Name: microfluidic imaging flow cytometry by asymmetric-detection time-stretch optical microscopy (atom)
Uploaded: 2017-06-28T15:00:00
Description: Watch this Scientific Journal Video about Microfluidic Imaging Flow Cytometry by Asymmetric-detection Time-stretch Optical Microscopy ATOM at JoVE.com

We thank Mr. P. Yeung for preparing the MCF-7 for us. This work was partially supported by grants from the Research Grant Council of the Hong Kong Special Administration Region, China (Project no. 17259316, 17207715, 17207714, 17205215, and HKU 720112E), the Innovation and Technology Support Programme (ITS/090/14), and the University Development Fund of HKU.

1. Sample Preparation
<ol>
	<li>Sample preparation (adherent cells; MCF-7 cells)
	<ol>
		<li>Take out the cell culture dish from the incubator and drain the culture medium.</li>
		<li>Rinse the cells on a dish with 1x phosphate-buffered saline (PBS) to remove excessive culture medium.</li>
		<li>Add 3 mL of a solution of 0.25% trypsin to the culture dish (diameter of 100 mm) and put it in a 37 &#176;C, 5% CO2 incubator for 4 min. 
		NOTE: The trypsin dissolves the adhesive protein of th...

<ol>
	<li>Lau, A. K. S., Wong, T. T. W., Shum, H. C., Wong, K. K. Y., Tsia, K. K., Barteneva, N. S., Vorobjev, I. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Imaging Flow Cytometry: Methods and Protocols. , 23-45 (2016).</li><li>Goda, K., Tsia, K. K., Jalali, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Serial+time-encoded+amplified+imaging+for+real-time+observation+of+fast+dynamic+phenomena.">Serial time-encoded amplified imaging for real-time observation of fast dynamic phenomena.</a> Nature. 458 (7242), 1145-1149 (2009).</li><li>Goda, K., Jalali, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dispersive+Fourier+transformation+for+fast+continuous+single-shot+measurements.">Dispersive Fourier transformation for fast continuous single-shot measurements.</a> Nat Photon. 7 (2), 102-112 (2013).</li><li>Lau, A. K., Shum, H. C., Wong, K. K., Tsia, K. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optofluidic+time-stretch+imaging+-+an+emerging+tool+for+high-throughput+imaging+flow+cytometry.">Optofluidic time-stretch imaging - an emerging tool for high-throughput imaging flow cytometry.</a> Lab Chip. 16 (10), 1743-1756 (2016).</li><li>Lau, A. K. S., Tang, A. H. L., Xu, J., Wong, X. W., Y, K. K., Tsia, K. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optical+Time+Stretch+for+High-Speed+and+High-Throughput+Imaging+-+From+Single-Cell+to+Tissue-Wide+Scales.">Optical Time Stretch for High-Speed and High-Throughput Imaging - From Single-Cell to Tissue-Wide Scales.</a> IEEE J. Sel. Top. in Quant. Electron. 22 (4), (2016).</li><li>Lei, C., Guo, B., Cheng, Z., Goda, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optical+time-stretch+imaging:+Principles+and+applications.">Optical time-stretch imaging: Principles and applications.</a> Appl Phys Rev. 3 (1), 011102 (2016).</li><li>Lei, C., Guo, B., Cheng, Z., Goda, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optical+time-stretch+imaging:+Principles+and+applications.">Optical time-stretch imaging: Principles and applications.</a> Applied Physics Reviews. 3 (011102), (2016).</li><li>Goda, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+single-microparticle+imaging+flow+analyzer.">High-throughput single-microparticle imaging flow analyzer.</a> Proc Natl Acad Sci U S A. 109 (29), 11630-11635 (2012).</li><li>Goda, K., Solli, D. R., Tsia, K. K., Jalali, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Theory+of+amplified+dispersive+Fourier+transformation.">Theory of amplified dispersive Fourier transformation.</a> Physical Review A. 80 (4), 043821 (2009).</li><li>Goda, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+single-microparticle+imaging+flow+analyzer.">High-throughput single-microparticle imaging flow analyzer.</a> Proc Natl Acad Sci U S A. 109 (29), 11630-11635 (2012).</li><li>Lai, Q. T. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+time-stretch+imaging+flow+cytometry+for+multi-class+classification+of+phytoplankton.">High-throughput time-stretch imaging flow cytometry for multi-class classification of phytoplankton.</a> Opt. Express. 24 (25), 28170-28184 (2016).</li><li>Chen, C. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Deep+Learning+in+Label-free+Cell+Classification.">Deep Learning in Label-free Cell Classification.</a> Sci Rep. 6, 21471 (2016).</li><li>Fard, A. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nomarski+serial+time-encoded+amplified+microscopy+for+high-speed+contrast-enhanced+imaging+of+transparent+media.">Nomarski serial time-encoded amplified microscopy for high-speed contrast-enhanced imaging of transparent media.</a> Biomed Opt Express. 2 (12), 3387-3392 (2011).</li><li>Lau, A. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Interferometric+time-stretch+microscopy+for+ultrafast+quantitative+cellular+and+tissue+imaging+at+1+mum.">Interferometric time-stretch microscopy for ultrafast quantitative cellular and tissue imaging at 1 mum.</a> J Biomed Opt. 19 (7), 76001 (2014).</li><li>Mahjoubfar, A., Chen, C., Niazi, K. R., Rabizadeh, S., Jalali, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Label-free+high-throughput+cell+screening+in+flow.">Label-free high-throughput cell screening in flow.</a> Biomed Opt Express. 4 (9), 1618-1625 (2013).</li><li>Wong, T. T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Asymmetric-detection+time-stretch+optical+microscopy+(ATOM)+for+ultrafast+high-contrast+cellular+imaging+in+flow.">Asymmetric-detection time-stretch optical microscopy (ATOM) for ultrafast high-contrast cellular imaging in flow.</a> Sci Rep. 4, 3656 (2014).</li><li>Mata, T. M., Martins, A. A., Caetano, N. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microalgae+for+biodiesel+production+and+other+applications:+A+review.">Microalgae for biodiesel production and other applications: A review.</a> Renew Sustainable Energy Rev. 14 (1), 217-232 (2010).</li><li>Irigoien, X., Huisman, J., Harris, R. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Global+biodiversity+patterns+of+marine+phytoplankton+and+zooplankton.">Global biodiversity patterns of marine phytoplankton and zooplankton.</a> Nature. 429 (6994), 863-867 (2004).</li><li>Wei, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coherent+Laser+Source+for+High+Frame-Rate+Optical+Time-Stretch+Microscopy+at+1.0+&#181;m.">Coherent Laser Source for High Frame-Rate Optical Time-Stretch Microscopy at 1.0 &#181;m.</a> IEEE J. Sel. Top. Quantum Electron. 20 (5), 384-389 (2014).</li><li>Wei, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Breathing+laser+as+an+inertia-free+swept+source+for+high-quality+ultrafast+optical+bioimaging.">Breathing laser as an inertia-free swept source for high-quality ultrafast optical bioimaging.</a> Opt. Lett. 39 (23), 6593-6596 (2014).</li><li>Xu, Y., Wei, X., Ren, Z., Wong, K. K. Y., Tsia, K. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ultrafast+measurements+of+optical+spectral+coherence+by+single-shot+time-stretch+interferometry.">Ultrafast measurements of optical spectral coherence by single-shot time-stretch interferometry.</a> Sci Rep. 6, 27937 (2016).</li><li>Tsia, K. K., Goda, K., Capewell, D., Jalali, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Performance+of+serial+time-encoded+amplified+microscope.">Performance of serial time-encoded amplified microscope.</a> Opt. Express. 18 (10), 10016-10028 (2010).</li><li>Alix-Panabi&#232;res, C., Pantel, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Challenges+in+circulating+tumour+cell+research.">Challenges in circulating tumour cell research.</a> Nat Rev Cancer. 14 (9), 623-631 (2014).</li><li>Kling, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Beyond+counting+tumor+cells.">Beyond counting tumor cells.</a> Nat Biotech. 30 (7), 578-580 (2012).</li><li>Hodgkinson, C. 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There are several technical details that require special attention during the ATOM system setup. First, it is essential to note that asymmetric/oblique spectrally-encoded illumination could introduce residual phase-gradient components (i.e., the shadowing effect) in the absorption contrast and influence the enhancement of phase-gradient contrast in ATOM. Therefore, this effect of oblique illumination should be minimized. Second, it should be emphasized that the time-multiplexing or time-interleaving schemeinvolv...

Optical imaging presents a powerful tool and cell-based assay to (almost) non-invasively visualize the detailed spatial distribution of many cellular/subcellular components, thus uncovering a multitude of morphological, biophysical, and biomolecular signatures of cells. However, this ability to extract high-content information from single cells has generally been compromised when an enormous and heterogeneous population of cells had to be investigated. This marks a common trade-off in cell-based assays between measurement throughput and content. A notable example is that adding imaging capability to flow cytometry has resulted in a down-scaling of throughput by at least 1-2 orders of magnitude compared to that of the classical non-imaging flow cytometers. Although it could offer complex morphological single-cell analysis that is not possible with standard flow cytometers1, imaging flow cytometry generally lacks sufficient throughput to identify cellular heterogeneity with high statistical confidence. This is necessary for new discoveries in biology and for gaining an understanding of the pathogenesis of diseases. The key technical challenge lies in the inherent speed limit imposed by the common optical imaging strategies: laser-beam scanning, (e.g., by galvanometric mirrors), and/or image sensors (e.g., charge-coupled device (CCD) and complementary metal-oxide semiconductor (CMOS)). The laser scanning speed is intrinsically restricted by the mechanical inertia of the scanning mirrors, whereas the frame rate of CCD or CMOS is limited by the fundamental trade-off between imaging speed and sensitivity (i.e., increasing the frame rate leads to reduced signal detection sensitivity, and vice versa).
Based on an all-optical, ultrafast image-encoding mechanism, optical time-stretch imaging has been demonstrated as an attractive platform for high-throughput imaging flow cytometers, without need of the conventional image sensors or mechanical laser scanning2,3. Detailed descriptions of the working principle of time-stretch imaging can be found in references4,5,6,7. In brief, it consists of two interchangeable mapping steps: (i) spectral encoding (wavelength-space mapping), in which the spatial coordinates of the imaged specimen are mapped to different wavelengths across the spectrum of the light-pulsed beam8,9, and (ii) a dispersive Fourier transformation (wavelength-time mapping)9, in which the wavelength components of individual laser pulses are transformed (stretched) via group velocity dispersion (GVD) into temporal (wavelength-swept) waveforms (Figure 1). An important feature of time-stretch imaging is optical amplification, which plays a critical role in combatting the loss of sensitivity due to ultrafast photodetection and GVD loss, thus enhancing the image signal-to-noise ratio (SNR) without being contaminated by the photodetector noise9. Since each laser pulse encodes a line-scan of the imaged specimen, which is orthogonal to the unidirectional flow of the cells, an effective line-scan rate is determined by the laser repetition rate, which is typically beyond 10 MHz. This ultrafast operation enables blur-free, single-cell image capture at a throughput of 10,000-100,000 cells/s (i.e., 10-100 times higher than conventional imaging flow cytometry). As a result, time-stretch imaging could find unique applications in high-throughput, single-cell, image-based screening, especially when there is a need for identifying unknown heterogeneity or rare/aberrant cells within a sizable population (thousands to millions of cells), such as rare cancer cell screening10 or micro-algae classification11.
Time-stretch imaging predominantly relies on bright-field (BF) image capture, from which the image contrast is generated through light scattering and absorption from the cells2,3,9,10,11. Such label-free, single-cell imaging capabilities could bypass the detrimental effects associated with the fluorescent labels, such as cytotoxicity and photobleaching, and yet provide valuable information for single-cell analysis based on the cellular and sub-cellular texture and morphology. These label-free parameters are proven to be effective for the deep image classification of cells, especially when an enormous cell population is available11,12. However, in many occasions, BF imaging fails to provide sufficient contrast to reveal the detailed morphology of the label-free transparent cells. Different label-free, phase-contrast, time-stretch imaging modalities have been developed for enhancing the imaging contrast at ultrafast frame rates13,14,15. Among these techniques, asymmetric-detection time-stretch optical microscopy (ATOM) was developed to reveal the phase-gradient (differential-interference-contrast-(DIC)-like) contrast based on a concept similar to Schlieren photography, enabling the label-free, high-contrast imaging of single cells at an ultrahigh microfluidic speed (up to 10 m/s)16. This effect can be readily generated through oblique detection or illumination by partially blocking the image-encoded beam path or tilting the beam before photodetection. Another advantage of ATOM is its ability to simultaneously acquire two phase-gradient contrasts along opposite orientations. Intensity subtraction and summation of two opposite-contrast images yield the differential phase-gradient contrast and the absorption contrast, respectively, from the same line-scan. This work presents a detailed protocol describing the implementation of ATOM, including the establishment of the optical setup, the sample preparation, and the data acquisition and visualization. Specifically, this work demonstrates the ATOM operation with single-cell imaging of human blood cells, cancer cells, and phytoplankton (microalgae). This highlights the applicability of ATOM to imaging flow cytometry, not only in the biomedical arena, but also in marine and biofuel research17,18.

<table border="0" cellpadding="0" cellspacing="0" width="789">
	<tbody>
		<tr height="42">
			<td height="42" style="height:42px;width:207px;">Nikon Plan Fluorite Physiology Objectives 40X</td>
			<td style="width:71px;">Nikon</td>
			<td style="width:119px;">MRF07420</td>
			<td style="width:393px;">Objective lens (Obj2)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Olympus Plan Fluorite Objective, 0.75 NA, 0.51 mm WD, 40X</td>
			<td style="width:71px;">Olympus</td>
			<td>RMS40X-PF</td>
			<td>Objective lens (Obj1)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:207px;">N-BK7 Plano-Convex Lenses</td>
			<td style="width:71px;">Thorlabs</td>
			<td>LA1145-C</td>
			<td>For relaying spectral shower</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:207px;">FC/APC Fiber Collimation Package</td>
			<td style="width:71px;">Thorlabs</td>
			<td style="width:119px;">F220APC-1064</td>
			<td>For outputing and collecting laser pulses</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:207px;">Pellicle beamsplitter</td>
			<td style="width:71px;">Thorlabs</td>
			<td style="width:119px;">BP145B3</td>
			<td>For making beam replica</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:207px;">Protected silver mirror</td>
			<td style="width:71px;">Thorlabs</td>
			<td style="width:119px;">PF10-03-P01</td>
			<td>For reflecting light</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:207px;">800-1650nm 12GHz single mode DC-coupled NIR Photoreceiver</td>
			<td style="width:71px;">Newport</td>
			<td style="width:119px;">1544-B</td>
			<td>For converting light into electrical signal</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:207px;">Infiniium High-Performance Oscilloscope</td>
			<td style="width:71px;">Agilent</td>
			<td style="width:119px;">DSOX91604A</td>
			<td>To save the light-converted electrical signals</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:207px;">HI1060 optical fiber</td>
			<td style="width:71px;">Corning</td>
			<td style="width:119px;">HI1060</td>
			<td>Optical fiber for time-stretch</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:207px;">YTTERBIUM DOPED FIBER AMPLIFIER</td>
			<td style="width:71px;">Keopsys</td>
			<td style="width:119px;">KPS-STD-BT-YFA-37-BO-SM-111-FA-FA</td>
			<td>Optical in-line amplifier</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:207px;">Holographic grating</td>
			<td style="width:71px;">Wasatch Photonics</td>
			<td style="width:119px;">020305-6</td>
			<td>Grating</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:207px;">Infuse/Withdraw Syringe Pumps</td>
			<td style="width:71px;">Harvard Apparatus</td>
			<td style="width:119px;">PHD 2000</td>
			<td>Syringe pump for sample loading in micro-fluidic channels</td>
		</tr>
	</tbody>
</table>

microfluidic imaging flow cytometry by asymmetric-detection time-stretch optical microscopy (atom)

Scaling the number of measurable parameters, which allows for multidimensional data analysis and thus higher-confidence statistical results, has been the main trend in the advanced development of flow cytometry. Notably, adding high-resolution imaging capabilities allows for the complex morphological analysis of cellular/sub-cellular structures. This is not possible with standard flow cytometers. However, it is valuable for advancing our knowledge of cellular functions and can benefit life science research, clinical diagnostics, and environmental monitoring. Incorporating imaging capabilities into flow cytometry compromises the assay throughput, primarily due to the limitations on speed and sensitivity in the camera technologies. To overcome this speed or throughput challenge facing imaging flow cytometry while preserving the image quality, asymmetric-detection time-stretch optical microscopy (ATOM) has been demonstrated to enable high-contrast, single-cell imaging with sub-cellular resolution, at an imaging throughput as high as 100,000 cells/s. Based on the imaging concept of conventional time-stretch imaging, which relies on all-optical image encoding and retrieval through the use of ultrafast broadband laser pulses, ATOM further advances imaging performance by enhancing the image contrast of unlabeled/unstained cells. This is achieved by accessing the phase-gradient information of the cells, which is spectrally encoded into single-shot broadband pulses. Hence, ATOM is particularly advantageous in high-throughput measurements of single-cell morphology and texture &#8211; information indicative of cell types, states, and even functions. Ultimately, this could become a powerful imaging flow cytometry platform for the biophysical phenotyping of cells, complementing the current state-of-the-art biochemical-marker-based cellular assay. This work describes a protocol to establish the key modules of an ATOM system (from optical frontend to data processing and visualization backend), as well as the workflow of imaging flow cytometry based on ATOM, using human cells and micro-algae as the examples.

This work illustrates two single-cell imaging demonstrations by ATOM: one with mammalian cells (human peripheral blood mononuclear cells (PBMC) and breast cancer cells (MCF-7)) and another with phytoplanktons (Scenedesmus and Chlamydomonas). The first experiment was motivated by the growing interest in liquid biopsy for the detection, enumeration, and characterization of circulating tumor cells (CTCs) in the blood23. The ability to...

Watch this Scientific Journal Video about Microfluidic Imaging Flow Cytometry by Asymmetric-detection Time-stretch Optical Microscopy ATOM at JoVE.com

Microfluidic Imaging Flow Cytometry by Asymmetric-detection Time-stretch Optical Microscopy ATOM

This protocol describes the implementation of an asymmetric-detection time-stretch optical microscopy system for single-cell imaging in ultrafast microfluidic flow and its applications in imaging flow cytometry.

Microfluidic Imaging Flow Cytometry by Asymmetric-detection Time-stretch Optical Microscopy (ATOM)

Scaling the number of measurable parameters, which allows for multidimensional data analysis and thus higher-confidence statistical results, has been the ...

the overall goal of this protocol is to prepare and use an asymmetric detection time stretch optical microscopy system for label-free high contrast single-cell imaging in ultra-fast microfluidic flow. The main advantage of ATOM is that it's allows ultra-fast image capture with line scan rates of up to tens of megahertz while enhancing the image contrast on the unlabeled cells. ATOM enables complex morphological analysis of cellular and subcellular structures with an uncentered cell-based assays at up to 100, 000 cells per second, which is not possible with standard flow cytometry.to begin setting up the system use a fiber collimator to couple a broadband femto or pico second near IR pulsed laser to a single mode dispersive optical fiber connected to an optical amplifier. Illuminate a transmission diffraction grading with the laser to produce a spectral shower. Orient the grading close to the littrow configuration to maximize the diffraction efficiency.Configure a telescopic relay lens assembly in a 4f imaging system to direct the spectral shower onto the rear focal plane of an objective lens below a sample platform. Ensure that the spectral shower fills the rear aperture of the objective lens. Place another objective lens with a plane mirror at its rear aperture above the sample platform.Adjust the objective lenses until their focal planes overlap. Verify that the spectral shower double passes the image plane and follows the same path back to the grading. Place a microfluidic chip on the sample platform and ensure that the spectral shower falls across the microfluidic channel.Redirect the returned light with a beam splitter after it passes through the grading. Separate the returned light into two beams with another beam splitter. Use fiber collimators to couple the beams to single mode fibers of different lengths to introduce a time delay between beams.Connect the fibers to a real-time oscilloscope through a fiber coupler and a photodetector. Tune the optical amplifier gain until the signal-to-noise ratio of the optical signal is greater than 10 decibels. Then block approximately half of each returned beam with knife-edge beam blocks.Adjust the beam blocks until the measured optical power in each fiber is about half of the power before the block. Verify that the oscilloscope bandwidth and sampling rate are both high enough not to influence the image resolution. To begin the experiment dilute cell samples to between 10 to the 5th and 10 to the 6th cells per milliliter with phosphate buffered saline or spring water.Then load the cell solution into a 10 milliliter syringe. Connect the syringe to the microfluidic channel inlet. Direct the microfluidic channel outlet to a centrifuge tube.Secure the syringe in a syringe pump and set the flow rate appropriately for the channel width. Choose the number of data points to be saved for the experiment. Then acquire and save the optical signal data.Digitize and export the data from the oscilloscope to a computer. Process the data into 2D images and extract a library of parameters from the images. Import the images in parameter library into a visualization program.Assign a parameter of interest to each axis and select the data set to be displayed as a scatter plot. Check the cell images associated with each group in the plot to identify trends. Use manual gating or display additional datasets for further analysis as needed.ATOM was used to acquire high contrast single-cell images of human cells and phytoplankton. Characteristic cell structures such as vacuoles, pyrenoids, and flagella, are visible in the phytoplankton images. Parameters such as cell size and circularity were determined from the ATOM images to classify cells for cytometric analysis.The classification results can be displayed as 2D scatter plots. Here volume versus circularity was plotted for an MCF7 shown in yellow and PBMC shown in red. Two clusters were observed for MCF7.By identifying the high contrast images corresponding to individual data points, the lower cluster was found to correspond to cell fragments and debris. Once mastered the imaging system can be set up in two to three hours if it is performed properly. The imaging procedures can be done within an hour.Don't forget to pay special attention to eye safety while working with the laser source and laser beam alignment. Precautions such as wearing safety goggles should always be taken while performing these procedures. While attempting this procedure remember to monitor the optical beam alignment throughout the whole imaging system setup process to ensure optimal imaging quality.While this technique can lend insight into the detection and quantification of rare or apparent cells during disease process, it can also be applied to cell type classification, within large and heterogeneous cell populations. This technique is particularly advantageous when looking to overcome the throughput limitation of imaging cytometry, while preserving the image quality. After watching this video, you should have good understanding of how to implement ATOM from the system setup to the imaging procedures.

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Research

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Electrical Engineering

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Unit 1

Operational Amplifiers

SCIENTISTS IN ACTION

Fabricating Metamaterials Using the Fiber Drawing Method

Metamaterials are man-made composite materials, fabricated by assembling components much smaller than the wavelength at which they operate 1. They owe their electromagnetic properties to the structure of their constituents, instead of the atoms that compose them. For example, sub-wavelength metal wires can be arranged to possess an effective electric permittivity that is either positive or negative at a given frequency, in contrast to the metals themselves 2. This unprecedented control over the behaviour of light can potentially lead to a number of novel devices, such as invisibility cloaks 3, negative refractive index materials 4, and lenses that resolve objects below the diffraction limit 5. However, metamaterials operating at optical, mid-infrared and terahertz frequencies are conventionally made using nano- and micro-fabrication techniques that are expensive and produce samples that are at most a few centimetres in size 6-7. Here we present a fabrication method to produce hundreds of meters of metal wire metamaterials in fiber form, which exhibit a terahertz plasmonic response 8. We combine the stack-and-draw technique used to produce microstructured polymer optical fiber 9 with the Taylor-wire process 10, using indium wires inside polymethylmethacrylate (PMMA) tubes. PMMA is chosen because it is an easy to handle, drawable dielectric with suitable optical properties in the terahertz region; indium because it has a melting temperature of 156.6 &deg;C which is appropriate for codrawing with PMMA. We include an indium wire of 1 mm diameter and 99.99% purity in a PMMA tube with 1 mm inner diameter (ID) and 12 mm outside diameter (OD) which is sealed at one end. The tube is evacuated and drawn down to an outer diameter of 1.2 mm. The resulting fiber is then cut into smaller pieces, and stacked into a larger PMMA tube. This stack is sealed at one end and fed into a furnace while being rapidly drawn, reducing the diameter of the structure by a factor of 10, and increasing the length by a factor of 100. Such fibers possess features on the micro- and nano- scale, are inherently flexible, mass-producible, and can be woven to exhibit electromagnetic properties that are not found in nature. They represent a promising platform for a number of novel devices from terahertz to optical frequencies, such as invisible fibers, woven negative refractive index cloths, and super-resolving lenses.

Metamaterials at terahertz frequencies offer unique opportunities, but are challenging to fabricate in bulk. We adapt the fabrication procedure for microstructured polymer optical fibers to inexpensively fabricate metamaterials potentially on an industrial scale. We produce polymethylmethacrylate fibers containing ~10 &mu;m diameter indium wires separated by ~100 &mu;m, which exhibit a terahertz plasmonic response.

Metamaterials are man-made composite materials, fabricated by assembling components much smaller than the wavelength at which they operate 1. They owe ...

Determining 3D Flow Fields via Multi-camera Light Field Imaging

In the field of fluid mechanics, the resolution of computational schemes has outpaced experimental methods and widened the gap between predicted and observed phenomena in fluid flows. Thus, a need exists for an accessible method capable of resolving three-dimensional (3D) data sets for a range of problems. We present a novel technique for performing quantitative 3D imaging of many types of flow fields. The 3D technique enables investigation of complicated velocity fields and bubbly flows. Measurements of these types present a variety of challenges to the instrument. For instance, optically dense bubbly multiphase flows cannot be readily imaged by traditional, non-invasive flow measurement techniques due to the bubbles occluding optical access to the interior regions of the volume of interest. By using Light Field Imaging we are able to reparameterize images captured by an array of cameras to reconstruct a 3D volumetric map for every time instance, despite partial occlusions in the volume. The technique makes use of an algorithm known as synthetic aperture (SA) refocusing, whereby a 3D focal stack is generated by combining images from several cameras post-capture 1. Light Field Imaging allows for the capture of angular as well as spatial information about the light rays, and hence enables 3D scene reconstruction. Quantitative information can then be extracted from the 3D reconstructions using a variety of processing algorithms. In particular, we have developed measurement methods based on Light Field Imaging for performing 3D particle image velocimetry (PIV), extracting bubbles in a 3D field and tracking the boundary of a flickering flame. We present the fundamentals of the Light Field Imaging methodology in the context of our setup for performing 3DPIV of the airflow passing over a set of synthetic vocal folds, and show representative results from application of the technique to a bubble-entraining plunging jet.

A technique for performing quantitative three-dimensional (3D) imaging for a range of fluid flows is presented. Using concepts from the area of Light Field Imaging, we reconstruct 3D volumes from arrays of images. Our 3D results span a broad range including velocity fields and multi-phase bubble size distributions.

In the field of fluid mechanics, the resolution of computational schemes has outpaced experimental methods and widened the gap between predicted and ...

Atom Probe Tomography Studies on the Cu(In,Ga)Se2 Grain Boundaries

Compared with the existent techniques, atom probe tomography is a unique technique able to chemically characterize the internal interfaces at the nanoscale and in three dimensions. Indeed, APT possesses high sensitivity (in the order of ppm) and high spatial resolution (sub nm).
Considerable efforts were done here to prepare an APT tip which contains the desired grain boundary with a known structure. Indeed, site-specific sample preparation using combined focused-ion-beam, electron backscatter diffraction, and transmission electron microscopy is presented in this work. This method allows selected grain boundaries with a known structure and location in Cu(In,Ga)Se2 thin-films to be studied by atom probe tomography.
Finally, we discuss the advantages and drawbacks of using the atom probe tomography technique to study the grain boundaries in Cu(In,Ga)Se2 thin-film solar cells.

Atom Probe Tomography Studies on the CuIn,GaSe2 Grain Boundaries

In this work, we describe the use of the atom-probe tomography technique for studying the grain boundaries of the absorber layer in a CIGS solar cell. A novel approach to prepare the atom probe tips containing the desired grain boundary with a known structure is also presented here.

Compared with the existent techniques, atom probe tomography is a unique technique able to chemically characterize the internal interfaces at the ...

Analyzing the Movement of the Nauplius 'Artemia salina' by Optical Tracking of Plasmonic Nanoparticles

We demonstrate how optical tweezers may provide a sensitive tool to analyze the fluidic vibrations generated by the movement of small aquatic organisms. A single gold nanoparticle held by an optical tweezer is used as a sensor to quantify the rhythmic motion of a Nauplius larva (Artemia salina) in a water sample. This is achieved by monitoring the time dependent displacement of the trapped nanoparticle as a consequence of the Nauplius activity. A Fourier analysis of the nanoparticle&#39;s position then yields a frequency spectrum that is characteristic to the motion of the observed species. This experiment demonstrates the capability of this method to measure and characterize the activity of small aquatic larvae without the requirement to observe them directly and to gain information about the position of the larvae with respect to the trapped particle. Overall, this approach could give an insight on the vitality of certain species found in an aquatic ecosystem and could expand the range of conventional methods for analyzing water samples.

Analyzing the Movement of the Nauplius &#039;Artemia salina&#039; by Optical Tracking of Plasmonic Nanoparticles

We use optical tracking of plasmonic nanoparticles to probe and characterize the frequency movements of aquatic organisms.

We demonstrate how optical tweezers may provide a sensitive tool to analyze the fluidic vibrations generated by the movement of small aquatic organisms. A ...

Coherent anti-Stokes Raman Scattering (CARS) Microscopy Visualizes Pharmaceutical Tablets During Dissolution

Traditional pharmaceutical dissolution tests determine the amount of drug dissolved over time by measuring drug content in the dissolution medium. This method provides little direct information about what is happening on the surface of the dissolving tablet. As the tablet surface composition and structure can change during dissolution, it is essential to monitor it during dissolution testing. In this work coherent anti-Stokes Raman scattering microscopy is used to image the surface of tablets during dissolution while UV absorption spectroscopy is simultaneously providing inline analysis of dissolved drug concentration for tablets containing a 50% mixture of theophylline anhydrate and ethyl cellulose. The measurements showed that in situ CARS microscopy is capable of imaging selectively theophylline in the presence of ethyl cellulose. Additionally, the theophylline anhydrate converted to theophylline monohydrate during dissolution, with needle-shaped crystals growing on the tablet surface during dissolution. The conversion of theophylline anhydrate to monohydrate, combined with reduced exposure of the drug to the flowing dissolution medium resulted in decreased dissolution rates. Our results show that in situ CARS microscopy combined with inline UV absorption spectroscopy is capable of monitoring pharmaceutical tablet dissolution and correlating surface changes with changes in dissolution rate.

Coherent anti-Stokes Raman Scattering CARS Microscopy Visualizes Pharmaceutical Tablets During Dissolution

Coherent anti-Stokes Raman scattering (CARS) microscopy is combined with an intrinsic flow-through dissolution setup to allow in situ and real-time visualization of the surface of pharmaceutical tablets undergoing dissolution. Using this custom-built setup, it is possible to correlate CARS videos with drug dissolution profiles recorded using inline UV absorption spectroscopy.

Traditional pharmaceutical dissolution tests determine the amount of drug dissolved over time by measuring drug content in the dissolution medium. This ...

Writing Bragg Gratings in Multicore Fibers

Fiber Bragg gratings in multicore fibers can be used as compact and robust filters in astronomical and other research and commercial applications. Strong suppression at a single wavelength requires that all cores have matching transmission profiles. These gratings cannot be inscribed using the same method as for single-core fibers because the curved surface of the cladding acts as a lens, focusing the incoming UV laser beam and causing variations in exposure between cores. Therefore we use an additional optical element to ensure that the beam shape does not change while passing through the cross-section of the multicore fiber. This consists of a glass capillary tube which has been polished flat on one side, which is then placed over the section of the fiber to be inscribed. The laser beam enters the fiber through the flat surface of the capillary tube and hence maintains its original dimensions. This paper demonstrates the improvements in core-to-core uniformity for a 7-core fiber using this method. The technique can be generalized to larger multicore fibers.

We describe a technique for inscribing identical fiber Bragg gratings into each core of a multicore fiber. This is achieved by introducing an additional surface into the optical path to mitigate lensing by the curved surface of the fiber cladding.

Fiber Bragg gratings in multicore fibers can be used as compact and robust filters in astronomical and other research and commercial applications. Strong ...

Dynamic Pore-scale Reservoir-condition Imaging of Reaction in Carbonates Using Synchrotron Fast Tomography

Underground storage permanence is a major concern for carbon capture and storage. Pumping CO2 into carbonate reservoirs has the potential to dissolve geologic seals and allow CO2 to escape. However, the dissolution processes at reservoir conditions are poorly understood. Thus, time-resolved experiments are needed to observe and predict the nature and rate of dissolution at the pore scale. Synchrotron fast tomography is a method of taking high-resolution time-resolved images of complex pore structures much more quickly than traditional &#181;-CT. The Diamond Lightsource Pink Beam was used to dynamically image dissolution of limestone in the presence of CO2-saturated brine at reservoir conditions. 100 scans were taken at a 6.1 &#181;m resolution over a period of 2 hours. The images were segmented and the porosity and permeability were measured using image analysis and network extraction. Porosity increased uniformly along the length of the sample; however, the rate of increase of both porosity and permeability slowed at later times.

Synchrotron fast tomography was used to dynamically image dissolution of limestone in the presence of CO2-saturated brine at reservoir conditions. 100 scans were taken at a 6.1 &#181;m resolution over a period of 2 h.

Underground storage permanence is a major concern for carbon capture and storage. Pumping CO2 into carbonate reservoirs has the potential to dissolve ...

Novel Photoacoustic Microscopy and Optical Coherence Tomography Dual-modality Chorioretinal Imaging in Living Rabbit Eyes

Photoacoustic ocular imaging is an emerging ophthalmic imaging technology that can noninvasively visualize ocular tissue by converting light energy into sound waves and is currently under intensive investigation. However, most reported work to date is focused on the imaging of the posterior segment of the eyes of small animals, such as rats and mice, which poses challenges for clinical human translation due to small eyeball sizes. This manuscript describes a novel photoacoustic microscopy (PAM) and optical coherence tomography (OCT) dual-modality system for posterior segment imaging of the eyes of larger animals, such as rabbits. The system configuration, system alignment, animal preparation, and dual-modality experimental protocols for in vivo, noninvasive, label-free chorioretinal imaging in rabbits are detailed. The effectiveness of the method is demonstrated through representative experimental results, including retinal and choroidal vasculature obtained by the PAM and OCT. This manuscript provides a practical guide to reproducing the imaging results in rabbits and advancing photoacoustic ocular imaging in larger animals.

This manuscript describes the novel setup and operating procedure of a photoacoustic microscopy and optical coherence tomography dual-modality system for noninvasive, label-free chorioretinal imaging of larger animals, such as rabbits.

Photoacoustic ocular imaging is an emerging ophthalmic imaging technology that can noninvasively visualize ocular tissue by converting light energy into ...

Generation of Size-controlled Poly (ethylene Glycol) Diacrylate Droplets via Semi-3-Dimensional Flow Focusing Microfluidic Devices

Uniform and size-controllable poly (ethylene glycol) diacrylate (PEGDA) droplets could be produced via the flow focusing process in a microfluidic device. This paper proposes a semi-three-dimensional (semi-3D) flow-focusing microfluidic chip for droplet formation. The polydimethylsiloxane (PDMS) chip was fabricated using the multi-layer soft lithography method. Hexadecane containing surfactant was used as the continuous phase, and PEGDA with the ultraviolet (UV) photo-initiator was the dispersed phase. Surfactants allowed the local surface tension to drop and formed a more cusped tip which promoted breaking into tiny micro-droplets. As the pressure of dispersed phase was constant, the size of droplets became smaller with increasing continuous phase pressure before dispersed phase flow was broken off. As a result, droplets with size variation from 1 &#181;m to 80 &#181;m in diameter could be selectively achieved by changing the pressure ratio in two inlet channels, and the average coefficient of variation was estimated to be below 7%. Furthermore, droplets could turn into micro-beads by UV exposure for photo-polymerization. Conjugating biomolecules on such micro-beads surface have many potential applications in the fields of biology and chemistry.

Generation of Size-controlled Poly ethylene Glycol Diacrylate Droplets via Semi-3-Dimensional Flow Focusing Microfluidic Devices

Here, we present a protocol to illustrate the fabrication processes and verifying experiments of a semi-three-dimensional (semi-3D) flow-focusing microfluidic chip for droplet formation.

Uniform and size-controllable poly (ethylene glycol) diacrylate (PEGDA) droplets could be produced via the flow focusing process in a microfluidic device. ...

Simultaneous Measurement of Turbulence and Particle Kinematics Using Flow Imaging Techniques

Numerous problems in scientific and engineering fields involve understanding the kinematics of particles in turbulent flows, such as contaminants, marine micro-organisms, and/or sediments in the ocean, or fluidized bed reactors and combustion processes in engineered systems. In order to study the effect of turbulence on the kinematics of particles in such flows, simultaneous measurements of both the flow and particle kinematics are required. Non-intrusive, optical flow measurement techniques for measuring turbulence, or for tracking particles, exist but measuring both simultaneously can be challenging due to interference between the techniques. The method presented herein provides a low cost and relatively simple method to make simultaneous measurements of the flow and particle kinematics. A cross section of the flow is measured using a particle image velocimetry (PIV) technique, which provides two components of velocity in the measurement plane. This technique utilizes a pulsed-laser for illumination of the seeded flow field that is imaged by a digital camera. The particle kinematics are simultaneously imaged using a light emitting diode (LED) line light that illuminates a planar cross section of the flow that overlaps with the PIV field-of-view (FOV). The line light is of low enough power that it does not affect the PIV measurements, but powerful enough to illuminate the larger particles of interest imaged using the high-speed camera. High-speed images that contain the laser pulses from the PIV technique are easily filtered by examining the summed intensity level of each high-speed image. By making the frame rate of the high-speed camera incommensurate with that of the PIV camera frame rate, the number of contaminated frames in the high-speed time series can be minimized. The technique is suitable for mean flows that are predominantly two-dimensional, contain particles that are at least 5 times the mean diameter of the PIV seeding tracers, and are low in concentration.

The technique described herein offers a low cost and relatively simple method to simultaneously measure particle kinematics and turbulence in flows with low particle concentrations. The turbulence is measured using particle image velocimetry (PIV), and particle kinematics are calculated from images obtained with a high-speed camera in an overlapping field-of-view.

Numerous problems in scientific and engineering fields involve understanding the kinematics of particles in turbulent flows, such as contaminants, marine ...