This work was supported by the Max Planck Society, an Alexander-von-Humboldt Professorship, and the Deutsche Forschungsgemeinschaft (CRC 1181). We thank Stefanie Schaffer at Universit&#228;tsklinikum Erlangen for providing Laz388 cells and for useful discussions. We thank Simone Ihloff and Maksim Schwab at MPL for technical support.

<ol>
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The authors have nothing to disclose.

One of the most crucial aspects to obtaining useful iSCAT data is the ability to find the correct focal position at the coverslip surface, and, furthermore, to hold this position for long periods of time. Failing to do so will result in broadened PSFs, weak iSCAT signals, and drift-associated artifacts in dynamics analyses. It turns out that finding the focal plane on a clean, bare coverslip surface is not an easy task as surface features are not visible against the large reference beam background (see Figure 4d).
Raw iSCAT images are often obscured by background signals that arise from wavefront impurities in the excitation source, and can hinder one&#39;s ability to find the correct imaging plane. Active wavefront subtraction is a useful way to circumvent this issue and subsequently monitor the iSCAT focus during a measurement16. One way to accomplish this is through spatial sample modulation. In brief, a function generator applies a 50 Hz square wave to the external control port of the piezo stage, resulting in a spatial sample modulation at the applied frequency (290 nm amplitude). Synchronous camera acquisitions are triggered from the same source, and, when combined through lock-in principles, result in a wavefront-compensated image14,16. The resulting image typically shows the surface roughness of the coverslip (Figure 4e). Small features remaining on the glass after cleaning can be used to bring the microscope into focus. Parameters used for this active background subtraction step may be changed according to the frame rate, exposure time, or hardware.
As mentioned above, the use of a high-quality beam splitter in the iSCAT setup (step 1.2.1.) is recommended, as imaging artefacts like ghosting or interference arising from thin planar beam splitters will influence the image and disturb the measurement. Figure 7 shows a comparison between a high-quality and low-quality beam splitter. Both raw iSCAT images show the same area on the coverslip containing some residual particles. The same iSCAT setup was used to capture both images, only the beam splitter was exchanged. Figure 7a shows the image formed on the camera by use of a thicker (5 mm), AR-coated, and wedged beam splitter. Due to the wedged design, the reflected beam from the back surface of the beam splitter is anti-parallel to the reflection arising from the front surface and is not entering the objective. No interference artefacts occur. Figure 7b shows the same field of view on the sample but this time a thinner (1 mm) planar beam splitter was used. The two reflections from front and back surfaces of the beam splitter are parallel and propagate to the camera. Interference artefacts are clearly visible.
<img alt="Figure 7" class="xfigimg" src="/files/ftp_upload/58486/58486fig7.jpg" /> 
Figure 7: Comparison of iSCAT images produced with high- and low-quality beam splitters. (a) Resulting raw iSCAT image by use of a 5 mm thick, AR-coated, and wedged beam splitter. (b) Resulting raw iSCAT image of the same area by use of a 1 mm thick planar beam splitter. Both beam splitters have the same splitting ratio (50% reflection, 50% transmission). Interference artefacts arising from Fresnel reflections are clearly observed in the image produced with the 1 mm thick planar beam splitter. Scale bars: 2 &#181;m. <a href="https://www.jove.com/files/ftp_upload/58486/58486fig7large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
In this protocol we describe a wide-field illumination scheme for iSCAT as it is fast, easy to realize and allows for parallel sensing over a large area14. Another common approach is to use acousto-optic deflectors (AODs) and scan a confocal beam across the sample12,17. This approach avoids the need for high-quality wavefronts but is more experimentally complex than conventional wide-field imaging. Furthermore, the speed of confocal illumination is limited by that of AODs. Depending on the desired experimental parameters, either confocal or wide-field illumination schemes can, in principle, be utilized to detect single proteins secreted from living cells.
As discussed throughout the protocol, it is imperative to minimize lateral mechanical fluctuations in the sample stage of the microscope. Even nanometer deviations in the position of the sample can lead to variations in consecutive camera frames and induce significant extraneous noise in the differential image. It is therefore recommended to use a mechanically stable microscope stage and a damped optical table (step 1.1.1.) and to cover the setup with optical curtains or panels during an experiment (step 3.5.).
An active focus stabilization scheme could also be considered for long-term measurements. In this approach, a second laser is incorporated into the microscope in a total internal reflection (TIR) arrangement, and subsequently imaged onto a quadrant photodiode. Changes in the system&#39;s focus translate into lateral displacements of the TIR laser spot on the quadrant diode, which can then be used in an active feedback loop to control the z-axis of the piezo stage26. Long-term vertical drift effects are thus eliminated.
Several modifications and extensions can be applied to the presented technique to address specific experimental needs. For example, commercial microscope stage incubators are available that could readily be incorporated into the iSCAT microscope for long-term imaging of cells. Other techniques can also be implemented to complement iSCAT imaging, such as confocal or TIR fluorescence microscopies17. To adapt on the system under study, iSCAT secretion measurements can be carried out in other cell media such as DMEM or DPBS, however, the pH indicator phenol red should be avoided as it can disturb the experiment due to absorption of the laser light. Additionally, supplements like fetal calf serum (FCS) or human platelet lysate (hPL) contain proteins that may interfere with iSCAT detection. Depending on the desired sensitivity of the experiment, these supplements should be excluded from the microscopy medium.
iSCAT relies on an analyte&#39;s ability to scatter light&#8212;a property that is intrinsic to all proteins&#8212;and is thus inherently nonspecific. Nevertheless, some degree of specificity is possible as iSCAT signals scale linearly with protein mass14,27,28. This allows for the calibration of an iSCAT system using standard protein samples, such as bovine serum albumin (BSA) and fibrinogen14,27,28. In fact, very recently, Young et al.28 have extended on the work of Piliarik &#38; Sandoghdar14 and have shown that iSCAT can be used to determine the molecular weight of proteins as small as streptavidin (53 kDa) with a mass resolution of 19 kDa and an accuracy of about 5 kDa. Several conventional approaches can further complement iSCAT by providing an extra level of specificity. As an example, enzyme-linked immunosorbent assays (ELISA), and/or other surface modifications, restrict protein binding events so that only the target protein is detected16.
In this protocol, we described how iSCAT microscopy can be used to investigate cellular secretions at the single protein level with subsecond temporal resolution16. The technique is general and can be implemented on any commercial or home-built microscope. In contrast to single-molecule fluorescence approaches, the method does not suffer from photobleaching or blinking effects but it still achieves single-protein sensitivity. These features make iSCAT a powerful tool in the field of biosensing and microscopy. Future applications will focus on elucidating complex cellular interactions such as immunological response to a stimulus or cellular communication.

Secreted proteins play a significant role in various physiological processes1. Because of this, they are routinely studied as a collective ensemble (proteomics) or as individual entities2,3. Proteomics traditionally investigates the entire set of proteins present in a particular biological system by way of e.g., enzyme-linked immunosorbent assays (ELISA), flow cytometry, or mass spectrometry4,5,6. Single proteins, on the other hand, are generally detected using a variety of techniques that are based on fluorescence7,8, plasmonics9,10, or cryogenic electron11 microscopies. All of these techniques use complex instruments, labeling, or both and often lack dynamics information as they only deliver long-term information about the system under study.
Here we use iSCAT12,13 microscopy to sense individual secretory proteins with sub-second temporal resolution14. Importantly, the technique detects the weak scattered signal intrinsic to every protein12,14. The amount of light that a small bioparticle scatters scales with its polarizability. Assuming that the shape of a protein can be approximated by an effective scattering sphere14,15,16, and that different proteins have very similar refractive indices, the measured signal can be directly connected to the molecular weight (MW) of the protein. The empirical calibration of iSCAT contrast versus molecular weight by reference measurements allows one to distinguish proteins of different sizes. iSCAT experiments can readily be complemented by fluorescence microscopy17,18, immunosorbent reagents, as well as fluorescent or scattering labels to allow for a specific detection of any protein of interest14,17,19.
In principle, iSCAT functions by amplifying a protein&#8217;s weak scattered light via interferometric mixing with a secondary reference wave. The detected intensity (<img alt="Equation 1" src="/files/ftp_upload/58486/58486eq1.jpg" />) in an iSCAT microscope is described by
<img alt="Equation 2" src="/files/ftp_upload/58486/58486eq2.jpg" />
where <img alt="Equation 3" src="/files/ftp_upload/58486/58486eq3.jpg" />&#160;is the incident intensity, <img alt="Equation 4" src="/files/ftp_upload/58486/58486eq4.jpg" />&#160;is a coefficient for the contribution of the reference wave, <img alt="Equation 5" src="/files/ftp_upload/58486/58486eq5.jpg" />&#160;signifies the scattering strength of the nano-object under study, and <img alt="Equation 6" src="/files/ftp_upload/58486/58486eq6.jpg" />&#160;is the phase shift between the scattered and reference waves14. Either the transmitted or back-reflected incident light is typically used as a reference wave, where in each case <img alt="Equation 7" src="/files/ftp_upload/58486/58486eq7.jpg" />&#160;accounts for the transmissivity or reflectivity of the sample chamber, respectively. The term <img alt="Equation 8" src="/files/ftp_upload/58486/58486eq8.jpg" />&#160;is proportional to the protein&#8217;s scattering cross section and can be neglected compared to the cross term. Thus, setting <img alt="Equation 9" src="/files/ftp_upload/58486/58486eq9.jpg" />&#160;for complete destructive interference, the detected light is given by <img alt="Equation 10" src="/files/ftp_upload/58486/58486eq10.jpg" />&#160;where <img alt="Equation 11" src="/files/ftp_upload/58486/58486eq11.jpg" />&#160;is the reference intensity and <img alt="Equation 12" src="/files/ftp_upload/58486/58486eq12.jpg" />&#160;is the interference intensity.
iSCAT microscopy offers an excellent method to study biological processes at the single-molecule level. As an example, we investigate Laz388 cells &#8212; an Epstein-Barr virus (EBV) transformed B lymphocyte cell line20,21 &#8212; as they secrete proteins such as IgG antibodies16. However, the method is general and can be applied to a variety of other biological systems. iSCAT is inherently unspecific and can detect any protein or nanoparticle or it can be extended with common surface functionalization methods for specific or multiplexed detection. Its simplicity and ability to be combined with other optical techniques, such as fluorescence microscopy, make iSCAT a valuable complementary tool in cell biology.

<table border="0" cellpadding="0" cellspacing="0" style="width:1081px;" width="1083">
	
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:255px;">Item/Device</td>
			<td style="width:152px;"></td>
			<td style="width:161px;"></td>
			<td style="width:513px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">100x / 1.46 NA objective</td>
			<td>Zeiss</td>
			<td>420792-9800-000</td>
			<td>alpha Plan Apochromat oil immersion</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">20x / 0.4 NA objective</td>
			<td>Leica</td>
			<td>566049</td>
			<td>N Plan</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Piezo Stage</td>
			<td>PI</td>
			<td>P-517k020</td>
			<td>3-axis stage with 100x100x10&#181;m range</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Diode laser (445 nm)</td>
			<td>Lasertack</td>
			<td>PD-01236</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Optics/Optomechanics</td>
			<td>Thorlabs/Newport</td>
			<td>-</td>
			<td>lenses, mirrors, posts, mounts</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Pinhole</td>
			<td>Thorlabs</td>
			<td>P30H</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">LED light source</td>
			<td>Thorlabs</td>
			<td>MCWHL5</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Shortpass filter (580 nm)</td>
			<td>Omega Optical</td>
			<td>580SP</td>
			<td>to modify the spectrum of the LED for fluorescence excitation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Longpass filter (500 nm)</td>
			<td>Thorlabs</td>
			<td>FEL0500</td>
			<td>to modify the spectrum of the LED for fluorescence excitation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">70R/30T beam splitter</td>
			<td>Newport</td>
			<td>20Q20BS.1</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Economy beam splitter</td>
			<td>Thorlabs</td>
			<td>EBS1</td>
			<td>used for the comparison of fringe effects</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Wedged plate beam splitter</td>
			<td>Thorlabs</td>
			<td>BSW26</td>
			<td>used for the comparison of fringe effects</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Shortpass dichroic mirror (550 nm)</td>
			<td>Edmund Optics</td>
			<td>66249</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">8R/92T beam splitter</td>
			<td>Thorlabs</td>
			<td>BP108</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">CMOS camera</td>
			<td>Photonfocus</td>
			<td>MV1-D1024E-160-CL</td>
			<td>for iSCAT aquisition</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">CMOS cameras</td>
			<td>Mightex</td>
			<td>SCE-B013-U</td>
			<td>for bright field / fluorescence aquisition</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Longpass filter (600 nm)</td>
			<td>Thorlabs</td>
			<td>FELH0600</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Computer</td>
			<td>Fujitsu Siemens&#160;</td>
			<td>-</td>
			<td>Core i7 Processor, 16 GB RAM, SSD</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Acquisition Software</td>
			<td>LabVIEW</td>
			<td>-</td>
			<td>LabVIEW 2016 Suite</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Analysis Software</td>
			<td>Matlab</td>
			<td>-</td>
			<td>Matlab 2014 Suite</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Plasma Cleaner</td>
			<td>Diener</td>
			<td>Diener pico</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Incubator</td>
			<td>Binder</td>
			<td>Model CB</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Centrifuge</td>
			<td>Eppendorf</td>
			<td>5810R</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Reagent/Material</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">RPMI 1640 medium</td>
			<td>Gibco</td>
			<td>11835063</td>
			<td>without phenol red</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">HEPES Buffer Solution (1M)</td>
			<td>Sigma Aldrich</td>
			<td>59205C</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Cover slides</td>
			<td>Marienfeld</td>
			<td>107052</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Glass bottom culture dishes</td>
			<td>ibidi</td>
			<td>81158</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Fluorescent Microspheres</td>
			<td>Invitrogen</td>
			<td>F8821</td>
			<td>used for calibration</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Immersol immersion oil</td>
			<td>Zeiss</td>
			<td>444960</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Propidium iodide stain</td>
			<td>Invitrogen</td>
			<td>R37108</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Small pipette tips</td>
			<td>Eppendorf</td>
			<td>30075005</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Flexible pipette tips</td>
			<td>Eppendorf</td>
			<td>5242956003</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Ethanol, 99.8%</td>
			<td>Fisher Scientific</td>
			<td>E/0650DF/15</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sodium hydroxide, pellets</td>
			<td>Sigma Aldrich</td>
			<td>221465</td>
			<td>for preparing 0.2M NaOH solution</td>
		</tr>
	</tbody>
</table>

label-free imaging of single proteins secreted from living cells via iscat microscopy

We demonstrate interferometric scattering (iSCAT) microscopy, a method capable of detecting single unlabeled proteins secreted from individual living cells in real time. In this protocol, we cover the fundamental steps to realize an iSCAT microscope and complement it with additional imaging channels to monitor the viability of a cell under study. Following this, we use the method for real-time detection of single proteins as they are secreted from a living cell which we demonstrate with an immortalized B-cell line (Laz388). Necessary steps concerning the preparation of microscope and sample as well as the analysis of the recorded data are discussed. The video protocol demonstrates that iSCAT microscopy offers a straightforward method to study secretion at the single-molecule level.

A schematic of an iSCAT microscope is shown in Figure 4a. Representative bright-field, fluorescence, and raw iSCAT images are shown in Figure 4b, 4c, and 4d, respectively16. Figure 4e and 4f show the results of background removal and differential post processing; two adsorbed proteins are visible as diffraction-limited spots in Figure 4f. Figure 6 shows a histogram of the detected proteins over the course of 125 s. These data were obtained by applying a peak-seeking algorithm to the captured images to count the binding events and catalog their contrast16. A total number of 503 proteins were detected.
Next, secreted species are identified by comparison with reference measurements carried out on purified protein solutions, or through additional measurements with functionalized glass surfaces14,16. The iSCAT data, thus, directly visualize cellular secretion dynamics on a subsecond scale16. As an example, we have previously found that IgG antibodies are a major fraction of the Laz388 secretome and are released from the cell at a rate of ca. 100 molecules per second16. Additionally, other particles spanning a range of 100 kDa - 1000 kDa are secreted by the cells16. The described method can be further employed e.g., to investigate the spatial concentration gradient of secretions surrounding a cell16, or to determine the temporal dynamics of cellular lysis16.
<img alt="Figure 6" class="xfigimg" src="/files/ftp_upload/58486/58486fig6.jpg" /> 
Figure 6: Quantification of secreted proteins by a single Laz388 cell. The histogram shows detected proteins during a time period of 125 s. Contrast values are accumulated in 1 x 10-4 contrast bins (blue bars). A total of 503 individual proteins were counted during this measurement. The experiment was repeated 10 times with similar results. This figure has been adapted from McDonald, M.P. et al.16. Copyright 2018 American Chemical Society. <a href="https://www.jove.com/files/ftp_upload/58486/58486fig6large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Label-Free Imaging of Single Proteins Secreted from Living Cells via iSCAT Microscopy at JoVE.com

Label-Free Imaging of Single Proteins Secreted from Living Cells via iSCAT Microscopy

We present a protocol for the real-time optical detection of single unlabeled proteins as they are secreted from living cells. This is based on interferometric scattering (iSCAT) microscopy, which can be applied to a variety of different biological systems and configurations.

We demonstrate interferometric scattering (iSCAT) microscopy, a method capable of detecting single unlabeled proteins secreted from individual living ...

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16.8K Views.  Max Planck Institute for the Science of Light (MPL). We present a protocol for the real-time optical detection of single unlabeled proteins as they are secreted from living cells. This is based on interferometric scattering (iSCAT) microscopy, which can be applied to a variety of different biological systems and configurations.

Video: Label-Free Imaging of Single Proteins Secreted from Living Cells via iSCAT Microscopy

Compact Quantum Dots for Single-molecule Imaging

Single-molecule imaging is an important tool for understanding the mechanisms of biomolecular function and for visualizing the spatial and temporal heterogeneity of molecular behaviors that underlie cellular biology 1-4. To image an individual molecule of interest, it is typically conjugated to a fluorescent tag (dye, protein, bead, or quantum dot) and observed with epifluorescence or total internal reflection fluorescence (TIRF) microscopy. While dyes and fluorescent proteins have been the mainstay of fluorescence imaging for decades, their fluorescence is unstable under high photon fluxes necessary to observe individual molecules, yielding only a few seconds of observation before complete loss of signal. Latex beads and dye-labeled beads provide improved signal stability but at the expense of drastically larger hydrodynamic size, which can deleteriously alter the diffusion and behavior of the molecule under study.
Quantum dots (QDs) offer a balance between these two problematic regimes. These nanoparticles are composed of semiconductor materials and can be engineered with a hydrodynamically compact size with exceptional resistance to photodegradation 5. Thus in recent years QDs have been instrumental in enabling long-term observation of complex macromolecular behavior on the single molecule level. However these particles have still been found to exhibit impaired diffusion in crowded molecular environments such as the cellular cytoplasm and the neuronal synaptic cleft, where their sizes are still too large 4,6,7.
Recently we have engineered the cores and surface coatings of QDs for minimized hydrodynamic size, while balancing offsets to colloidal stability, photostability, brightness, and nonspecific binding that have hindered the utility of compact QDs in the past 8,9. The goal of this article is to demonstrate the synthesis, modification, and characterization of these optimized nanocrystals, composed of an alloyed HgxCd1-xSe core coated with an insulating CdyZn1-yS shell, further coated with a multidentate polymer ligand modified with short polyethylene glycol (PEG) chains (Figure 1). Compared with conventional CdSe nanocrystals, HgxCd1-xSe alloys offer greater quantum yields of fluorescence, fluorescence at red and near-infrared wavelengths for enhanced signal-to-noise in cells, and excitation at non-cytotoxic visible wavelengths. Multidentate polymer coatings bind to the nanocrystal surface in a closed and flat conformation to minimize hydrodynamic size, and PEG neutralizes the surface charge to minimize nonspecific binding to cells and biomolecules. The end result is a brightly fluorescent nanocrystal with emission between 550-800 nm and a total hydrodynamic size near 12 nm. This is in the same size range as many soluble globular proteins in cells, and substantially smaller than conventional PEGylated QDs (25-35 nm).

We describe the preparation of colloidal quantum dots with minimized hydrodynamic size for single-molecule fluorescence imaging. Compared to conventional quantum dots, these nanoparticles are similar in size to globular proteins and are optimized for single-molecule brightness, stability against photodegradation, and resistance to nonspecific binding to proteins and cells.

Single-molecule imaging is an important tool for  understanding the mechanisms of biomolecular function and for visualizing the  spatial and temporal ...

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 ...

Single Wavelength Shadow Imaging of Caenorhabditis elegans Locomotion Including Force Estimates

This study demonstrates an inexpensive and straightforward technique that allows the measurement of physical properties such as position, velocity, acceleration and forces involved in the locomotory behavior of nematodes suspended in a column of water in response to single wavelengths of light. We demonstrate how to evaluate the locomotion of a microscopic organism using Single Wavelength Shadow Imaging (SWSI) using two different examples.
The first example is a systematic and statistically viable study of the average descent of C. elegans in a column of water. For this study, we used living and dead wildtype C. elegans. When we compared the velocity and direction of nematode active movement with the passive descent of dead worms within the gravitational field, this study showed no difference in descent-times. The average descent was 1.5 mm/sec &#177; 0.1 mm/sec for both the live and dead worms using 633 nm coherent light.
The second example is a case study of select individual C. elegans changing direction during the descent in a vertical water column. Acceleration and force are analyzed in this example. This case study demonstrates the scope of other physical properties that can be evaluated using SWSI while evaluating the behavior using single wavelengths in an environment that is not accessible with traditional microscopes. Using this analysis we estimated an individual nematode is capable of thrusting with a force in excess of 28 nN.
Our findings indicate that living nematodes exert 28 nN when turning, or moving against the gravitational field. The findings further suggest that nematodes passively descend in a column of water, but can actively resist the force of gravity primarily by turning direction.

Single Wavelength Shadow Imaging of Caenorhabditis elegans Locomotion Including Force Estimates

The technique presented here measures the path of freely swimming microscopic species using single wavelength exposure. C. elegans are used to demonstrate shadow imaging as an inexpensive alternative to costly microscopes. This technique can be adapted to accommodate various orientations, environments and species to measure direction, speed, acceleration and forces.

This study demonstrates an inexpensive and straightforward technique that allows the measurement of physical properties such as position, velocity, ...

Measurement of Scattering Nonlinearities from a Single Plasmonic Nanoparticle

Plasmonics, which are based on the collective oscillation of electrons due to light excitation, involve strongly enhanced local electric fields and thus have potential applications in nonlinear optics, which requires extraordinary optical intensity. One of the most studied nonlinearities in plasmonics is nonlinear absorption, including saturation and reverse saturation behaviors. Although scattering and absorption in nanoparticles are closely correlated by the Mie theory, there has been no report of nonlinearities in plasmonic scattering until very recently. 
Last year, not only saturation, but also reverse saturation of scattering in an isolated plasmonic particle was demonstrated for the first time. The results showed that saturable scattering exhibits clear wavelength dependence, which seems to be directly linked to the localized surface plasmon resonance (LSPR). Combined with the intensity-dependent measurements, the results suggest the possibility of a common mechanism underlying the nonlinear behaviors of scattering and absorption. These nonlinearities of scattering from a single gold nanosphere (GNS) are widely applicable, including in super-resolution microscopy and optical switches. 
In this paper, it is described in detail how to measure nonlinearity of scattering in a single GNP and how to employ the super-resolution technique to enhance the optical imaging resolution based on saturable scattering. This discovery features the first super-resolution microscopy based on nonlinear scattering, which is a novel non-bleaching contrast method that can achieve a resolution as low as l/8 and will potentially be useful in biomedicine and material studies.

Saturable and reverse saturable scattering were discovered in isolated plasmonic particles and adopted as a novel non-bleaching contrast method in super-resolution microscopy. Here the experimental procedures of detecting and extracting nonlinear scattering are explained in detail, as well as how to enhance resolution with the aid of saturated excitation microscopy.

Plasmonics, which are based on the collective oscillation of electrons due to light excitation, involve strongly enhanced local electric fields and thus ...

Use of a Multi-compartment Dynamic Single Enzyme Phantom for Studies of Hyperpolarized Magnetic Resonance Agents

Imaging of hyperpolarized substrates by magnetic resonance shows great clinical promise for assessment of critical biochemical processes in real time. Due to fundamental constraints imposed by the hyperpolarized state, exotic imaging and reconstruction techniques are commonly used. A practical system for characterization of dynamic, multi-spectral imaging methods is critically needed. Such a system must reproducibly recapitulate the relevant chemical dynamics of normal and pathological tissues. The most widely utilized substrate to date is hyperpolarized [1-13C]-pyruvate for assessment of cancer metabolism. We describe an enzyme-based phantom system that mediates the conversion of pyruvate to lactate. The reaction is initiated by injection of the hyperpolarized agent into multiple chambers within the phantom, each of which contains varying concentrations of reagents that control the reaction rate. Multiple compartments are necessary to ensure that imaging sequences faithfully capture the spatial and metabolic heterogeneity of tissue. This system will aid the development and validation of advanced imaging strategies by providing chemical dynamics that are not available from conventional phantoms, as well as control and reproducibility that is not possible in vivo.

A multi-compartment dynamic phantom is used to simulate some biology of interest for metabolic studies using hyperpolarized magnet resonance agents.

Imaging of hyperpolarized substrates by magnetic resonance shows great clinical promise for assessment of critical biochemical processes in real time. Due ...

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 ...

Hand Controlled Manipulation of Single Molecules via a Scanning Probe Microscope with a 3D Virtual Reality Interface

Considering organic molecules as the functional building blocks of future nanoscale technology, the question of how to arrange and assemble such building blocks in a bottom-up approach is still open. The scanning probe microscope (SPM) could be a tool of choice; however, SPM-based manipulation was until recently limited to two dimensions (2D). Binding the SPM tip to a molecule at a well-defined position opens an opportunity of controlled manipulation in 3D space. Unfortunately, 3D manipulation is largely incompatible with the typical 2D-paradigm of viewing and generating SPM data on a computer. For intuitive and efficient manipulation we therefore couple a low-temperature non-contact atomic force/scanning tunneling microscope (LT NC-AFM/STM) to a motion capture system and fully immersive virtual reality goggles. This setup permits &#34;hand controlled manipulation&#34; (HCM), in which the SPM tip is moved according to the motion of the experimenter&#39;s hand, while the tip trajectories as well as the response of the SPM junction are visualized in 3D. HCM paves the way to the development of complex manipulation protocols, potentially leading to a better fundamental understanding of nanoscale interactions acting between molecules on surfaces. Here we describe the setup and the steps needed to achieve successful hand-controlled molecular manipulation within the virtual reality environment.

We demonstrate the precise manipulation of individual organic molecules on a metal surface with the tip of a scanning probe microscope driven in 3D by the experimenter's hand using a motion capture system and fully immersive virtual reality goggles.

Considering organic molecules as the functional building blocks of future nanoscale technology, the question of how to arrange and assemble such building ...

Sub-nanometer Resolution Imaging with Amplitude-modulation Atomic Force Microscopy in Liquid

Atomic force microscopy (AFM) has become a well-established technique for nanoscale imaging of samples in air and in liquid. Recent studies have shown that when operated in amplitude-modulation (tapping) mode, atomic or molecular-level resolution images can be achieved over a wide range of soft and hard samples in liquid. In these situations, small oscillation amplitudes (SAM-AFM) enhance the resolution by exploiting the solvated liquid at the surface of the sample. Although the technique has been successfully applied across fields as diverse as materials science, biology and biophysics and surface chemistry, obtaining high-resolution images in liquid can still remain challenging for novice users. This is partly due to the large number of variables to control and optimize such as the choice of cantilever, the sample preparation, and the correct manipulation of the imaging parameters. Here, we present a protocol for achieving high-resolution images of hard and soft samples in fluid using SAM-AFM on a commercial instrument. Our goal is to provide a step-by-step practical guide to achieving high-resolution images, including the cleaning and preparation of the apparatus and the sample, the choice of cantilever and optimization of the imaging parameters. For each step, we explain the scientific rationale behind our choices to facilitate the adaptation of the methodology to every user's specific system.

We present a method for achieving sub-nanometer resolution images with amplitude-modulation (tapping mode) atomic force microscopy in liquid. The method is demonstrated on commercial atomic force microscopes. We explain the rationale behind our choices of parameters and suggest strategies for resolution optimization.

Atomic force microscopy (AFM) has become a well-established technique for nanoscale imaging of samples in air and in liquid. Recent studies have shown ...

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.

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.

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

All-electronic Nanosecond-resolved Scanning Tunneling Microscopy: Facilitating the Investigation of Single Dopant Charge Dynamics

The miniaturization of semiconductor devices to scales where small numbers of dopants can control device properties requires the development of new techniques capable of characterizing their dynamics. Investigating single dopants requires sub-nanometer spatial resolution, which motivates the use of scanning tunneling microscopy (STM). However, conventional STM is limited to millisecond temporal resolution. Several methods have been developed to overcome this shortcoming, including all-electronic time-resolved STM, which is used in this study to examine dopant dynamics in silicon with nanosecond resolution. The methods presented here are widely accessible and allow for local measurement of a wide variety of dynamics at the atomic scale. A novel time-resolved scanning tunneling spectroscopy technique is presented and used to efficiently search for dynamics.

We demonstrate an all-electronic method to observe nanosecond-resolved charge dynamics of dopant atoms in silicon with a scanning tunneling microscope.

The miniaturization of semiconductor devices to scales where small numbers of dopants can control device properties requires the development of new ...