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Sensors and Actuators A 279 (2018) 367–375

Contents lists available at ScienceDirect

Sensors and Actuators A: Physical


journal homepage: www.elsevier.com/locate/sna

A portable, optical scanning microsystem for large field of view, high


resolution imaging of biological specimens
Georgia Korompili a,b , Georgios Kanakaris a , Christos Ampatis a , Nikos Chronis a,b,∗
a
Institute of Nanotechnology and Nanoscience, N.C.S.R. Demokritos, Athens, Greece
b
Department of Materials Science and Technology, University of Crete, Irakleion, Greece

a r t i c l e i n f o a b s t r a c t

Article history: Adapting medical technology for use at the point of care, demands the development of portable, robust
Received 13 January 2018 and accurate systems for the early diagnosis and monitoring of a wide range of diseases. Microscopy at the
Received in revised form 3 June 2018 point of care, fueled by recent advances in micro-optics, micro-electronics and micro-electromechanical
Accepted 17 June 2018
systems, is an emerging and promising field. However, imaging devices already developed remain rather
Available online 24 June 2018
sophisticated and bulky, mainly because of failure to address the most challenging technical limitation:
to combine large field-of-view (FOV) with high resolution imaging of biological specimens. To address
Keywords:
this need, we developed a portable, optical scanning microsystem that can image - with approximately
Point-of-care
Microscopy
1 ␮m resolution- large areas (6 mm × 40 mm) from various biological samples. This is achieved through
Large field of view the use of a microfabricated - 2D lens array that scans a sample in 1 direction in few minutes. We
Optical imaging demonstrated that our system can image blood smear and identify single white blood cells immobilized
Lens array in a microfluidic chip.
© 2018 Elsevier B.V. All rights reserved.

1. Introduction for progress monitoring and treatment adjustment in the case of


HIV-infected patients and patients undergoing chemotherapy for
Early diagnosis and accurate continuous monitoring of the cancer treatment. Whole slide blood imaging and cell population
progress of a disease are both considered of critical impor- counting represent irreplaceable steps of the diagnostic procedure
tance. However, time consuming procedures and costly equipment in many cases. The conventional diagnostic process of Malaria,
required in many cases, act as serious obstacles in the early common infection in sub-Saharan region, is based on microscopic
screening of a disease. Though, in the developed world advanced examination of stained peripheral blood smears. The standard pro-
infrastructure and well-trained healthcare professionals are avail- cess requires examination of the entire smear slide with light
able, the cost of healthcare can still be prohibitive for patients microscope to detect infected cells [4,5]. For HIV infected indi-
to seek diagnosis. In low-resources settings, access to medical viduals, CD4+ T cell concentration is a common test to perform to
equipment may not even be available [1]. To address these issues, define the response of the immune system to antiretroviral therapy.
there is an emerging trend to adapt a patient-centered health- Cell count can be accurately extracted through microscopy imag-
care [2]. The use of point-of-care devices is part of this trend with ing of a drop of patient’s blood (1–10 ␮l), though flow cytometry
excellent application in the field of microscopy imaging of biolog- remains the gold standard [6]. In tuberculosis-endemic countries,
ical specimens [3]. Recent technological advances in micro-optics, the low-cost, fast and accurate microscopy imaging of smears of
micro-electronics and micro-electromechanical systems (MEMS) non-concentrated sputum with Ziehl-Neelsen staining is the most
have the potential to improve screening and detection of a wide common diagnostic test [7]. Other hematologic diseases, such as
range of diseases at the point-of-care in primary health care settings sickle cell anemia also require microscopy imaging for highly spe-
in both low and high-resource countries. cific diagnosis. In both low and high-resource countries, frequent
Microscopy imaging is the gold standard for the diagnosis of counting of white blood cells is required for patients undergoing
malaria, tuberculosis and sickle cell anemia, while it is also used chemotherapy or radiation therapy for cancer treatment as low
white blood cell counts often represent an important side effect.
In general, in vitro biological specimen imaging such as blood
film or sputum is considered as the most promising field of applica-
∗ Corresponding author. tion for automated and miniaturized medical instrumentation that
E-mail address: chronis@umich.edu (N. Chronis).

https://doi.org/10.1016/j.sna.2018.06.034
0924-4247/© 2018 Elsevier B.V. All rights reserved.
368 G. Korompili et al. / Sensors and Actuators A 279 (2018) 367–375

could be used at the point of care [8]. High accuracy, in terms of imaging. To be effective at the point-of-care, evolved technologies
specificity and sensitivity, low cost, portability, ease of use and low need to be simple [19]. Our approach proposes the use of a specially
power consumption are the specifications imposed by the World patterned mini-lens array combined with a simple, one direction
Health Organization for devices used at the point-of-care in poor- (1D) scanning system for whole slide, high resolution imaging of
resources settings [9]. Though a large number of devices have been a biological specimen. The large FOV (290 ␮m) and high numeri-
developed in the field of automated portable imaging systems, cal aperture (NA∼0.7) of the used sapphire ball lenses reduce the
unfortunately, so far, none of them has succeeded in complying number of required images – approximately 400 images for a 4 cm
with all criteria. Particularly, concerning the technical limitations long sample surface in 1X magnification. The simplicity of the pro-
and challenges met, major problem is the need to combine high posed portable system – one direction scanning and one layer of
resolution with large FOV imaging of the biological sample [8]. mini-lenses (1 mm in diameter) – render it compact, inexpensive
To address this need, two main approaches have been widely and with low power requirements. It is, therefore, ideal for use in
studied: (a) whole slide scanning [10–12] and (b) lens-free imag- poor resources areas.
ing techniques [13–16]. In particular, a certain number of evolved
devices perform 2 or 3 direction scanning to cover an extended
2. Materials and methods
area of tissue or blood sample [11,12]. In these approaches, sophis-
ticated motorized systems and complicated optical systems are
We developed an imaging, scanning platform (Fig. 1) that com-
employed, resulting in an increased cost of manufacturing. In cases
prises of three components: (a) an optical, scanning head that
where scanning components are excluded, medium or large format
images the specimen of interest (b) a motorized, translation stage
detectors have to be used instead [13], increasing furthermore the
that is responsible for moving the optical head along the specimen
production cost. In case of non-scanning devices, the resolution is
(1D scanning) and (c) an external white light LED array (Edmund
limited by the pixel size of the large format detector in use, much
Optics, #66-830) that provides homogeneous illumination of the
larger than desired resolution of at least a few micrometers. To com-
entire specimen. The optical head is an assembly of a 10.7 Mpixel
pensate large pixel size of these sensors – approximately 10 ␮m –
monochrome CMOS sensor (Imaging Source, DMM 27UJ003-ML)
the existing approaches make use of complicated and bulk optical
and of a custom-made mini-lens array. The optical head is attached
systems or sophisticated software algorithms for image infor-
to the translation stage that is connected to a computer-controlled,
mation extraction. Consequently, time and computational power
stepper motor through a lead screw. The specimen – typically blood
requirements radically increase. It is also a fact that the samples
sample inserted in a microfluidic chamber or sitting on a glass slide
tested need to be rather sparse to reduce possible loss of informa-
or coverslip – is placed at a short distance (∼0–500 ␮m) from the
tion due to actual low resolution efficiency [13]. The same problems
optical head and it is illuminated by the LED array light source. The
of augmented computational power demands and sparse sample
CMOS/mini-lens array assembly moves in one direction and has a
requirements are encountered in approaches of lens-free imaging
travelling distance of approximately 40 mm. This configuration cre-
systems [13–16]. In the aforementioned platforms, image process-
ates a 40 mm x 6 mm image of the specimen. The distances between
ing algorithms are used to detect particles in a sample, based on the
the mini-lens array, the CMOS sensor and the specimen are con-
shadow produced by the particles. Thus, provided accuracy may be
trolled by two step motors (20 ␮m step, 3 mm range) that allow
highly affected by the sample density and result in a large number
us to obtain a sharp, focused image of the sample. The focusing
of lost particles in case of dense specimens. Preprocessing of blood
procedure is performed prior to every scan.
is therefore a demand and a possible obstacle in areas where the
necessary laboratory equipment is unavailable.
With the advent of mobile phones, their extensive use and their 2.1. The optical, scanning head
fast technological development, there has been an integration of
phone cameras in devices for cytological or histological specimen The optical, scanning head is responsible for image acquisition
imaging. These devices, though assuring portability and autonomy, process. It comprises of a microfabricated lenslens array, a 10.7
incorporate complicated and expensive optical systems to perform Mpixel CMOS camera (of 1.67 ␮m square pixels) and two, com-
high resolution imaging by radically decreasing the detection area puter controlled, stepper motors that control the distance between
[17,18]. Though phone cameras provide high quality imaging, they the sample, the lens array and the detector. The two stepper motors
are restricted for a short range of applications and are incapable of are used to achieve sharp in-focus images as well as to operate in
providing extended region imaging, unless combined with a scan- different magnification modes – from 1X up to 4X magnification.
ning system. The operational principle of the entire scanning system is based on
Rapid progress in microfabrication technology resulted in an the special design of the lens array. 36 sapphire ball lenses of high
emerging trend towards the use of micro-lens arrays. The integra- numerical aperture (NA∼0.7), refractive index of 1.67 and 1 mm
tion of high numerical aperture micro-lenses in optical systems, in diameter (EDMUND OPTICS #43-638) are placed on top of a
benefits of high resolving power, large FOV imaging and radically specially patterned silicon die to form the array of mini-lenses.
decreases cost of manufacturing. The inevitable problem of whole The mini-lens array is fabricated using standard microfabrica-
slide imaging related to the use of micro-lens arrays is caused by tion techniques (supplementary Fig. 1). A 400 ␮m thick, silicon
the existence of undetected areas of the imaged specimen due to wafer is Deep Reactive Ion Etched (DRIE) to create 960 ␮m in
the blind regions between neighbor lenses in an array. To mitigate diameter, wafer-through holes [20]. After the etching process is
this challenge, in some cases a multilayer lens-array assembly is completed, individual dies are glued with a UV curable optical adhe-
employed, improving also provided resolution, while a sophisti- sive (NORLAND 60, refractive index 1.62) on thin, glass coverslips
cated, 2 or 3 direction- scanning system can additionally be used of standard thickness (#1, 130–170 ␮m) to form the wells upon
[12]. Such an approach increases the manufacturing cost of the which the lenses are placed. The same adhesive is used to fill the
equipment, while it is rather questionable whether it meets the wells and secure the lenses on top of the wells.
criteria of compactness and portability. The design of the lens array is the key element of the operation
Despite the numerous approaches that already exist, the field of the entire system. The wells are patterned so that all mini-lenses
still presents a challenge as there has been no approach that could in the array are equally spaced with an edge-to-edge distance of
overcome the aforementioned obstacles and provide a general pur- 50 ␮m. The lens array is placed with a tilt angle of ␸ = 17◦ with
pose, portable, low-cost device for high resolution and wide FOV respect to the scanning direction. This tilted design assures that
G. Korompili et al. / Sensors and Actuators A 279 (2018) 367–375 369

Fig. 1. (a) Schematic of the architecture of the portable scanning microsystem, (b) photograph of the prototype and close-up view of the optical head. The size of the prototype
is 21 cm × 8 cm × 11 cm and it weights ∼1 kg, (c) schematic of the optical/scanning head illustrating the imaging principle.

Fig. 2. (a) Top view schematic and picture of the lens array. The black dotted outline indicates the effective imaging area of the CMOS sensor, the green rectangular represents
the silicon chip; (b) The tilt (17◦ ) of the mini-lens array and the overlap between the FOV of neighboring lenses are crucial for covering blind areas between the lenses; (c)
Estimation of the FOV of a lens (∼290 ␮m) based on a grid of lines imaged with the CMOS sensor in 1X magnification mode. The FOV is the diameter of the disc area where
light intensity is not lower than 90% of its maximum value (center of the lens).

the diameter of the FOV of one lens – estimated approximately at The calculation of the tilt angle ␸ was based on the geometry
290 ␮m – has an overlap with the FOV of the neighboring lenses by of the array, where (␸ = (0.8 x lens FOV diameter) / (Lens diame-
a factor of 20% (Fig. 2). Thus, by performing one direction scanning, ter + Lenses distance). The measurement of the FOV was performed
there are no undetected areas of the sample. with the use of a lines grid projection over the CMOS surface. The
370 G. Korompili et al. / Sensors and Actuators A 279 (2018) 367–375

estimated 290 ␮m FOV is the diameter of the disc surface where new scan. During scanning, the device performs only one direction
light intensity is not lower than 90% of its maximum value – located translation of the optical head.
at the center of the lens. Based on working principle the characterization procedure
The quality of the produced image is dependent on the manufac- needs to define the error induced by the motorized stage during
turing and assembly process of the optical head components (see scanning. Any imperfections or misalignments in the assembly of
supplementary material). The characterization procedure aims at the components of the stage may result in a defocusing error due
accurately defining the uniformity of the assembled mini-lens array to non-parallel move of the optical head with respect to the sample
in terms of resolution and contrast. Ideally, we require a perfectly holder. Image curvature focus measure [22] was used to quantify
uniform array in the sense that all lenses are focused on the same the defocus error induced for 26 equally spaced (1000 ␮m) posi-
plane and they provide an image of the sample with the same res- tions along the scanning range.
olution, magnification and contrast. In order to quantify the optical
performance of the scanner and the uniformity of the lens array, we 2.3. The illumination source
conducted two experiments: (a) we measured the contrast across
the mini-lens array (36 imaging units) and (b) we measured the The illumination source is a square homogeneous light source
in-focus factor for each lens as they are not located in the same (EDMUND OPTICS, part number #66-830) with 5 cm side length.
plane within the array. The in-focus factor is a measurement of The light source covers the entire imaged area and does not need
focus that represents the ability of each lens to focus the image to move during scanning. This light source consists of an LED array
to the CMOS sensor. It has its maximum value at the best focused (operated at 24 V) covered by a diffuser. The emitted light is homo-
image plane. The defocusing error in each case can be extracted as geneously diffused onto the biological sample and it is distributed
the subtraction of the in-focus factor from 1, which is the maximum over a surface 6% wider than the surface of the source. The entire
normalized in-focus factor. For quantifying the resolution and con- scanner along with the light source is placed inside a PMMA opaque
trast, a line-pairs pattern of a chrome film (100 nm thick) deposited enclosure to prevent ambient light from entering the scanner.
on glass slide was imaged in 1X and 4X magnification mode. The The distance between the light source and the sample affects
contrast (C), obtained from greyscale images from each lens, was the contrast of the produced image. If that distance is short, then
based on the Michelson formula [21]: C = standard deviation of the images obtained from neighboring lenses and projected to overlap-
light intensity gradient/ mean of light intensity gradient. ping areas on a CMOS sensor – a phenomenon known as crosstalk.
For quantifying the defocusing error, a series of images from a Crosstalk is frequently encountered in micro-lens arrays [25] and
whole blood smear test were obtained by varying the mini-lens affects image quality as the original image appears blurred. In the
array to CMOS distance from 500 ␮m up to 1500 ␮m with a step case of a non-collimated light source, such as an LED array, increas-
of 20 ␮m. An image processing algorithm based on image curva- ing the distance between the LED array and the sample can reduce
ture focus measure [22] for the automatic detection of the sharpest crosstalk, as diverging rays originating from the LED array do not
image was used [23,24]. reach the sample. To select the minimum LED-sample distance
where crosstalk is adequately reduced, we measured the contrast
2.2. The motorized, translation stage of the produced image at different distances.

A motorized, translation stage is responsible for the movement 3. Results


of the optical, scanning head across the scanning direction. It com-
prises of a step motor, a lead screw upon which the optical head 3.1. Magnification range of the optical head
is sliding, a motor driver to control the step motor, an electron-
ics board with an Arduino UNO Microcontroller and a flat sample The proposed imaging platform can operate at 1X-4X magni-
holder located on top of the stage, where the biological specimen fication range. An image curvature focus measure algorithm was
is placed. The stepper motor providing 200 steps per revolution is used to automatically select the best focal plane and determine the
connected through a motor flex coupler with the leadscrew. The positions of the lens array and the CMOS sensor with respect to the
scanning head is able to move with a minimum 5 ␮m step for cov- sample (Fig. 3).
ering a distance of 40 mm maximum range. This scanning head
is moving right beneath the sample – either typical microfluidic 3.2. Resolution at maximum (4X) and minimum (1X)
chamber or glass slide – across its long axis. It is kept in place dur- magnification
ing scanning with the use of two flexible strips. A window of the
sample holder allows optical access to the specimen from the side The resolution of our system at 1X and 4X magnification was
of the scanning head, with the lens-array being able to move close experimentally measured using a custom-made resolution pattern
to the sample and achieve high magnification. (Fig. 4). The design of the resolution pattern was similar to the
The sample holder can host a standard glass slide of 1951 USAF resolution test chart. It was patterned on a thin Cr film
60 mm x 22 mm, however the scanned surface is defined by the using e-beam lithography. The maximum optical resolution was
CMOS sensor size and the maximum possible scanning range of the approximately 0.98 ␮m and 1.95 ␮m at 4X and 1X magnification
stepper motor. Thus, the surface that can be scanned has 5.7 mm respectively.
width – equal to the length of the CMOS sensor – and 40 mm length
– equal to the maximum scanning range, rendering the device ideal 3.3. Sharpness and contrast uniformity of the images produced by
for use with microfluidic biochips respectively wide and long. the lenses of the array
The maximum adequate step for the entire chip scanning with-
out undetected areas is defined by the design of the lens array and The image curvature focus factor was measured for each lens
by the overlap between neighboring lenses. Based on the theoret- using a smear blood test when the lens array is at the closest posi-
ical study of the lens-array properties the maximum allowed step tion to the sample – 0 ␮m lens to sample distance. At this position
size should not exceed 0.6*FOV Diameter = 174 ␮m at 1X magnifi- of maximum magnification and resolution the out-of-focus error of
cation. the lenses of the array is expected to be maximized. 31 lenses – out
To eliminate repeatability error between different scans, the of 36 – were selected for this experiment, as those lenses captured
device is programmed to return to ‘zero position’ before executing a images that fitted entirely into the CMOS effective detection area.
G. Korompili et al. / Sensors and Actuators A 279 (2018) 367–375 371

Fig. 3. The distances of the lens array and the CMOS detector with respect to the sample are determined with the use of image curvature based autofocus algorithm. The
magnification range (1X-4X) was calculated by the projection on the CMOS effective area of 10 ␮m width, chrome, line pairs patterned on glass slide.

Fig. 4. A photograph of the resolution line pattern as imaged through a single lens at 1X (A) and 4X (B) magnification and their corresponding light intensity profiles. The red
line in the images indicates the length where the intensity profile was quantified. A minimum line width of 1.95 ␮m and 0.98 ␮m was detected at 1X and 4X magnification
respectively.

The best focused image produced by the array was selected as the than 5%) are attributed to differences in the pattern of smear blood
one that the averaged out-of-focus factor (averaged from all lenses) cells monitored in each position as no noticeable drift is present.
was minimum. At this image, defocusing error, measured for each The precision of the step motor employed allows for automatic
lens separately, was less than 20% while the contrast was within stitching of the images acquired by each lens during scanning. Since
12% of its maximum value (Fig. 5). no repeatability step error is present, the images of the specimen
can be cropped in the borders of FOV of each lens and stitched
automatically to produce 36 images of the sample, each one corre-
3.4. Sharpness imaging uniformity along scanning direction
sponding to a different optical unit in the lens array (Fig. 6).
The image curvature based autofocus algorithm was used to
quantify the defocusing error induced during scanning. This error is 3.5. Minimizing crosstalk
presented as the variations of the in-focus factor measured for one
lens in the array in equally spaced (1 mm) positions of the optical Crosstalk is a significant drawback of lens arrays [25,26] as it
head for a smear blood test 25 mm long. The slight variations (less deteriorates image quality. It can be minimized by using collimated
372 G. Korompili et al. / Sensors and Actuators A 279 (2018) 367–375

Fig. 5. In-focus factor normalized for each lens within the array, as measured by images obtained from a blood smear test (left); Contrast of the image produced by each lens
of the array (right); 5 lenses were excluded from this experiment as they did not produce high quality images.

Fig. 6. (a) De-focusing error versus position of the optical head along the scanning direction. The de-focusing error was induced by fabrication imperfections or assembly
misalignments in the components of the motorized scanning stage. The in-focus factor – measured for one lens across the scanning length – remains for all positions of the
optical head within 5% of the best in-focus image. (b) Stitching of 20 images acquired from one lens in the array with a scanning step of 100 ␮m. The resulting image monitors
an area of the sample 2 mm long. Precision stepping allows for automatic stitching of the images.
light sources. The same result can be accomplished by placing a blood cells captured and detected. The chip comprises of two 16 ␮m
non-collimated light source at a large distance from the sample. In thick chambers of 1 ␮l total volume each, functionalized with
order to quantify the crosstalk, we measured the contrast in our human CD45 biotinylated antibody to capture white blood cells
system for different distance between the LED source and the sam- (WBCs). Red blood cells (RBCs) were washed away. The 40 mm long
ple (Fig. 7). The best contrast was obtained at distances of 40 cm and chip was scanned with our device within a few minutes. The images
above. For practical reasons, we used a distance of 22 cm, where the acquired were automatically processed to produce the entire image
contrast was ∼0.89 and it was adequate to clearly image blood cells of the scanned surface (Fig. 8).
from a blood smear test. The image processing algorithm comprises of the following
steps: (a) cropping of the FOV of each lens, (b) vignetting effect
3.6. Image mosaicing and cell detection correction for each cropped image, (c) automatic stitching of the
images of each lens and mosaicing of the entire image. Vignetting
As a proof of concept for the operation of the device we present effect induced by the spherical surface of the lenses is reduced
the image acquired from a typical microfluidic chip with white through measurement of the sharpness of gradient distribution
G. Korompili et al. / Sensors and Actuators A 279 (2018) 367–375 373

Fig. 7. Normalized contrast versus light source to sample distance (A). Larger distances result in less crosstalk and clearer images as diverging rays do not reach the mini-lens
array (B).

Fig. 8. (a) Schematic of the microfluidic chip with 2 parallel chambers used for the experiment. The dotted square indicates the scanned surface. (b) Stitched image of the 4 cm
long microfluidic chip of two parallel chambers. (c) Zoom-in of the image in the region of inlets. (d) WBCs captured in the microfluidic chamber (e) automatically detected
WBCs (indicated with an arrow) with Sobel operator image segmentation algorithm.
374 G. Korompili et al. / Sensors and Actuators A 279 (2018) 367–375

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Studies, Cambridge, 2008. G. Korompili holds a diploma in Electrical and Electronic Engineering from National
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[5] A. Moody, Rapid diagnostic tests for malaria parasites, Clin. Microbiol. Rev. 15 the field of bioMEMS, under supervision of prof. Chronis Nikos. Her research inter-
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G. Korompili et al. / Sensors and Actuators A 279 (2018) 367–375 375

micro-optics systems, microflidic systems as well as automated microsystems for tronics and its application on process development and point of care devices. He is
various biological applications. currently working in consumer products industry as product design-prototype and
process development engineer.
G.P. Kanakaris is a Mechanical Engineer specializing in mechanical design and
biotechnology instrument development. He has acquired his M.Sc. from the National Professor Chronis received a Bachelor in Engineering (B.E.) in mechanical engineer-
Technical University of Athens, 2011. His research interests include high through- ing in 1998, from the Aristotle University of Thessaloniki with honors (graduated 1st
put proteomic measurement platforms as well as Point of Care Systems for in vitro out of 145 students in his class). He completed his Ph.D. in mechanical engineering
diagnostics. He is currently a PhD candidate in the field of proteomic measurement from the University of California at Berkeley (USA) in 2004. From 2004–2006, he held
technologies. a post-doctoral research position at Rockefeller University, New York, (USA). In 2006,
he became a faculty at the Department of Mechanical Engineering at the University
C. Ampatis is a mechanical engineer with specialization in aeronautics, control of Michigan, Ann Arbor. He is the co-author of more 60 journal and peer-reviewed
systems and robotics. He holds two M.Sc. diplomas in the aforementioned fields, conference publications and inventor in 3 patents. Dr. Chronis is the recipient of the
acquired from National Technical University of Athens during 2010 and 2012 respec- prestigious NIH Director’s New Innovator Award.
tively. His research interests include axial compressor design and performance, wind
tunnel design, multi-rotor aerial vehicles design and performance, as well as mecha-

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