimized. Even in theory and simula-
tions, smaller refinements need to be
incorporated. For example, the refractive
indices and dispersion due to small
absorption within the fabrication mate-
rials are likely causes of the variance;
hence, characterization and prediction of
these properties is needed. The efficien-
cy and FWHM of any filter depend both
on the optical alignment as well as
properties of the underlying materials.
While the filters themselves can be
fabricated and coupled to a globar
source, great care must be taken in
alignment. Alignment concerns can
likely be resolved with the same dy-
namic approaches as used in an interfer-
ometer but beam collimation (restricted
with an aperture similar to that in an FT-
IR spectrometer) and its effect on
spectra need to be studied. Spectra from
the filter wheel show higher noise
compared to a conventional single-
element spectrometer, which is several
thousand fold larger in area and lower
resolution due to the broad spectral
bandwidth. Hence, further optimization
is needed for routine spectroscopy. As
with all frequency selection methods via
coherent processes, polarization is intro-
duced into the beam. An alternative to
GMRFs might be to use a conventional
grating/slit monochromator, where serial
adjustment of the monochromator slit
position illuminates the sample one
wavelength at a time. While such a
method would suffice in principle, the
GMRF approach has a number of
advantages. By using the described
approach, efficiency at all wavenumbers
can be optimized, frequencies are indi-
vidually selectable, ruling cost is much
lower, and large wavelength regions can
be covered in a single part (filter wheel).
The fundamental limitation of a globar
FIG. 4. Components and results from DF-IR imaging. (A) Schematic of a designed filter. (B) Characterization of the designed filter by
microscopy and atomic force microscopy shows the ability to fabricate structures as per design and their uniformity. (C) The imperfect
prediction and fabrication capabilities at this early stage, however, do present challenges in translating the narrowband predicted
performance (for example, on the left) to actual filter performance (right). (D) Tens of filters can be placed on a single substrate and
fabricated together on the same optical path using the concept of a filter wheel. (E) Schematic of setup for characterization of the filter,
spectroscopy or for comparison with FT-IR imaging. (F) An absorbance image from an unoptimized system showing the antisymmetric CH
stretching band absorbance of an SU-8 sample. The image size is approximately 500 lm 3 500 lm. White levels indicate a higher beam
attenuation and gray/black levels indicate little to no attenuation.

in terms of flux remains. For filters, the
use of an aperture and polarizer further
decreases total available intensity.
Hence, the need for higher intensity
sources is not addressed and actually
becomes more acute in using filters.
Tunable lasers are an obvious choice
and two routes, discussed next, stand out
in their potential for IR imaging.
Spectrometer Components for DF-
IR Imaging: Lasers. Quantum Cas-
cade Lasers. Quantum cascade lasers
(QCLs)103,104 are a class of unipolar
lasers based on inter-sub-band transi-
tions in a semiconductor heterostructure.
Most common embodiments involve
using InGaAs/AlInAs/InP composites105
that are active at wavelengths longer
than ~3 lm. The most effective ap-
proach in this direction is emerging in
the form of an external cavity (EC)
QCL. A grating is coupled to a free-
running semiconductor laser to select a
specific band and tune the entire device
into a single-band source. The setup
consists of three components: the gain
element (QCL chip), collimating mir-
rors, and grating.106 In principle, the
setup is similar to the combination of a
grating-based spectrometer and source.
The major advantage, however, is that
exceptionally narrowband light of un-
precedented intensity can be obtained.
QCLs function at room temperature,107
the source is compact, and, in principle,
it can become fairly inexpensive after
further development. Lasers have been
widely used for spectroscopic analy-
ses108 for a number of years and,
similarly, various studies have used
QCLs for IR spectroscopy109–113 as well
as microscopy and imaging.114,115 The
most widely reported studies in spec-
troscopy have been focused on using the
narrow-band properties and high inten-
sity of the QCL to profile specific
species, aqueous environments116–118
or the integrated and compact instru-
mentation119,120 that may be developed
for specific experimental configura-
tions121 or applications.122–124 The tech-
nology has made rapid progress,
specifically in spectral properties and
power.125
A large effort in the QCL-related
fields has been in the modeling, mea-
surements, and optical properties of
these devices. Imaging and microscopy
instruments as well as applications have
lagged significantly. Since their initial
demonstration more than 15 years ago,47
the technology has matured and there
are several commercial vendors offering
QCL systems. Though realized around
the same time, the maturation of IR
imaging technology has been consider-
ably faster, given the long history of IR
microscopy. It is curious that combining
the two technologies has received lim-
ited attention. The first factor in this lack
of progress may be the limited spectral
range, high cost, and restricted avail-

APPLIED SPECTROSCOPY 1099

focal point review

FIG. 5. USAF 1951 optical resolution target absorption images (cycle 3, elements 5 and 6) as acquired by three different instruments. As
opposed to chrome-on-glass targets, these samples were designed to be a cross-linked photolithographic polymer (SU-8) on polished
barium fluoride substrates. Top row: QCL þ bolometer system without diffuser plate. Middle row: QCL þ bolometer system with rotating
diffuser plate. Bottom row: commercial FT-IR instrument. [Reproduced with permission from Ref. 126, copyright American Chemical
Society.]

ability of stable, packaged QCL sources
that are usable. The second is more
fundamental. While QCL manufacturing
technology is making rapid progress in
developing broadband output devices
appropriate for spectroscopy, turning
them into viable sources for microscopy
will likely require substantial further
work on the part of spectroscopy and
imaging scientists. Based on preliminary
experiments thus far, a QCL cannot
simply be integrated into existing mi-
croscopes in the manner that FPAs were
integrated into single-point IR mapping
microscopes. Though the single point-
to-FPA detector transition required
opening the apertures and changes in
software, the beam size, spectroscopy,
noise characteristics of the spectrometer,
and optical performance of the micro-
scope were not changed. These would
all have to be reconsidered in using a
QCL source. We illustrate one aspect
from our work126 in Fig. 5. The coupling
of the laser to a microscope required
beam expansion, reduction of spatial
coherence, and new optical elements for
illumination. Without these measures,
coherence makes data interpretation
difficult; even with this design, illumi-
nation and recording are not trivial. The
beam intensity and size, as well as its
polarization, coherence, and narrowband
emission all present significantly new
challenges that are discussed and would
require a careful analysis of the perfor-
mance of an integrated system and a
likely re-design of existing microscopy
systems to be of significant value. An
excellent recent example of integrating
the unique advantages of this technology
in designing instruments is available in
the near-field microscopy arena,127
while new opportunities may lie in
photoacoustic spectroscopy applica-
tions.128 The challenge for spectrosco-
pists would be to integrate the new
sources with a better understanding of
their potential and of the implications of
the limited-wavelength, coherence, and
polarization for spectroscopic imaging.
The challenge for QCL device manu-
facturers obviously lies in extending the
wavelength coverage, providing com-
pact and integrated sources with seam-
less transition between wavelengths, and
high beam stability. Complementary
sources to cover shorter wavelengths
(,3.5 lm) will also be required to
complete the mid-IR spectral coverage
common for spectroscopy. This area is
likely to remain very productive and
important for imaging in the coming
years.
Other Laser Sources. While QCLs
produce mid-IR light directly, the con-
siderable advances in powerful sources
in other spectral regions as well as
photonic fibers can also be leveraged

1100 Volume 66, Number 10, 2012

using frequency conversion.129,130 A
complete discussion of these sources
and their potential for imaging is beyond
the scope of this article but compilation
of the fundamentals of several potential
technologies131 and recent advances are
available.132 The development of appro-
priate materials such as periodically
poled lithium niobate (LiNbO3) and the
emergence of NIR sources have been
most crucial to the development of
tunable mid-IR sources by optical para-
metric generation (OPG). Advances in
materials processing, microfabrication
technology, and understanding of these
systems has led to other candidates and
materials for frequency conversion. Spe-
cific examples of successful technolo-
gies are using, for example, GaAs,133
which promises to considerably extend
the capability of this approach. The most
successful example of application is in
coupling with a sub-micron scanning
sensor134 and the commercial translation
to nanoscale imaging,135,136 demonstrat-
ing that a system built from these
sources may also be viable for micro-
spectroscopy.
An excellent example of the potential
of this approach is demonstrated in the
coupling of an OPG-based system with a
conventional IR microscope and
FPA.137 The flux allowed the acquisition
of images with sufficient SNR in ~1 ls
of acquisition, thereby considerably
reducing the contributions from thermal
background radiation and providing new
opportunities for noise rejection. The
primary limitations at present are the
relatively coarse spectral resolutions
attainable (~10 cm-1) that cannot be
arbitrarily changed, pulse-to-pulse sta-
bility, and complexity of the setup.
Though pulses may be spectrally broad-
er, spectroscopy can be performed by
spacing the tuned peak wavenumber
closer to provide a quasi-resolution that
is comparable to those typically used for
condensed-phase imaging. Further, in
principle, computation can be used to
recover the true spectrum at higher
resolution using signal processing tech-
niques. The sources will likely imply
shot-noise-limited performance, though
such an analysis has not been reported
for imaging systems. Though the capa-
bility to image across the entire mid-IR
bandwidth exists with OPG-based sys-
tems, a source with consistent spectral
performance over the range is difficult to
achieve in practical terms. Alternative
materials with new crystals, for exam-
ple, cadmium selenide (with an idler
tuning range of 1160–850 cm-1), are
becoming available. A comparison of IR
imaging with a laser and thermal source
has not been reported in terms of
spectral or spatial performance, though
spectra were found to be in reasonable
agreement in qualitative terms.137 In
addition to the optical and performance
issues discussed for QCLs, cost is an
additional factor in these systems. While
the compact packaging and ability to use
the same material for a variety of
applications and wavelengths exists for
QCLs, indirect production of mid-IR
light inherently requires a larger capital
cost and complexity of instrumentation
for phase matching. In the opinion of the
author, the rapid development of QCLs
and their relative simplicity will eventu-
ally lead to their adoption over other
laser technologies.
Compressed Sensing and Recon-
struction. As seen in the discussion of
the previous section, there is significant
value in acquiring only a limited set of
data. The obvious trade-off is that the
spectral range and resolution of acquired
data would also be limited. This trade-
off can be mitigated to some extent by
the use of modern computational power
and algorithms. Computational ap-
proaches to spectral reconstruction are
an emerging area in which fewer data
are acquired than would be dictated by
classical sampling considerations and
the deficiency in data quantity can be
compensated by estimation algorithms.
The estimation algorithms at one ex-
treme can be completely blinded to
spectroscopic details and use signal
processing approaches that, essentially,
operate to optimize entropy. Methods at
the other extreme perform reconstruc-
tions of full spectral detail using a
knowledgebase, either of expected spec-
tra for the problem or a general
understanding of spectral features, to
predict missing details in the data.
Applications in data reconstruction have
also been reported for temporal mea-
surements an interpolation sense, for
example, to obtain time-resolved mea-
surements with better accuracy.138 The
APPLIED SPECTROSCOPY
reconstruction approach has also been
proposed139 as an alternative to recov-
ering SNR and circumventing some
limitations of classical FT-IR approach-
es in some cases. An important conclu-
sion was that reconstructions are
relatively noise free. While not explicitly
stated in the study, the important
implication for imaging measurements
(in which sensitivity is often limited by
SNR) can be that the inaccuracy in
reconstruction may be smaller than the
noise for rapidly acquired data. Hence, it
may actually be advantageous to acquire
a smaller set of spectral points at high
SNR and reconstruct the entire dataset
rather than acquiring the entire data set
at some low SNR. A demonstration of
this possibility has not been reported.
Reconstruction approaches have been
reported in spectroscopy but have not
been extensively applied; their applica-
tion to imaging data can provide signif-
icant benefit. In most cases, data are
spectrally sparse, data acquisition times
are long, and storage requirements are
vast. At the same time, much is known
about specific applications, for example,
using the data to determine tissue
types.140 In one study,141 a representa-
tion for IR absorption spectra was
developed using a learned dictionary
(Fig. 6, top row). A sparse representa-
tion of this dictionary is used as prior
knowledge in regularizing the com-
pressed sensing inverse problem. The
reduced measurement during acquisition
was modeled as a process of interfero-
gram truncation, providing a benefit for
data acquisition in terms of a reduced set
of data as well as the centerburst to
enhance the SNR at the cost of the
sharper spectral components. The model
was implemented using low-pass filter-
ing and down-sampling in the spectral
domain as dictated by the measurement
process. Spectra could be obtained that
closely resembled the spectra acquired
without truncation (Fig. 6, middle row).
In any reconstruction, there is no doubt
that signal is lost and an estimate of the
true signal is obtained. The critical
measure of success then becomes
whether the task at hand is accom-
plished. The developed approach was
tested in its ability to predict cell types
in a number of tissue samples and the
results were compared to those obtained
1101
focal point review

FIG. 6. Reconstruction of data from a small number of spectral measurements. (Top) The basis of the approach relies on reconstructing
spectra from a representation of the data as a combination of sparsely measured data, parameters from a dictionary of known samples,
and correlation coefficients. (Middle, left) Different parameters of the process result in reconstructed spectra (dashed lines) that may be
lower resolution or closer to the recorded data (solid line). (Bottom, left) Gray colors indicate different cell types deduced from IR data
measured at full resolution while the same information is sought from a reconstructed data set (bottom, right).

1102 Volume 66, Number 10, 2012

with full data acquisition. Hence, a
number of tissues, which contained
multiple cell types and were drawn from
different patients reflecting the natural
variance expected in the task, were used
as a test bed. A down-sample factor of
four was found to be adequate for
accurate tissue classification and
matched the performance of the data
dacquire at full resolution. The method
also provided an improvement in the
SNR of the reconstructed signal, though
the effect of this improvement on
enhancing classification accuracy142
was not evaluated. The work was
important in demonstrating that data
storage and acquisition times in FT-IR
imaging can be significantly reduced
while preserving data quality by em-
ploying compressed sensing. Spatial
correlation and spatial–spectral correla-
tions may similarly be useful in specific
cases. Approaches such as the one
reported are likely to evolve with
increasing sophistication.
These studies represent a significant
untapped area of inquiry in IR imaging,
especially with the emergence of DF-IR
approaches. Spectral reconstructions
from a smaller measured set and strat-
egies for sparse acquisition are likely to
become more prominent. We strongly
emphasize that there is a difference
between recording spectroscopic imag-
ing data and estimating it via recon-
struction approaches, however. While
the former can offer the greatest confi-
dence, the latter offer speed. Care must
be exercised in evaluating the relative
merits of the approaches and claims
must be tempered accordingly. It is not
correct to assume, given the excellent
quality and speed of reconstruction with
modern computers and advanced algo-
rithms, that one is superior to another.
When the outcome of the imaging study
relies on conclusions to be drawn from
the data but the data itself are of limited
interest, reconstruction approaches are
especially relevant, for example, in rapid
tissue or polymer identification when the
range of possible solutions is limited. In
general, reconstruction methods are
ideally suited for repeated imaging of
similar samples in which rigorous vali-
dation of the approach can be conducted
to optimize both the parameters of
reconstruction as well as determine the
optimal results. This topic engenders
another direction that is likely to evolve
for imaging in the convergence of signal
processing, theory, and spectral recon-
struction with details of the experiment,
as seen in some areas of spectrosco-
py.143 Computation, as used thus far, not
only represents a necessity for imaging
data analysis but can potentially tie
together emerging instrumentation, the-
ory, sensing, and analysis.
Microscopy Optics. While we have
hitherto focused on describing spectral
recording approaches, the other aspect
of IR imaging lies in the optics of image
formation. While several studies in IR
microscopy and imaging have used
predictions from optical microscopy, a
complete model of the IR microscope
was not available until recently.144 A
model for light propagation in an
imaging instrument is important to both
the understanding of image quality as
well as to the rational design of
improved instruments that optimize
quality. Theoretical models for instru-
mentation, based on ray (geometric)
optics, have been proposed to describe
IR microscopy for many years. Most
efforts concentrated on the angular
dependence of data related to focusing
and corrections to measurements such as
dichroic ratios.145 Similarly, other meth-
ods of understanding spectral depen-
dence on sampling geometry in
conventional spectroscopy have often
focused on molecular properties in thin
films or at interfaces.146 It must be
recalled that sample path lengths as well
as microscopic features are often at the
scale of the wavelength of light; hence,
frameworks based on geometric (ray)
optics that have been largely used in
spectroscopy until now are inadequate in
the investigation of effects associated
with light–matter interaction. Full elec-
tromagnetic models capture all of the
physics of image formation but are also
significantly complex. They are most
useful when a precise prediction of a
combination of specific microscopy
optics–sample is desired. For many
other purposes, a simpler model suffices,
especially to understand the effects of
the optics of the microscope on the
recorded data. The first attempt in this
direction recently reported,144 in the
author’s opinion, the simplest approach
APPLIED SPECTROSCOPY
to microscopy that incorporates all the
phenomena of interest, forgoing full
electromagnetic modeling in favor of
the conceptually simpler and computa-
tionally easier model based on scalar
wave theory. We capture the major
aspects of this theory in the next section.
While details of the theory are described
in the original publication, the salient
features and critical equations are cap-
tured here in a simplified notation for
comparison with other studies and for
the sake of completeness.
In the scalar wave theory model, the
electric field at every plane in the
microscope is explicitly calculated. For
simplicity, consider a monochromatic
component of the field with a wavenum-
ber t̄, and complex amplitude U. Since
the spectral frequencies in any measure-
ment are independent, the approach can
simply be extended to the entire band-
width of the instrument. The field, in any
spatial plane for any wavenumber, is
expressed as a superposition of plane
waves described by functions of the form
U(f) expfi2p[f.r þ fz (f) z]g where f =
(fx, fy) and r = (rx, ry) are the two-
dimensional frequency and spatial coor-
dinate vectors, respectively, in Cartesian
coordinates. The function fz is defined
such that j f j2 þ fz(f)2 = t̄2, implying that
the individual plane waves satisfy the
Helmoltz equation.147 The microscopy
system is assumed to be linear; hence,
summation of individual plane waves can
be employed to reconstruct the field and
all linear transformations of the field. For
each plane wave constituting the field,
the amplitude determines its quantitative
contribution and the phase determines its
relative position. Both the amplitude and
phase are necessary and sufficient for a
complete description of the field. Subse-
quently, a plane wave decomposition can
be achieved via the two-dimensional
Fourier transform. Each plane wave
constituting the field has a specific
direction, or ‘‘angle’’ of propagation,
and therefore the plane wave decompo-
sition described above also describes the
‘‘angular spectrum’’ of the field. Com-
plete description of light propagation,
hence, consists of the related contribu-
tions of the three spatial coordinates,
spectral wavenumber as well as individ-
ual amplitudes and phases describing the
angular spectrum. The term ‘‘spatial
1103
focal point review
frequency’’ is also used to describe f and
this arises from the spatial Fourier
transform interpretation of the fields.
In the most general sense, the goal of
modeling an IR imaging instrument is to
relate the field at the detector UD(f) to the
sample S(f) via a function, or an operator
A(f1, f2). The operator incorporates the
details of the specific instrument. For-
mally, the relation between the detector
field, the sample, and the instrument is
described using the equation
Z the image plane field U1(f) is
UD ðf 2 Þ ¼ d2 f1 Aðf 1 ; f 2 ÞSðf 1 Þ ð2Þ
The operator A(f1, f2) can be decom-
posed into constituent operators pertain-
ing to various aspects of light propaga-
tion in air, through substrates and
samples as well as optical components,
as follows. The propagation of the field
U1(f) in a plane to the field U2(f) in a
plane at a distance d in free space is
given by the equation
Z The imaging system consists of the
U2 ðf 2 Þ ¼ d2 f1 Kd ðf 1 ; f 2 ÞU1 ðf 1 Þ ð3Þ
where the operator Kd(f1, f2) is defined as
Kd ðf 1 ; f 2 Þ ¼ dðf 1 - f 2 Þei2pfz ðf 1 Þd
The operator for the interferometer can
be described in terms of a pair of
propagation operators as
1 mines spectral data quality, with small
Id1 ;d2 ðf 1 ; f 2 Þ ¼ ½Kd1 ðf 1 ; f 2 Þ
2 The field at the source is assumed to be
þ Kd2 ðf 1 ; f 2 Þ
The Schwarzschild optic can be mod-
eled as a Fresnel lens, which imparts a
quadratic phase factor to the incident
field, and is described by the operator
2 sample, S(f), the instrument parameters,
GC ðr1 ; r2 Þ ¼ dðr1 -r2 ÞQC ðr1 Þe-ipt̄r1 =Lf
ð6Þ
where Lf is the focal length of the
Schwarzschild and QC(r) is a pupil
function

b 1 a,r,b
Qa ðrÞ ¼ ð7Þ
0 else
The quadratic phase factor converts each
plane wave incident on the Schwarzs-
child optic into a spherical wave con-
1104 Volume 66, Number 10, 2012
verging on its focal plane. The phase
relation between incident plane waves
and the imparted quadratic phase deter-
mines the final image position and size.
Combining propagation operators and
the lens functions allows us to construct
an operator relating the scalar field in the
image plane of the lens to the field in the
object plane. If the object plane is at a
distance d1 from the lens and the image
plane is at a distance d2, then the relation
between the object plane field U0(f) and
U1 ðfÞ ¼ QtNA
tNAin ðfÞU0 ð-MC fÞ
out
ð8Þ
where MC = d2/d1 is the magnification
of the system. The above expression is
for a Schwarzschild focusing light on to
a sample (i.e., the ‘‘condenser’’). The
corresponding expression for the collec-
tor Schwarzschild (focusing lens) is
U1 ðfÞ ¼ QtNA
tNAin ðMC fÞU0 ð-MC fÞ ð9Þ
out
condenser, C1, the focusing lens, C2,
and the detector collection lens, CD. The
interaction of the incident field, U1(f),
with a thin sample, S(f), resulting in the
field U2(f) can simply be described as a
ð4Þ product in the spatial domain or, equiv-
alently, a convolution in spatial frequen-
cy as
Z tion.148 An optimal pixel size, which
U2 ðf 2 Þ ¼ d2 f1 U1 ðf 2 -f 1 ÞSðf 1 Þ ð10Þ
ð5Þ Uz0 (f). Light from the source passes
through the interferometer, is focused on
the sample, and is propagated via the
microscope to the detector. Combining
the operators described above allows us
to construct an expression relating the
and the detector field, UzD (f), as follows:
1 imaging with a synchrotron in which
UzDðfÞ¼ QCD ðfÞQC2 ð-MC fÞ
2 there is sufficient flux to over-sample the
Z   spatial domain, the use of a globar for
2 f1
3 d f1 QC1 -
MC 1
3f1 þ exp½i2pfz ðf 1 Þð2d2 -2d1Þg
 
f1
3 Uz0 ðf 1 ÞS þ M C2 M CD f
M C1
ð11Þ
This equation describes an IR imaging
system, based on an interferometer in
this case, under the scalar wave model.
The same formalism may be extended to
DF-IR systems as well to account for the
effect of different spatial frequencies of
features in the sample. While details on
the validation and use of the model are
available elsewhere,144 a crucial result is
highlighted here.
The model was used to predict the
behavior of two different optical ar-
rangements as well as to obtain insights
into the performance of imaging sys-
tems: a high numerical aperture (NA)
system (743, NA = 0.65) and a
commercially available low NA system
(153, NA = 0.5) in terms of imaging a
standard chrome-on-glass USAF target.
Data from optical microscopy were used
to simulate the object and simulations
were compared with experiments (Fig.
7). The major conclusion was that the
higher NA provided higher quality
images, as expected, but that the sam-
pling frequency at the detector was the
limiting factor in the performance of
current imaging systems. The correct
pixel size for sampling the image
without loss of detail was shown to be
~403 smaller than previously believed.
To date, there is one report of an HD
imaging instrument with a globar
source144 and one report of an applica-
balances the throughput, which deter-
pixels, which determines spatial image
quality, was determined at the highest
usable wavenumber in most spectra to
be ~1.1 lm. This is approximately two-
fold larger than that reported for a
synchrotron HD imaging system59 be-
cause of a careful optimization of
throughput, maximum wavenumber,
and the needs of the tissue system. As
opposed to studies of HD spectroscopic
HD imaging requires maximizing
throughput for the highest desired reso-
lution. The two studies illustrate the
success as well as the need to carefully
understand the requirements, trade-offs,
and performance using system modeling
to make intelligent spectrometer design
decisions.
FIG. 7. (A) The original object consists of a set of bars of sizes with transmittance indicated to the left. Absorbance images from
simulations (at 3950 cm-1) are shown for the focusing Schwarzschild with a (B) NA = 0.65, (F) NA = 0.50, and (G) NA = 0.50. The effective
sample pixel size at the detector in (B) and (F) is 1.1 lm, whereas the pixel size in (G) is 5.5 lm. Measured absorbance images (also
at 3950 cm-1) are shown with configurations (C) NA = 0.65, pixel size = 1.1 lm and (H) NA = 0.50, pixel size = 5.5 lm. (D), (E), (I), and (J)
show magnified regions from corresponding images. [Reproduced with permission from Ref. 144, copyright Society for Applied
Spectroscopy.]

Given the improvement in image
quality, there is immense interest in the
optical setup and use of this configura-
tion. The decreased pixel size, however,
results in a substantial loss in throughput
and the SNR of the resulting data is
poor. Synchrotrons and DF-IR sources
may well be the answer as a hardware
solution. A signal-processing approach
to reducing noise (see section on noise
reduction later in this article) can also be
implemented. Ultimately, the choice
between conventional and HD imaging
will be determined by the necessity of
HD imaging or of high spectral SNR.
Spatial averaging could be a compro-
mise in some cases and other methods
that could potentially be useful have
been previously discussed.149 Currently,
almost all commercial instruments rou-
tinely provide approximately the same
optical setup (0.5 NA, 153 objective).
The demonstration of HD imaging has
already spurred a number of different
instrument configurations. While the
diversity in image quality using different
lenses is obvious, the spatial and spectral
domains are intimately related in the
recorded data and changing the lens
changes the quality and content of the
recorded data. A more complete theory
is needed to understand this convolution
of optics, sample structure, and recorded
data. A framework for this approach is
discussed in the next section.
DATA INTERPRETATION:
THEORY
Infrared microscopy and imaging
have long been considered to be simple
adjuncts to optical microscopy. The
recorded data are usually considered to
be a simple extension of the IR spec-
troscopy of bulk materials, with the
additional trivial consideration that data
are selectively obtained from specific
points on the sample. Other than reflect-
ing species concentration, the spatial
structure of the sample was not thought
to play a major role in the recorded data.
The first major hint that there may be
additional considerations arose almost at
the same time FT-IR imaging with a
focal plane array was first reported.150 It
is only during the past three years,
however, that the full import of struc-
ture–spectra relationships has been
quantitatively explored by significant
advances in theory and a number of
experimental studies. It is now widely
recognized that there are differences in
the data recorded from a bulk measure-
ment and a microscopic measurement,
as there are between homogeneous and
heterogeneous samples in a microscope.
These differences arise from light focus-
ing at the point of interaction with the
sample as well as from the microstruc-
ture of samples on the scale of the

APPLIED SPECTROSCOPY 1105

focal point review
wavelength. Recent work has provided a
framework to understand these effects as
a function of spatial and spectral prop-
erties of the sample.
In this section, we focus on discussing
the forward problem, i.e., predicting the
spectra recorded from a sample in a
microscope. In particular, it is interest-
ing to understand how spectra from
heterogeneous materials in a microscope
differ from those that would have been
recorded from the bulk of the same
material using conventional spectrosco-
py. These differences are often termed to
be errors, distortions, or artifacts. We
would emphasize here that these terms
should not be used. There is ample
understanding, from the theory summa-
rized below and form confirmatory
experimental evidence, to indicate that
the spectral dependence on optical
configuration and sample microstructure
ed.151 Just as for the scalar wave theory where B is the angular spectrum in a
case, the sample is assumed to be a transverse plane. Next, we set up
linear system consisting of multiple boundary conditions at each layer inter-
layers of varying (complex) refractive face. Gauss’ law for electricity leads to
indices. This conceptual position allows
ðlÞ ðlÞ
a simplification of the general problem sx Bx ðsx ; sy ; t̄Þ þ sy By ðsx ; sy ; t̄Þ
of light–sample interaction into under- ðlÞ ðlÞ
standing light transport between pairs of þ sz Bz ðsx ; sy ; t̄Þ ¼ 0 ð15Þ
homogeneous layers. The approach is
general in that it can isolate heterogene- and
ity within layers, allowing for the ðlÞ ðlÞ
extension of the same framework to sx B̂x ðsx ; sy ; t̄Þ þ sy B̂y ðsx ; sy ; t̄Þ
heterogeneous samples. The electromag- ðlÞ ðlÞ
- sz B̂z ðsx ; sy ; t̄Þ ¼ 0 ð16Þ
netic field can be described as consisting
of a linear combination of plane waves,
Faraday’s law and Ampere’s law require
each of which satisfy Maxwell’s equa-
that the transverse components of the
tions at the boundaries as the entire
electric and magnetic fields be continu-
system is linear. Hence, the studies
ous. Hence,
employ the same approach as the scalar
wave framework in this case and ðlÞ ðlÞ
ðzðlÞ -zðl-1Þ Þ ðlÞ
Bx e½i2pt̄sz þ B̂x
analyze the response of the system to a ðlþ1Þ ½-i2pt̄sðlþ1Þ ðzðlÞ -zðlþ1Þ Þ
ðlþ1Þ
single plane wave first. The total re- ¼ Bx þ B̂x e z

is deterministic and reliably reproduc- sponse of the system to illumination ð17Þ

ible. Hence, there are no errors or would then be the sum of each of these
artifacts that arise from light–matter individual plane wave responses.
ðlÞ ðlÞ
ðzðlÞ -zðl-1Þ Þ ðlÞ
interactions and it would not be correct Let the electric, E, and magnetic, H, By e½i2pt̄sz þ B̂y
to term them as such. Rigorous electro- fields at a position, r, = (x, y, z)T be ðlþ1Þ ðlþ1Þ ½-i2pt̄sðlþ1Þ ðzðlÞ -zðlþ1Þ Þ
¼ By þ B̂y e z
magnetic models analyzing the interac- represented by their complex amplitudes
tion of light with heterogeneous samples and the permittivity and permeability of ð18Þ
have quantitatively predicted recorded free space be denoted by e0 and l0,
spectra as a function of experimental respectively. Let the real and imaginary and
parameters, clearly indicating that a parts of the refractive index of a single   ðlÞ ðlÞ
ðlÞ ðlÞ ðlÞ ðl-1Þ
deeper understanding of the recorded layer be denoted by n(t̄) and k(t̄), sy Bz -sz By e½i2pt̄sz ðz -z Þ
data is sorely needed. In fact, IR respectively. For homogeneous layers,  ðlÞ 
ðlÞ ðlÞ
microscopy is an unusually rich area of the electric and magnetic fields can be þ sy B̂z þ sz B̂y
investigation in the general realm of written as  
ðlþ1Þ ðlþ1Þ ðlþ1Þ
microscopy because the spectral diver- ¼ sy Bz -sz By
sity and unique light–matter interactions Eðr; t̄; tÞ ¼ E0 ei2pt̄sr ð12Þ  ðlþ1Þ 
ðlþ1Þ ðlþ1Þ
in the mid-IR spectral range give rise to þ sy B̂z þ sz B̂y
interesting theoretical questions and and
ðlþ1Þ
instrument-design tradeoffs. We divide rffiffiffiffiffi 3 e½-i2pt̄sz ðzðlÞ -zðlþ1Þ Þ ð19Þ
e0
further discussion to summarize the Hðr; t̄; tÞ ¼ ðs 3 E0 Þei2pt̄sr ð13Þ
framework for predicting the spectral l0   ðlÞ ðlÞ
ðlÞ ðlÞ ðlÞ ðl-1Þ

response of homogeneous materials, sz Bx -sx Bz e½i2pt̄sz ðz -z Þ

where s = (sx, sy, sz)T and jsj = e(t) =  
which indicate the effects of focusing, ðlÞ ðlÞ ðlÞ
k[n(t) þ ik(t)]2. The temporal depen- þ -sz B̂x -sx B̂z
as well as heterogeneous materials,
dence of the fields is not explicitly  
which additionally describe the effect ðlþ1Þ ðlþ1Þ ðlþ1Þ
denoted above for notational simplicity. ¼ sz Bx -sx Bz
of scattering at interfaces and light
The field in the lth layer (between zl-1  
transport within the sample structure. ðlþ1Þ ðlþ1Þ ðlþ1Þ
and zl) is given by - sz B̂x þ sx B̂z
Details of the theory are described in the
original publications. Here, we repro- EðlÞ ðx; y; z; t̄Þ ðlþ1Þ
3 e½-i2pt̄sz ðzðlÞ -zðlþ1Þ Þ ð20Þ
duce the critical equations, for parallel- ZZ n
ðlÞ
ism with other studies and for the sake ¼ t̄
ðl-1Þ
BðlÞðsx ;sy ; t̄Þe½i2pt̄sz ðz-z Þ
of completeness. Finally, note that there is no incoming
R2
Theory for Homogeneous Samples. ðlÞ ðlÞ
o light from the last boundary (L) and
ðlÞ Þ
A rigorous electromagnetic model to þ B̂ ðsx ;sy ; t̄Þe½-i2pt̄sz ðz-z therefore,
describe light–sample interaction and its ðLÞ
effect on recorded data has been report- 3 e½i2pt̄ðsx xþsy yÞ dsx dsy ð14Þ B̂ ðsx ; sy ; t̄Þ ¼ 0 ð21Þ

1106 Volume 66, Number 10, 2012

FIG. 8. Comparison of the rescaled absorbance spectra from the same toluene film acquired in two different configurations, in
transmission mode on a BaF2 substrate and in transmission-reflection (transflection) mode on a gold substrate. Simply changing the
thickness of the film changes the recorded data. [Reproduced with permission from Ref. 151, copyright American Chemical Society.]

The equations above summarize the
complete set of boundary conditions
for analyzing a multi-layer sample
consisting of homogeneous layers. As-
signing refractive indices and thickness
to each layer allows for a complete
solution for the system of equations. It is
notable that the solution does not require
any empirical parameters or adjust-
ments. Hence, it can generally be used
to predict the behavior of any specific
system. A number of cases are consid-
ered in the complete report on this
subject.151 One example is highlighted
While extracting absorbance from spec-
tra measured by a specific configuration
is discussed in the next section, this
forward modeling can be used to
compare two different experimental
configurations. If spectral dependence
on thickness were to be calculated, in
the example discussed here, highly
accurate measurements could be made
by switching from reflectance-based
sampling (Au substrate) to measuring
transmittance of the sample on a BaF2
substrate. Distortions in transflectance
measurements of samples that can be
transverse heterogeneity in the film can
always be assumed to be of finite area.
Hence, the structure of the object can be
reasonably approximated by its two-
dimensional Fourier series. The proper-
ties of the heterogeneous layer can be
characterized by a transversely varying
complex refractive index or equivalently
by its permittivity, e, which follows its
spatial structure. Truncating the Fourier
series of e and e-1 to a finite number of
coefficients gives
NX
U -1 NX
W -1

(Fig. 8) to illustrate the observed considered to be layered have been eðx; y; ṽÞ » /p;qðṽÞe½iðpUxþqWyÞ
dependence of the spectral response on experimentally noted elsewhere155,156 p¼-NU q¼-NW
sample parameters and sampling config- and could be understood in terms of ð22Þ
uration. Spectra are re-scaled by thick- interference between the propagating
ness, as would be appropriate for Beer’s and reflecting waves. The importance and
law, and compared to the ideal (obtained of the analysis based on first principles
from tabulated values of the imaginary is that quantitative predictions and ½eðx; y; ṽÞ-1
part of the refractive index). Deviations evaluations can now be made, which
from the ideal demonstrate that the can provide an understanding of how NX
U -1 NX
W -1

optical effects of anomalous disper-
sion152 can result in recorded spectra
with significantly shifted band peaks
and severely distorted relative intensi-
ties. The use of an aperture changes the
optical configuration and similar effects
were observed and quantified.153 The
quantitative accuracy of these measure-
ments as well as chemical specificity
(e.g., drawing conclusions regarding
hydrogen bonding or packing from peak
shifts) is compromised even when using
sophisticated spectral correction154 that
does not explicitly take into account the
optical phenomena in image formation.
recorded data are related to structure for » wp;q ðṽÞe½iðpUxþqWyÞ
the first time. p¼-NU q¼-NW
Theory for Heterogeneous Sam- ð23Þ
ples. While the previous formulation
provided insight into layered samples, Due to the periodic nature of the sample,
one approach to understanding thin films an incident plane wave exp[i(dx þ ry)]
of heterogeneous materials could be to is shifted only by integer spatial fre-
model spectra from each pixel indepen- quencies, resulting in plane waves with
dently. In heterogeneous films, however, spatial frequency components given by
light scatters, thus affecting neighboring
pixels as well and a more complete up ¼ pU þ d ð24Þ
description of the interaction of light
with sample morphology is needed.157 and
For any IR imaging experiment with
present day microscopes, the region of wq ¼ qW þ r ð25Þ

APPLIED SPECTROSCOPY 1107

focal point review
XX
The electric and magnetic fields can be ¼ -i2pt̄ /p-p 00;q-q 00 ðt̄Þ well as its effect on the spectrum
represented using plane wave decompo- p 00 q 00 recorded by pixels relative to the
sitions as 3 Yp 00;q 00 ðz; t̄Þ þ iup Kp;q ðz; t̄Þ ð33Þ position of the scattering interface (Fig.
9). First, spectral contributions from a
ðDÞ
E ðx; y; z; t̄Þ and scattering pixel can be observed in
2 3 neighboring pixels where there is no
X X Xp;q ðz; t̄Þ dJp;q ðz; t̄Þ sample. The scattering contribution can
¼ 4 Yp;q ðz; t̄Þ 5e½iðup xþwq yÞ be significant and can be calculated for
dz
p q Zp;q ðz; t̄Þ XX particular materials and vibrational
¼ i2pt̄ /p-p 00;q-q 00ðt̄ÞXp 00;q 00 ðz; t̄Þ modes for different distances. Second,
ð26Þ p 00 q 00
recorded data demonstrate a positional
and þ iwq Kp;q ðz; t̄Þ ð34Þ dependence both in intensities of bands
and in the position of peak absorbance.
HðDÞ ðx; y; z; t̄Þ These expressions can be reorganized Since normalization is a common prac-
2 3 into a matrix differential equation of the tice in spectroscopic analysis, the effect
rffiffiffiffiffi X X Ip;q ðz; t̄Þ form is compounded on absorbance ratios. A
e0 4 Jp;q ðz; t̄Þ 5e½iðup xþwq yÞ
¼ 2 3 baseline offset is also observed for
l0 p q K ðz; t̄Þ dXðz; t̄Þ
p;q pixels in the vicinity of the interface.
6 dz 7 Third, peak positions are not substan-
ð27Þ 6 7
6 7 2 3 tially altered and may be more reliable
6 dYðz; t̄Þ 7
6 7 Xðz; t̄Þ for chemical identification. Again, the
Note that the electric and magnetic fields 6 dz 7 6 Yðz; t̄Þ 7
6 7 results indicate that caution must be
are not necessarily orthogonal in the 6 dIðz; t̄Þ 7 ¼ i2pt̄Uðt̄Þ6 7
4 Iðz; t̄Þ 5
presence of transverse heterogeneity, but 6 7 exercised in interpreting small wave-
6 7
can be related using Faraday’s law and 6 dz 7 Jðz; t̄Þ number shifts in spectra from imaging
6 7
Ampere’s law, resulting in 6 dJðz; t̄Þ 7 data. Finally, we note that these predic-
4 5 tions are made for transmission mode
rffiffiffiffiffi dz
l0 measurements and will be substantially
r 3 Eðr; t̄Þ ¼ i2pt̄ Hðr; t̄Þ ð28Þ affected by the interference of the
e0 ð35Þ
propagating and reflected waves in a
and The above matrix equation couples the transflection geometry.
rffiffiffiffiffi electric and magnetic fields. It is possi-
e0 ble to decouple these equations by INFORMATION RETRIEVAL
r 3 Hðr; t̄Þ ¼ -i2pt̄eðr; t̄Þ Eðr; t̄Þ
l0 computing the eigenvalues and eigen- Even in one of the first applications of
ð29Þ vectors of U and find X, Y, I, and J in IR imaging,150 it was apparent that both
terms of the eigenvalues and eigenvec- the imaginary and the real part of the
Expanding the above equations provides tors. The boundary conditions for each refractive index influence recorded data.
a system of equations that completely component can be evaluated in the same In an elegant accompanying experiment,
describe light–matter interactions in an manner as those for homogeneous layers the real part of the refractive index was
IR microscope given above. Therefore, we can solve changed (with small changes in the
the matrix equation and find the electric imaginary part) and baseline offsets
dXp;q ðz; t̄Þ (E) and magnetic (H) field at every were seen to largely disappear as indices
¼ i2pt̄Jp;q ðz; t̄Þ plane in the heterogeneous sample as were matched (Fig. 10). Even at that
dz
well as any underlying substrate. Just as early stage of the technology, it was
þ iup Zp;q ðz; t̄Þ ð30Þ in previous formalisms, the fields and cautioned that spectral changes indica-
intensities at the detector can again be tive of molecular interaction should be
dYp;q ðz; t̄Þ computed by propagating light via the interpreted with caution at interfaces as
¼ -i2pt̄Ip;q ðz; t̄Þ intervening optics. The detector intensi-
dz they may arise from purely optical
ty is the recorded data, which can be effects due to the refractive index
þ iwq Zp;q ðz; t̄Þ ð31Þ
calculated given the source and sample mismatch. Thus, information extraction
properties, and compared to observa- from spectroscopic imaging data sets is
Kp;q ðz; t̄Þ tions or ideal predictions. This frame- not a straightforward process of treating
work provides a powerful mechanism to a spectrum from each pixel as an
1 understand the behavior of IR imaging independent measurement comparable
¼ ½up Yp;q ðz; t̄Þ-wq Xp;q ðz; t̄Þ
2pt̄ systems as well as effects on the to a spectrum from a conventional
ð32Þ recorded data of specific structures. spectrometer. The same scattering ef-
A key finding of this work lies in fects are present in bulk measurements
dIp;q ðz; t̄Þ understanding the spatial extent of using a non-imaging spectrometer and
dz scattering by a single sharp interface as could be used to understand structure

1108 Volume 66, Number 10, 2012

FIG. 9. (A) Pixels in the vicinity of an idealized edge are examined for responses from a single material. (B) Spectra (colors correspond
to the arrows indicating positions in (A)) demonstrate baseline offsets, relative changes in band intensities, and shifts in peak positions.
(C) Detailed examination in the fingerprint region shows the effect of scattering on the apparent position and relative ratio of peak
absorbance. [Reproduced with permission from Ref. 157, copyright American Chemical Society.]

formation, for example, to monitor the
relationship between reaction, phase
separation, and ordering in complex
systems.158,159 While one aspect of these
effects is obviously useful and can be
developed for specific applications, ex-
tracting spectra that resemble those that
would be measured using bulk spectros-
copy of the materials in the micro-
domains is worthwhile to separate the
effects of microstructure and chemical
content and realize the ideal of purely
chemical information at specific sample
locations. As the forward modeling
results in the previous section indicate,
spectral response from microdomains
within samples of wavelength-compara-
ble dimensions complicate interpreta-
tion. Hence, we focus this first section
on approaches to recover purely chem-
ical information from recorded data and
term this the absorption spectrum to
distinguish it from the recorded spec-
trum.
The delineation between these two
types of useful spectra is an important
distinction and cannot be over-empha-
sized here. The recorded data contain
effects arising from both the real part of
the refractive index (scattering, for
example) and the imaginary part (ab-
sorption). They also contain the effects
of the ‘‘interaction’’ term due to the
relationship of the two components of
the refractive index and especially due to
anomalous dispersion. While the record-
ed data can be used directly to extract
information, classical spectroscopic
analyses have focused on relating the
absorbance to specific molecular content
via chemometric methods. We do not
focus on chemometric methods here as
there are several excellent compilations
describing the same for spectroscopy,160
in general, and for imaging,161,162 in
particular. The extraction of absorption
spectra from recorded data occurs prior
to the application of chemometric meth-
ods. Unless information is extracted in
terms of the underlying molecular con-
tent and the contributions of structure
recognized, in general, the application of
chemometric methods cannot provide
the correct results.
Extracting Spatial and Spectral
Information. Three major groups of
efforts can be discerned in the area of
extracting information from recorded
data. In the first, an understanding of
the underlying physics of the problem is
targeted and the goal is to recover the
spectral and spatial structure of the
sample as accurately as permitted by
the measurements via maps of the real
and imaginary parts of the refractive
index. We term these ‘‘analytic’’ ap-
proaches. In the second, a sufficient
recovery of absorption spectra is target-
ed to achieve the desired molecular
identification or understanding. Ap-
proaches in this stream may range from
simple signal processing approaches to
more complex representations of the
sample and optics but the underlying
light–matter interaction is not directly
targeted for the specific sample. We
term these ‘‘model-based’’ approaches as
they necessarily idealize the sample to a

APPLIED SPECTROSCOPY 1109

focal point review
was simply to visualize the presence of
prints and organic material, which is
easily accomplished without the need
for any extensive spectral analysis (Fig.
11A). The power of IR imaging is
apparent in further analysis, however.
The spatial specificity of the technique
leads to enhanced spectral sensitivity
when a material of interest can be
localized, for example in particulate
trace evidence within prints. Again
spectral features may be used to identify
a molecular species associated with the
particulate matter. In this case, the
explosive RDX is easily detected using
vibrational modes that are clearly indic-
ative of this material and not found in
most other materials. Delving further,
simply examining the absorbance at a
common vibrational mode such as CH
stretching allows facile detection of
other trace evidence such as fibers.
Fibers, by themselves, form a very
important class of forensic interest and
their molecular identification can prove
powerful. The recorded spectrum from a
fiber that has the same diameter as the
FIG. 10. Refractive index mismatches cause baseline offsets and apparent absorption in a wavelength of light, however, demon-
polymer dispersed liquid crystal. Chemically specific absorbance (top, left) and apparent strates the effects of light scattering and
absorbance (baseline offset) arising from optical mismatch of refractive indices can be diffraction that make molecular identifi-
observed in recorded data. The application of a voltage along the light propagation direction cation difficult. Thus, as the complexity
aligns liquid crystals in the microdomains, thereby changing the refractive index and
matching the real part of the index closely to the surrounding matrix. Matching the refractive of the problem and the need for
indices eliminates the baseline offset in spectra and the apparent absorbance at the information increase, the methods re-
interface that arises from scattering. [Reproduced from Ref. 158, copyright American quire progressively more effort. The first
Chemical Society.] years of IR imaging technology proved
very successful in applications without
simple geometric structure such as a the last approach but there is limited significant efforts in understanding the
sphere and/or idealize the optics to a insight into the properties of the sample data as simpler applications (such as
visualizing the structure of materials164
simple plane wave. The third set of and no assurance that the most accurate
or measuring diffusion165) were target-
approaches is essentially what largely molecular information contained in the
ed. Today, instrumentation is mature
exists today in commercial instruments’ data is extracted. The model-based
and the next level of complexity is being
software and consists of simple baseline approaches lie in the middle of these
targeted for information extraction.
and offset correction or fitting a more extremes. While they can be very Hence, approaches to extract absorption
complex shape to the spectrum. We term effective for some samples, based on spectra from recorded data are going to
these ‘‘ad hoc’’ approaches as they rely careful selection of the model, they do become more commonly reported and
largely on a subjective decision made by not offer a general solution and require used.
the investigator and only have a loose some computational effort to extract The need for such methods is illus-
rationale in the selection of a particular information. trated in the spectra from the particulate
approach. The benefit of the first set is Analytic Approaches. Both the suc- matter in Fig. 11, and the effect of shape
clearly in the accuracy of understanding cesses of IR imaging and the need for is clearly evident in the predictions of
and purity of information available but further analytic approaches are perhaps recorded data in the spectra of fibers and
also requires significant effort in algo- best illustrated with a case study, as spheres. Spectra from the same material
rithms and computation. Analogous to shown in Fig. 11. Here, IR imaging is are significantly affected, which can lead
the development of the forward predic- applied for latent print analysis.163 Oils to erroneous conclusions. Fiber analysis
tion, it is essentially a solution of the and skin can be visualized easily from by IR microscopy166 is widely reported
inverse problem. The speed of informa- absorption spectra using appropriate and can be used easily for major classes
tion extraction is the obvious benefit of vibrational modes. The first goal here of materials. Finer distinctions in mo-

1110 Volume 66, Number 10, 2012

FIG. 11. (A) RGB image of a fingerprint obtained using oil, protein, and particulate matter-specific absorbance modes, respectively. (B)
Expanded view of the box in A. (C) Spectra of the components showing the bands indicative of the specific components. (D) A single fiber
can be seen in the print with a particle next to it. The trace evidence can also be idealized to be cylindrical or spherical in shape. Modeling
predicts the shape dependence of spectra, dramatically altering the recorded data for the same material. [Reproduced with permission from
Refs. 163 (A–D, copyright Springer), 167 (cylinder spectra, copyright American Chemical Society), and 168 (sphere spectra, copyright
Society for Applied Spectroscopy).]

APPLIED SPECTROSCOPY 1111

focal point review

FIG. 12. The state of the art in available algorithms can successfully estimate the correct absorbance and refractive index from samples of
known shapes. Reconstructions and true values of the complex refractive index are shown for fibers of radius 5 lm (A–C) and 10 lm (D–F).
[Reproduced with permission from Ref. 167, copyright American Chemical Society.]

lecular content and changes, however,
are not easily measurable or quantitative
and require special sample preparation.
Clearly, if absorbance spectra cannot be
extracted, recorded data would not
provide accurate information, for exam-
ple on polarization to understand mo-
lecular structure or surface modi-
fications—both of which are important
considerations in fibers. While forward
modeling (Fig. 11D) indicates that
recorded spectra are difficult to use
directly, the same can be extended to
predict dynamic spectral changes, ef-
fects on molecular orientation, or surface
modifications, though no studies have
been reported. More useful would be the
extraction of absorption spectra from
recorded data. An algorithm that enables
this recovery from cylindrical objects
that have physical dimensions of the
order of the wavelength of light has been
formulated.167 Spectra clearly corre-
sponding to the bulk spectra of materials
could be recovered and the effect of
optical phenomena could be removed. A
similar effort for spheres168 is reported
and demonstrates a similar success in
recovering molecular information.
As the studies for spheres and cylin-
ders indicate, the use of analytic ap-
proaches for spectral extraction can be
greatly simplified by knowledge of the
sample. If the sample thickness is known
a priori, for example, iterative tech-
niques can be used to estimate the
absorbance from IR imaging data for
thin films. In the absence of thickness
information, co-estimating both geome-
try and spectra is difficult and conver-
gence to the correct result is not always
guaranteed. Hence, an intelligent strate-
gy is required to extract knowledge
optimally, and no simple approach exists
that is valid in all cases. In the case of
uniform films, for example, reflection
fringes can be used to estimate the real
part of the refractive index and thick-
ness, which can be subsequently used to
inform the recovery of the imaginary
part of the refractive index at other
spectral positions. Despite the successes
noted above for specific cases and the
suggested approximations from the ho-
mogeneous case, simultaneously recov-
ering both the geometry and spectra of
samples using IR imaging is an open
problem and the subject of current
research. One example of the potential
of the success of this approach can be
seen in Fig. 12, which demonstrates the
extraction of absorption spectra from
cylindrical objects. We do not discuss
other approaches under development
here but it is clear that the near future
will see the emergence of practical
algorithms and their integration with
instrumentation. It must be noted that
the recovery of spectral information is
dependent on the quality and extent of
input information. High SNR, extended
wavelength, and larger spatial areas than

1112 Volume 66, Number 10, 2012

the sample would need to be measured
to assure more accurate data recovery. It
is expected that future instrumentation
will be designed with the goal of
recovering such information rather than
simply acquiring data of the highest
SNR and will be based partly on the
insights offered by analytical approaches
to recover molecular spectra. The com-
putational burden on IR imaging will
undoubtedly increase with the use of
these algorithms, and effective strategies
(both hardware and software) will be
needed to extract molecular spectra.
Model-Based Approaches. While the
theory and corresponding approaches
described above are effective in recov-
ering absorption data, approximations
have also been proposed to model real
samples as consisting of absorbing and
scattering objects. With a definite object
and simplified optical interactions, facile
fitting to scattering features observed in
spectra can be conducted very rapidly,
largely because the specifics of the
particular sample do not have to be
modeled. Considerable recent interest
has focused on Mie-type scattering and
absorption.169 The forward problem in
this approach is rather straightforward in
that the scattering of specific objects is
well described in books.170 The inverse
implementation for imaging is interest-
ing. Details of the procedure are avail-
able in the studies described here; hence,
we will summarize only the most
interesting features of this approach.
One of the popular means to correct
for the effects of scattering on spectra
has been essentially to model the effects
for given properties of the sample and
build a lookup table. Matching observed
with known spectra can then be em-
ployed to correct for the observed
changes compared to what may be
expected in the absence of such chang-
es.171,172 Using spheres, spectral distor-
tion could be demonstrated, compared to
the bulk spectrum of the same polymer
film.173 The topic is relatively recent in
the field of microscopy, though it has
been recognized for spectroscopic mea-
surements in other applications of IR
spectroscopy.174 Variations on the use
of a scattering model have been pro-
posed. For example, resonant Mie scat-
tering (RMieS) was claimed to be
corrected using an improved iterative
algorithm. The application of full Mie
theory considerably enhances the com-
putational load, which was alleviated by
using graphical processing unit (GPU)-
based processing.175 Another caveat in
iterative methods is noise accumulation,
which was avoided by using a curve-
fitting step. To date, no modifications
have been reported in the illumination
and collection optics associated with the
extraction. This extension is likely
possible and the models could become
more sophisticated. The increasing so-
phistication, however, will deprive
methods of their computational simplic-
ity and abilities in straightforward ap-
plication. At the extreme, they will
involve the same effort as analytical
approaches. Hence, it is difficult to
foresee that significant conceptual effort
in increasing the sophistication of the
models will result in more accurate
analyses. Rather, in the opinion of the
author, a diversity of models will likely
be available and significant efforts will
be spent in choosing one and validating
it for use in a specific application.
The use of models to understand
spectra and extract absorbance data is
often stated as a correction. The author
of this manuscript is not in favor of
using the term ‘‘correct.’’ The spectra are
already correct in that they correctly
reflect the underlying chemical and
physical (which are both related) struc-
tures. A better term would be to
‘‘extract’’ absorption spectra since the
absorption measure is obtained from the
recorded spectrum in which absorption
and scattering are co-mingled. Hence, in
this manuscript, we employ the term
extraction and urge readers to do the
same.
Significant caution should be exer-
cised in employing model-based ap-
proaches to extract absorption spectra.
To extract spectra accurately, the under-
lying structure of the sample must fit the
model and approximations precisely to
be valid under all conditions. For
example, the extended multiplicative
scatter correction approach was careful-
ly developed and validated for a specific
set of samples with a clear validation
endpoint (indistinguishable performance
in the calibration and test set).176 The
algorithm, obviously, should not be
applied to all types of spectra that may
APPLIED SPECTROSCOPY
include other optical phenomena nor
should accuracy in extracting chemical
information be claimed in the absence of
a strict and valid endpoint. Simply
obtaining spectra that seem to be
accurate does not guarantee that the
intensities, band shapes, and positions
are indeed correct. If rigorous tests for
applicability are not conducted, the
extracted spectrum may change (other
than simple Beer’s law re-scaling) with
thickness of the sample, or change in the
optical setup or with spectral resolution.
Since model-based approaches are es-
sentially an empirical test, not only
should the ideal sample be tested but
all possible combinations of thickness,
optical effects, range of sample proper-
ties, and their variations with optical
setups must be tested against a gold
standard. While model-based approach-
es are convenient and useful, this
stringent and onerous requirement for
robustness is a likely barrier to their
effective use. More sophisticated models
of beam propagation and acquisition are
needed and model-based approaches
being replaced by analytical approaches
will likely be a future trend.
Ad Hoc Approaches. The simplest
approach to extracting absorbance from
measured spectra, and the first good
approximation in many cases, remains to
choose points across a band and remove
the baseline offset. The underlying
assumption in this approach is that the
effects of refractive index mismatch did
not significantly change the recorded
data’s peak absorbance, position, or
shape beyond the noise level. This type
of approach, in conjunction with elimi-
nating spectral features that likely did
not benefit from this approach, provided
excellent results in tissue classification,
for example.177 The success in that
study does not imply success for all
cases, whereas there is no guarantee that
more complicated methods to remove
the effects of scattering would perform
significantly better. Analytical absorp-
tion extraction methods will be better, in
general, while model-based methods
may perform better or worse or may be
more effective in certain spectral regions
than in others. Success depends on the
optical setup and the characteristics of
the sample. Hence, it remains unclear
whether ad hoc approaches are any
1113
focal point review

FIG. 13. (A) Acquired high SNR data and simulated noisy spectra (peak-to-peak noise = 0.001, 0.01, 0.1, and 0.4 a.u.), showing the
degradation in data quality. Spectra are offset for clarity. (B) Spectra after noise reduction demonstrate the dramatic gains possible by
chemometric methods. (C) Noise reduction was implemented to classify breast tissue and application of noise rejection allowed the same
quality of classification (accuracy) to be recovered at higher noise levels. (D) In another example, image fidelity (here the nitrile stretching
vibrational mode at 2227 cm-1) is much enhanced as a result of spectral noise rejection. [Figures A and C reproduced with permission from
Ref. 188, copyright Royal Society of Chemistry. Figure D reproduced with permission from Ref. 184, copyright Society for Applied
Spectroscopy.]

better or worse than model-based ap-
proaches. In any case, the two approach-
es cannot perform any better than what
appropriate analytical modeling may
provide. Hence, the value of ad hoc
approaches will likely persist for excep-
tionally rapid but qualitative understand-
ing of the data in the absence of a
framework to correctly estimate optical
properties of the sample along with its
structure or as starting points for algo-
rithms solving the inverse problem.
Improving Imaging Data by Com-
putational Approaches. While the ap-
proaches above are focused on extract-
ing molecular data, other approaches can
be used in conjunction to estimate and
improve the spectral and spatial content
of information. The class of techniques
discussed below, hence, lies between
extracting information and chemomet-
rics. Among the approaches to improve
data, noise reduction strategies are of
most importance. While noise deter-
mines the quantification limits and
ultimate sensitivity of measurements,
reduction of noise has taken on added
importance with the advent of HD
imaging and computational algorithms
to extract absorbance. The second area
would be in the domain of enhancing the
clarity of an image or enhancing the
features in a manner similar to optical
microscopy.178 A note of caution must
be repeated in the use of computational
approaches to suppress noise or any
other enhancements. Over-processing
data may lead to such severe distortions
that the underlying information may
change. Even small implementations to
improve visualization must be under-
stood and interpreted correctly by the
practicing spectroscopist. In IR imaging,
the spectral and spatial domain are
clearly linked. Hence, changes or im-
provements in one affect the other. Two
areas that are likely to be the focus of
activities in this theme are discussed
next.
Noise Reduction. Spectral noise is a
significantly greater concern in imaging
compared to bulk spectroscopy. While
appropriate data collection by optimiz-
ing the optical and experimental param-
eters is the ideal route to obtaining the
highest SNR, limited time and resources
may not always make that possible.
Numerical methods for noise rejection
have been proposed and can be useful
for rapid acquisition of data. The
transformation may involve simple
smoothing since signals are generally
of lower frequencies while noise is both
high and low frequency, determining
correlations using point-wise179 or mul-
tivariate means, or statistical recon-
struction180 or wavelet transforms.181
Smoothing results in loss of spectral
detail but can enhance spectral sensitiv-
ity and provide lower noise images, is
rapid, and can be easily implemented.
To take advantage of the statistical
properties of many pixels in an imaging
experiment, however, transform meth-
ods may be able to preserve both
spectral and spatial quality. In transform
or reconstruction methods, successful
noise rejection first involves recognizing
a property of noise that is distinct from
that of the signal. Second, the noisy data
need to be transformed such that the

1114 Volume 66, Number 10, 2012

 FIG. 14.
characteristic spectral features are col-
lected in some components of the
transformed space and noise is isolated
in others. Third, a cut-off needs to be
selected such that the information-rich
components can be identified. Finally,
an inverse transform of the components
identified as bearing information needs
to be conducted to recover high SNR
data. The type and quantity of available
data often dictates the optimal method.
The use of the multivariate covariance
method is especially interesting when
large numbers of spectra are available,
which is usually the case for spectro-
scopic imaging data, for example, prin-
cipal components analysis. 183 One
example of the potential of this approach
can be seen using a method based on a
modified principal components analysis,
termed the minimum noise fraction
(MNF),183 which has been used for
several different systems and demon-
strates broad efficacy.184–187 While the
need for an observer to select eigenim-
ages for transformation was often an
impediment, this process can be effec-
Overview of IR imaging and developing areas of activity.
tively automated and excellent reliability
can be obtained in recovering analytical
ability of measurements.188 The quality
improvement can be observed in Fig. 13.
Upon de-noising, significant recovery of
spectral and spatial details can be
observed. Though very successful, it
must be noted that any such method
results in loss of information (signal).
The goal should be to limit the loss to be
no larger than the uncertainty introduced
by measurement noise in the original
data set. Though analysis and image
quality are greatly improved, it must be
realized that the noise-reduced signal in
these cases contains a statistically esti-
mated SNR and users must be cautious
in drawing conclusions such as detection
limits or estimating the variance in the
data.189 While this approach to noise
reduction was not particularly required
for imaging with larger pixels, the HD
imaging approach has resulted in a large
reduction in the signal and the SNR. For
HD imaging, signal processing repre-
sents a useful tool that can be routinely
used.
APPLIED SPECTROSCOPY
Deconvolution. Several studies have
employed signal processing techniques
to improve image quality.190 The tech-
niques essentially rely on minimizing (or
maximizing) a cost function and can be
implemented without user input or
knowledge of the actual instrumentation
or sample. While these properties make
such methods robust and widely appli-
cable, they also lead to a general
smoothing of features and sharpening
of the related visualization parameters of
image details and contrast. While these
techniques are useful for visualization,
the images are estimates of the true
microstructure. The less information
about the optical setup such methods
contain, however, the greater is the
chance they may deviate from the true
sample structure. Given the recent
advances in theory and modeling as
well as the availability of computing
power, the best approach may be to use
the actual performance of the micro-
scope to inform the reconstruction. An
example of merging optical theory with
signal processing approaches is also
1115
focal point review
available.191 With the emergence of HD
imaging and development of nanoscale
imaging, the gap between imaging
modalities is closing. Hence, given the
ability to acquire data directly and the
uncertainty associated with structures
after reconstructions, simple techniques
to estimate smaller than wavelength
features are of diminishing value.
CONCLUDING REMARKS
This is an exciting time in the IR
imaging and microscopy field. New
theory and instruments have opened
new capabilities. One of the most critical
aspects of IR imaging technology is the
FPA. Mercury-cadmium-telluride
(MCT) FPAs are commonly employed
due to their wide spectral sensitivity and
good detection characteristics. While the
first generation’s problems of stability
and device reliability have largely been
addressed by chemical vapor deposition
technology and the MCT alloy chemis-
try is well-established, the overall de-
tector performance can be significantly
improved. The electronics for these
FPAs, in particular, are noisy and slow
compared to state-of-the art readouts
widely available in other spectral re-
gions. Ten-fold-lower noise in ten-fold-
faster readout electronics can potentially
provide video rate IR spectroscopic
imaging. The small format of available
arrays (128 3 128) can also be im-
proved. There are recent reports with
faster detectors and larger formats192
that will considerably enhance the
quality of available data. Even better
performance may be expected from
emerging technologies. While speed
and size will increase, the impetus for
the same has received a boost from
recent developments. Given the limited
flux from globar sources and smaller
beam sizes from the brighter sources,
significantly larger formats were not
thought to be very important. With the
advent of HD imaging, however, there is
significant value in pursuing smaller
pixel sizes and larger formats.
The availability of multiple new
components that are driven by sound
fundamental advances further portends
an acceleration of activity. New con-
cepts such as extraction of absorbance
by separating chemical and structural
effects as well as new computational
1116 Volume 66, Number 10, 2012
concepts such as compressed sensing
will not only change the practice of
spectroscopy but will bring computing
and instrumentation closer. While we
have not discussed applications here, the
development of new capabilities is likely
to transform applications as well. The
last major technological innovations in
IR imaging are almost ten years old. The
next cycle of advances is likely to come
from the application of new theory. As a
better understanding and availability of
the new components improves, new
optical configurations will likely be
seen. Hardware developments are likely
to enable new application areas and, in
turn, spur the development of faster
algorithms and signal-processing strate-
gies to store data, perform spectral
corrections, and extract information.
The various facets of IR imaging
technology and applications actually
form an integrated cycle as shown in
Fig. 14. For each of the major categories
in the inner circle, there are many
choices available to the spectroscopist
today in designing a particular study.
The cycle of development of theory
consisting of various approaches, indi-
vidual components integrated into high-
er performing instrumentation, and
algorithms and software for signal
processing and data management must
be tuned together with the application in
mind for an optimal solution. While
such an approach has not been commer-
cially demonstrated, several research
groups are working to include specific
aspects of each into their particular
solutions. Individual developments in
each of these aspects and the synergistic
integration of one or more of these
components are likely to prove the most
beneficial. Any of the factors can be
central to this integration but, in the
author’s opinion, we will likely see
evolution around applications. In princi-
ple, the recent advances make it possible
to analytically predict the performance
and utility of IR imaging for any
application for a given system design.
Hence, simulations from problem to
solution can be developed for the design
of instruments and analytical strategies
by a careful combination of hardware,
algorithms based on the physics of the
setup, and robust reconstruction to
provide the highest quality information.
In the opinion of the author, the
summary achievement of recent advanc-
es has been to enable the spectrometrist
or engineer to quantitatively measure,
model, and manufacture IR imaging
systems guided by rigorous application
of fundamental scientific principles. The
resulting benefits, in turn, are likely to
significantly enhance the applied spec-
troscopist’s ability to extract meaningful
information and solve important prob-
lems.
ACKNOWLEDGMENTS
The author would like to acknowledge the
contributions of colleagues and students who were
involved in various studies on which this review is
based, including Ira W. Levin, Stephen M. Hewitt,
P. Scott Carney, Brian Cunningham, Brynmor
Davis, Matthew Schulmerich, Michael J. Walsh,
Anil K. Kodali, Rohith K. Reddy, Thomas van
Dijk, Kevin Yeh, Matthew Kole, and Matthew
Gelber. Support for this work from the National
Institutes of Health (R01CA138882 and
1R01EB009745) and the National Science Foun-
dation (CHE 0957849) is gratefully acknowledged.
This article is dedicated to Prof. Peter Griffiths,
from whose works the author has greatly benefited,
on the completion of his term as the editor-in-chief
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