Name: a flexible chamber for time-lapse live-cell imaging with stimulated raman scattering microscopy
Uploaded: 2022-08-31T15:00:00
Description: Watch this Scientific Journal Video about A Flexible Chamber for Time-Lapse Live-Cell Imaging with Stimulated Raman Scattering Microscopy at JoVE.com

We want to thank the 2019 Undergraduate Senior Design Team (Suk Chul Yoon, Ian Foxton, Louis Mazza, and James Walsh) at Binghamton University for the design, fabrication, and testing of the microscope enclosure box. We thank Scott Hancock, Olga Petrova, and Fabiola Moreno Olivas at Binghamton University&#160;for helpful discussions. This research was supported by the National Institutes of Health under Award Number R15GM140444.

1. Build the microscope environmental enclosure
NOTE: This large microscope environmental enclosure is used to control the temperature of the microscope body and the imaging environment to be stabilized at 37 &#176;C (Figure 1A).
<ol>
	<li>Mark the locations of the feet of the SRS microscope frame and the motorized stage using a marker pen on the optical table. Mount two Iris Diaphragms in front of the Galvanometer scanner of the microscope and adjust to make th...

<ol>
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Time-lapse live-cell SRS microscopy is an alternative imaging technique for molecule tracking in a label-free manner. Compared to fluorescence labeling, SRS imaging is free from photobleaching, enabling long-term monitoring of molecules. However, to date, the live cell imaging system on an upright SRS microscopy is not commercially available. In this work, a live cell imaging system with a stable thermal-insulated microscope enclosure box and a flexible inner soft chamber was developed to enable transmitted SRS time-laps...

Optical microscopy is used to observe the microstructures of samples. Optical imaging is rapid, less invasive, and less destructive than other technologies1. Live-cell imaging with optical microscopy is developed to capture the dynamics of cultured live cells over a long period2. Different types of optical contrasts provide distinct information about biological samples. For instance, optical phase microscopy shows the subtle difference in the refractive indices across the sample3. Fluorescence microscopy is widely used to image specific biomolecules or cellular organelles. However, the broadband excitation and emission spectra of fluorescence usually result in spectral overlapping when multicolor imaging is performed4. Fluorescent molecules are light-sensitive and can be bleached after long-term, periodic light exposure. In addition, fluorescence labeling may change the biodistribution of the molecules in cells5. SRS microscopy is a label-free chemical imaging technology6. The contrast of SRS relies on the vibrational transition of specific chemical bonds. The vibrational frequency of a chemical bond often exhibits a narrow spectral bandwidth, making it feasible to image multiple Raman bands in the same samples7. SRS microscopy is a unique tool for live-cell imaging, providing multiple chemical contrasts in a label-free manner8.
While SRS imaging of unstained cells has been used for many studies, long-term time-lapse SRS imaging of live cells has not been widely adopted. One reason is that commercial open chambers cannot be directly used for SRS imaging because of their large thickness9,10,11,12. These chambers with a glass lid are mostly designed for brightfield or fluorescence imaging using a single high NA objective with a backward detection scheme. However, SRS imaging prefers transmitted detection using both a high NA objective and a high NA condenser, which leaves only a very short gap (typically a few millimeters) between the objective and the condenser. To overcome this problem, we designed a flexible chamber using a soft material to enable time-lapse SRS imaging of live cells using an upright microscope frame. In this design, the water dipping objective was enclosed in the soft chamber and can freely move in three dimensions for focusing and imaging purposes.
The optimal temperature for culturing most mammalian cells is 37 &#176;C, while the room temperature is always 10&#176; lower than this. Temperature higher or lower than 37 &#176;C has a dramatic effect on cell growth rate13. Therefore, temperature control of the cell culture environment is required in a live-cell imaging system. It is known that temperature instability will lead to defocusing issues during long-term imaging14. To achieve a stable 37 &#176;C environment, we built a large enclosure chamber to cover the entire microscope frame, including a thermal insulation layer underneath the microscope (Figure 1). Within the sizeable temperature-control chamber, the small flexible chamber helps to accurately maintain the physiological humidity and pH via the regulated air flow supplemented with 5% CO2 (Figure 2). The temperature and humidity of the chambers were measured to confirm that the double-chamber design provided the optimal cell culture condition for cell growth under long-term, periodic SRS imaging (Figure 3). We then demonstrated the application of the system for time-lapse imaging and tracking lipid droplets (LDs) in SKOV3 cancer cells (Figure 4, Figure 5, and Figure 6).

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>A lab-built SRS microscope</td>
			<td></td>
			<td></td>
			<td>https://rdcu.be/cP6ve</td>
		</tr>
		<tr>
			<td>HF2LI 50 MHz lock-in amplifer</td>
			<td>Zurich Instruments</td>
			<td>HF2LI</td>
			<td></td>
		</tr>
		<tr>
			<td>Iris diaphragm</td>
			<td>Thorlabs Inc</td>
			<td>SM1D12</td>
			<td></td>
		</tr>
		<tr>
			<td>Kinematic mirror mount</td>
			<td>Thorlabs Inc</td>
			<td>KM100</td>
			<td></td>
		</tr>
		<tr>
			<td>Microscope frame</td>
			<td>Nikon Inc</td>
			<td>FN-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Motorized microscopy stage</td>
			<td>Prior Scientific</td>
			<td>Z-Deck</td>
			<td></td>
		</tr>
		<tr>
			<td>Oil-immersion condenser (C-AA Achromat/Aplanat, NA 1.4)</td>
			<td>Nikon Inc</td>
			<td>MBL71405</td>
			<td></td>
		</tr>
		<tr>
			<td>Water-immersion objective (CFI75 Apo 25XC W 1300)</td>
			<td>Nikon Inc</td>
			<td>MRD77225</td>
			<td></td>
		</tr>
		<tr>
			<td>Materials and parts for the microscope enclosure (31&#39;&#39; x 29&#39;&#39; x 28&#39;&#39; L x W x H)</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Airtherm heater module</td>
			<td>World Precision Instruments (WPI)</td>
			<td>AIRTHERM-SAT-1W</td>
			<td></td>
		</tr>
		<tr>
			<td>Airtherm heater controller, CO2 and humidity monitor</td>
			<td>World Precision Instruments (WPI)</td>
			<td>AIRTHERM-SMT-1W</td>
			<td></td>
		</tr>
		<tr>
			<td>Air/CO2 mixer module</td>
			<td>World Precision Instruments (WPI)</td>
			<td>ECU-HOC-W</td>
			<td></td>
		</tr>
		<tr>
			<td>Flexible duct hose (2-1/2&#39;&#39; ID, 2-3/4&#39;&#39; OD)</td>
			<td>McMaster-Carr</td>
			<td>56675K71</td>
			<td></td>
		</tr>
		<tr>
			<td>High-temperature glass-mica ceramic, easy-to-machine (6&#39;&#39; x 6&#39;&#39;, 1/4&#39;&#39; thickness)</td>
			<td>McMaster-Carr</td>
			<td>8489K62</td>
			<td></td>
		</tr>
		<tr>
			<td>Polycarbonate sheets (thickness 0.25&#39;&#39;)</td>
			<td>McMaster-Carr</td>
			<td>8574K286</td>
			<td></td>
		</tr>
		<tr>
			<td>Silicone rubber sheets (36&#39;&#39; x 36&#39;&#39;, thickness 1/8&#39;&#39;)</td>
			<td>McMaster-Carr</td>
			<td>5827T43</td>
			<td></td>
		</tr>
		<tr>
			<td>Materials and parts for the Flexible chamber</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Hot plate</td>
			<td>McMaster-Carr</td>
			<td>31745K11</td>
			<td></td>
		</tr>
		<tr>
			<td>High-purity inline filter, 1/4 NPT</td>
			<td>McMaster-Carr</td>
			<td>6645T18</td>
			<td></td>
		</tr>
		<tr>
			<td>Hole saw (cutting diameter 1-7/8 inch)</td>
			<td>McMaster-Carr</td>
			<td>4066A34</td>
			<td></td>
		</tr>
		<tr>
			<td>Hole saw (cutting diameter 50 mm)</td>
			<td>McMaster-Carr</td>
			<td>4556A19</td>
			<td></td>
		</tr>
		<tr>
			<td>High-temperature silicone rubber tubing, soft, 2 mm ID, 5 mm OD</td>
			<td>McMaster-Carr</td>
			<td>5054K313</td>
			<td></td>
		</tr>
		<tr>
			<td>Inline filter (1/4 NPT, 40 micron)</td>
			<td>McMaster-Carr</td>
			<td>98385K843</td>
			<td></td>
		</tr>
		<tr>
			<td>Multipurpose 6061 Aluminum round tube (1/8&#39;&#39; wall thickness, 4&#39;&#39; OD)</td>
			<td>McMaster-Carr</td>
			<td>9056K42</td>
			<td></td>
		</tr>
		<tr>
			<td>Multipurpose 6061 Aluminum round tube (3/4&#39;&#39; wall thickness, 3-3/4&#39;&#39; OD)</td>
			<td>McMaster-Carr</td>
			<td>9056K47</td>
			<td></td>
		</tr>
		<tr>
			<td>Multipurpose 6061 Aluminum bar (12&#39;&#39; x 12&#39;&#39;, thickness 1/4&#39;&#39;)</td>
			<td>McMaster-Carr</td>
			<td>8975K142</td>
			<td></td>
		</tr>
		<tr>
			<td>Multipurpose 6061 Aluminum bar (8&#39;&#39; x 8&#39;&#39;, thickness 3/8&#39;&#39;)</td>
			<td>McMaster-Carr</td>
			<td>9246K21</td>
			<td></td>
		</tr>
		<tr>
			<td>Objective nosepiece (single)</td>
			<td>Nikon Inc</td>
			<td>FN-MN-H</td>
			<td></td>
		</tr>
		<tr>
			<td>Sample holder (modified)</td>
			<td>Prior Scientific</td>
			<td>HZ202</td>
			<td></td>
		</tr>
		<tr>
			<td>Ultra-thin natural rubber film (thickness 0.01&#39;&#39;)</td>
			<td>McMaster-Carr</td>
			<td>8611K13</td>
			<td></td>
		</tr>
		<tr>
			<td>Vacuum-sealable glass jar</td>
			<td>McMaster-Carr</td>
			<td>3231T44</td>
			<td></td>
		</tr>
		<tr>
			<td>Software</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>MATLAB</td>
			<td>MathWorks</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>ImageJ (Fiji)</td>
			<td></td>
			<td>imagej.net</td>
			<td></td>
		</tr>
		<tr>
			<td>ScanImage</td>
			<td>Vidrio Technologies, LLC</td>
			<td></td>
			<td>SRS imaging software</td>
		</tr>
		<tr>
			<td>Materials for live-cell imaging</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Cover glass bottom sterile culture dishes (Dia.x H, 50 x 7 mm)</td>
			<td>Electron Microscopy Sciences (EMS)</td>
			<td>70674-02</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM cell culture medium</td>
			<td>ThermoFisher Scientific</td>
			<td>11965092</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal bovine serum (FBS)</td>
			<td>ThermoFisher Scientific</td>
			<td>26140079</td>
			<td></td>
		</tr>
		<tr>
			<td>LysoSensor fluorescent dye DND-189</td>
			<td>ThermoFisher Scientific</td>
			<td>L7535 (Invitrogen)</td>
			<td></td>
		</tr>
		<tr>
			<td>Oleic acid</td>
			<td>MilliporeSigma</td>
			<td>364525</td>
			<td></td>
		</tr>
		<tr>
			<td>SKOV3 cell line</td>
			<td>ATCC</td>
			<td>HTB-77</td>
			<td></td>
		</tr>
	</tbody>
</table>

a flexible chamber for time-lapse live-cell imaging with stimulated raman scattering microscopy

Stimulated Raman scattering (SRS) microscopy is a label-free chemical imaging technology. Live-cell imaging with SRS has been demonstrated for many biological and biomedical applications. However, long-term time-lapse SRS imaging of live cells has not been widely adopted. SRS microscopy often uses a high numerical aperture (NA) water-immersion objective and a high NA oil-immersion condenser to achieve high-resolution imaging. In this case, the gap between the objective and the condenser is only a few millimeters. Therefore, most commercial stage-top environmental chambers cannot be used for SRS imaging because of their large thickness with a rigid glass cover. This paper describes the design and fabrication of a flexible chamber that can be used for time-lapse live-cell imaging with transmitted SRS signal detection on an upright microscope frame. The flexibility of the chamber is achieved by using a soft material - a thin natural rubber film. The new enclosure and chamber design can be easily added to an existing SRS imaging setup. The testing and preliminary results demonstrate that the flexible chamber system enables stable, long-term, time-lapse SRS imaging of live cells, which can be used for various bioimaging applications in the future.

We fabricated and assembled the flexible chamber system for time-lapse SRS imaging (Figure 1 and Figure 2), and then evaluated the performance of the system. The temperature inside the microscope environmental enclosure reached the expected 37 &#176;C within 1 h, which did not significantly affect the room temperature (Figure 3A). The temperature in the flexible chamber reached 37 &#176;C in 1.5 h, and it was stably maintained at 37...

Watch this Scientific Journal Video about A Flexible Chamber for Time-Lapse Live-Cell Imaging with Stimulated Raman Scattering Microscopy at JoVE.com

A Flexible Chamber for Time-Lapse Live-Cell Imaging with Stimulated Raman Scattering Microscopy

We report a stage-top, flexible environmental chamber for time-lapse imaging of live cells using upright stimulated Raman scattering microscopy with transmitted signal detection. Lipid droplets were imaged in SKOV3 cells treated with oleic acid for up to 24 h with a 3 min time interval.

Stimulated Raman scattering (SRS) microscopy is a label-free chemical imaging technology. Live-cell imaging with SRS has been demonstrated for many ...

The flexible environmental chamber technique enables time-lapse as SRS imaging with transmitted signal detection on an operating microscope frame. SRS microscopy used a high numerical aperture objective and a high ended condenser, leaving only a few millimeters gap where a conventional chamber cannot fit. A flexible chamber solve this problem.Researchers using SRS microscopy can easily adopt this technique. The flexible chamber can also be used on a dissecting or a sterile microscope to maintain the specimen under optimal physiological conditions. To begin, mark the locations of the feet of the SRS microscope frame and the motorized stage using a marker pen on the optical table.After removing microscope frame and stage from the optical table, lay the silicone rubber sheet on the table. Cut the silicone rubber along the marks using a knife. Remove small rubber pieces, and place the square mica ceramic sheets into the same locations.Then move the microscope frame and the stage back to the optical table and carefully align the feet onto the mica ceramic sheets along the marker lines. After realigning the SRS optical path, assemble the environmental enclosure on top of the thermal insulation foundation to cover the entire microscope frame, using five pieces of large polycarbonate sheets. Seal the edges and interfaces of the box using aluminum foil tape.Connect the flexible duct hose to the inlet and the outlet ports of the enclosure box to allow circulated, warm airflow pumped and controlled by the heater module. Mount the machined hollow cylindrical aluminum piece 1 to the nose piece of the objective using three set screws. Next, mount the machined hollow cylindrical aluminum piece 2 to the sample holder using four screws.Fit the sample holder with aluminum piece 2 onto the motorized stage and mount it using screws. Place the natural rubber film sleeve between the two machined aluminum pieces and mount it using rubber bands at each end. Connect the compressed CO2 cylinder to the gas mixer module using proper tubing and connectors.Set the CO2 input pressure at 20 to 25 psi. Use the built-in CO2 sensor and a controller to ensure the air mixer module can regulate and mix 5%CO2 into the airflow. Use inline filters to clean up the airflow.Using proper tubing and connectors, guide the mixed air to the pre-sterilized water bottle placed on the hotplate and then guide the humidified air to the flexible chamber. Set the hotplate at 37 degrees Celsius. Bubble the airflow in the warm water to increase the humidity of the airflow.Disconnect the machine aluminum piece 2 from the sample holder by removing the screws. Wipe all parts of the flexible chamber with 70%ethanol, including the nose piece, the sample holder, and water dipping objective. Decontaminate the entire enclosure system using a UV lamp placed in the enclosure for 20 to 30 minutes.Then load the cell culture dish. Remove the cover of the dish and immobilize it using the clamps. Lower the objective into the cell culture media for coarse focusing.Lower the aluminum piece 2 to enclose the flexible chamber and mount it to the sample holder using screws. Then insert the sensor. Set the air supply with 5%CO2 and 19%O2 for normal cell culture with an airflow rate of 200 cubic centimeters per minute and temperature to 37 degrees Celsius.Tune the laser wavelength to 805 nanometers to target the 2, 854 centimeter inverse Raman shift, which is attributed to the vibration of CH2 chemical bonds. Use low laser power to reduce photo damage to the cells. Adjust and focus the objective to achieve good SRS imaging of the cells using the focus button on the main controls panel of the software.To perform rapid focusing, set the pixel number to be 512 by 512 pixels with a pixel dwell time of 4.8 microseconds on the configuration panel. After achieving good focusing, set the imaging resolution to be 2048 by 2048 pixels for a 175 micrometers squared field of view for the acquisition of high quality images. Check the save function on the main controls panel and check the SRS channel on the channels panel.Set the interval time between two frames to be 180 seconds on the main controls channel. Set the acquisition number to 480 for time-lapse imaging over 24 hours. Start automated imaging acquisition using the loop function on the main controls panel.The performance of the flexible chamber system for time-lapse SRS imaging was evaluated. The temperature inside the microscope environmental enclosure reached the expected 37 degrees Celsius and did not significantly affect room temperature. The temperature in the flexible chamber reached 37 degrees Celsius in 1.5 hours and was stably maintained for at least 24 hours.The relative humidity in the flexible chamber reached 85%in one hour and could be maintained for at least 24 hours. The time-lapse SRS imaging of live SKOV3 cells showed the rapid and active movement of intracellular lipid droplets with a temporal resolution of three minutes. By the end of the 24 hour imaging session, the cells still showed normal morphology and density, indicating that the cells were healthy.Next, SKOV3 cells treated with oleic acid were imaged and lipid droplet accumulation was tracked over 10 hours. The lipid droplet amounts were quantified using the lipid droplet to cell body area ratio and total SRS intensity of the lipid droplets. The results indicate that the amount of lipid droplets kept increasing over 10 hours.Simultaneous forward SRS imaging of lipid droplets and backward two photon fluorescence imaging of lysosomes labeled with a fluorescence dye DND-189 was also demonstrated. A very low degree of colocalization of lipid droplets and lysosomes was observed. When attempting this protocol, keep in mind that focal drift is a common issue in live cell imaging.Refocusing may be needed after about two hours of time-lapse imaging. After its development, time-lapse SRS imaging has been used for various studies to track label-free molecules or labeled molecules with Raman text in live cells.

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Research

JoVE Journal

Bioengineering

Specimen Preparation, Imaging, and Analysis Protocols for Knife-edge Scanning Microscopy

Major advances in high-throughput, high-resolution, 3D microscopy techniques have enabled the acquisition of large volumes of neuroanatomical data at submicrometer resolution. One of the first such instruments producing whole-brain-scale data is the Knife-Edge Scanning Microscope (KESM)7, 5, 9, developed and hosted in the authors' lab. KESM has been used to section and image whole mouse brains at submicrometer resolution, revealing the intricate details of the neuronal networks (Golgi)1, 4, 8, vascular networks (India ink)1, 4, and cell body distribution (Nissl)3. The use of KESM is not restricted to the mouse nor the brain. We have successfully imaged the octopus brain6, mouse lung, and rat brain. We are currently working on whole zebra fish embryos. Data like these can greatly contribute to connectomics research10; to microcirculation and hemodynamic research; and to stereology research by providing an exact ground-truth. 
In this article, we will describe the pipeline, including specimen preparation (fixing, staining, and embedding), KESM configuration and setup, sectioning and imaging with the KESM, image processing, data preparation, and data visualization and analysis. The emphasis will be on specimen preparation and visualization/analysis of obtained KESM data. We expect the detailed protocol presented in this article to help broaden the access to KESM and increase its utilization.

The full process from brain specimen preparation to serial sectioning imaging using the Knife-Edge Scanning Microscope, to data visualization and analysis is described. This technique is currently used to acquire mouse brain data, but it is applicable to other organs, other species.

Major advances in high-throughput, high-resolution, 3D microscopy techniques have enabled the acquisition of large volumes of neuroanatomical data at ...

Time-lapse Fluorescence Imaging of Arabidopsis Root Growth with Rapid Manipulation of The Root Environment Using The RootChip

The root functions as the physical anchor of the plant and is the organ responsible for uptake of water and mineral nutrients such as nitrogen, phosphorus, sulfate and trace elements that plants acquire from the soil. If we want to develop sustainable approaches to producing high crop yield, we need to better understand how the root develops, takes up a wide spectrum of nutrients, and interacts with symbiotic and pathogenic organisms. To accomplish these goals, we need to be able to explore roots in microscopic detail over time periods ranging from minutes to days.
We developed the RootChip, a polydimethylsiloxane (PDMS)- based microfluidic device, which allows us to grow and image roots from Arabidopsis seedlings while avoiding any physical stress to roots during preparation for imaging1 (Figure 1). The device contains a bifurcated channel structure featuring micromechanical valves to guide the fluid flow from solution inlets to each of the eight observation chambers2. This perfusion system allows the root microenvironment to be controlled and modified with precision and speed. The volume of the chambers is approximately 400 nl, thus requiring only minimal amounts of test solution.
Here we provide a detailed protocol for studying root biology on the RootChip using imaging-based approaches with real time resolution. Roots can be analyzed over several days using time lapse microscopy. Roots can be perfused with nutrient solutions or inhibitors, and up to eight seedlings can be analyzed in parallel. This system has the potential for a wide range of applications, including analysis of root growth in the presence or absence of chemicals, fluorescence-based analysis of gene expression, and the analysis of biosensors, e.g. FRET nanosensors3.

This article provides a protocol for cultivation of Arabidopsis seedlings in the RootChip, a microfluidic imaging platform that combines automated control of growth conditions with microscopic root monitoring and FRET-based measurement of intracellular metabolite levels.

The root functions as the physical anchor of the plant and is the organ responsible for uptake of water and mineral nutrients such as nitrogen, ...

Creating Adhesive and Soluble Gradients for Imaging Cell Migration with Fluorescence Microscopy

Cells can sense and migrate towards higher concentrations of adhesive cues such as the glycoproteins of the extracellular matrix and soluble cues such as growth factors. Here, we outline a method to create opposing gradients of adhesive and soluble cues in a microfluidic chamber, which is compatible with live cell imaging. A copolymer of poly-L-lysine and polyethylene glycol (PLL-PEG) is employed to passivate glass coverslips and prevent non-specific adsorption of biomolecules and cells. Next, microcontact printing or dip pen lithography are used to create tracks of streptavidin on the passivated surfaces to serve as anchoring points for the biotinylated peptide arginine-glycine-aspartic acid (RGD) as the adhesive cue. A microfluidic device is placed onto the modified surface and used to create the gradient of adhesive cues (100% RGD to 0% RGD) on the streptavidin tracks. Finally, the same microfluidic device is used to create a gradient of a chemoattractant such as fetal bovine serum (FBS), as the soluble cue in the opposite direction of the gradient of adhesive cues.

A method for the assembly of adhesive and soluble gradients in a microscopy chamber for live cell migration studies is described. The engineered environment combines antifouling surfaces and adhesive tracks with solution gradients and therefore allows one to determine the relative importance of guidance cues.

Cells can sense and migrate towards higher concentrations of adhesive cues such as the glycoproteins of the extracellular matrix and soluble cues such as ...

Sample Drift Correction Following 4D Confocal Time-lapse Imaging

The generation of four-dimensional (4D) confocal datasets; consisting of 3D image sequences over time; provides an excellent methodology to capture cellular behaviors involved in developmental processes.&#160; The ability to track and follow cell movements is limited by sample movements that occur due to drift of the sample or, in some cases, growth during image acquisition. Tracking cells in datasets affected by drift and/or growth will incorporate these movements into any analysis of cell position. This may result in the apparent movement of static structures within the sample. Therefore prior to cell tracking, any sample drift should be corrected. Using the open source Fiji distribution 1 &#160;of ImageJ 2,3 and the incorporated LOCI tools 4, we developed the Correct 3D drift plug-in to remove erroneous sample movement in confocal datasets. This protocol effectively compensates for sample translation or alterations in focal position by utilizing phase correlation to register each time-point of a four-dimensional confocal datasets while maintaining the ability to visualize and measure cell movements over extended time-lapse experiments.

Time-lapse microscopy allows the visualization of developmental processes. Growth or drift of samples during image acquisition reduces the ability to accurately follow and measure cell movements during development. We describe the use of open source image processing software to correct for three dimensional sample drift over time.

The generation of four-dimensional (4D) confocal datasets; consisting of 3D image sequences over time; provides an excellent methodology to capture ...

From Fast Fluorescence Imaging to Molecular Diffusion Law on Live Cell Membranes in a Commercial Microscope

It has become increasingly evident that the spatial distribution and the motion of membrane components like lipids and proteins are key factors in the regulation of many cellular functions. However, due to the fast dynamics and the tiny structures involved, a very high spatio-temporal resolution is required to catch the real behavior of molecules. Here we present the experimental protocol for studying the dynamics of fluorescently-labeled plasma-membrane proteins and lipids in live cells with high spatiotemporal resolution. Notably, this approach doesn&#8217;t need to track each molecule, but it calculates population behavior using all molecules in a given region of the membrane. The starting point is a fast imaging of a given region on the membrane. Afterwards, a complete spatio-temporal autocorrelation function is calculated correlating acquired images at increasing time delays, for example each 2, 3, n repetitions. It is possible to demonstrate that the width of the peak of the spatial autocorrelation function increases at increasing time delay as a function of particle movement due to diffusion. Therefore, fitting of the series of autocorrelation functions enables to extract the actual protein mean square displacement from imaging (iMSD), here presented in the form of apparent diffusivity vs average displacement. This yields a quantitative view of the average dynamics of single molecules with nanometer accuracy. By using a GFP-tagged variant of the Transferrin Receptor (TfR) and an ATTO488 labeled 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine (PPE) it is possible to observe the spatiotemporal regulation of protein and lipid diffusion on &#181;m-sized membrane regions in the micro-to-milli-second time range.

Spatial distribution and temporal dynamics of plasma membrane proteins and lipids is a hot topic in biology. Here this issue is addressed by a spatio-temporal image fluctuation analysis that provides conceptually the same physical quantities of single particle tracking, but it uses small molecular labels and standard microscopy setups.

It has become increasingly evident that the spatial distribution and the motion of membrane components like lipids and proteins are key factors in the ...

Fluorescence-quenching of a Liposomal-encapsulated Near-infrared Fluorophore as a Tool for In Vivo Optical Imaging

Optical imaging offers a wide range of diagnostic modalities and has attracted a lot of interest as a tool for biomedical imaging. Despite the enormous number of imaging techniques currently available and the progress in instrumentation, there is still a need for highly sensitive probes that are suitable for in vivo imaging. One typical problem of available preclinical fluorescent probes is their rapid clearance in vivo, which reduces their imaging sensitivity. To circumvent rapid clearance, increase number of dye molecules at the target site, and thereby reduce background autofluorescence, encapsulation of the near-infrared fluorescent dye, DY-676-COOH in liposomes and verification of its potential for in vivo imaging of inflammation was done. DY-676 is known for its ability to self-quench at high concentrations. We first determined the concentration suitable for self-quenching, and then encapsulated this quenching concentration into the aqueous interior of PEGylated liposomes. To substantiate the quenching and activation potential of the liposomes we use a harsh freezing method which leads to damage of liposomal membranes without affecting the encapsulated dye. The liposomes characterized by a high level of fluorescence quenching were termed Lip-Q. We show by experiments with different cell lines that uptake of Lip-Q is predominantly by phagocytosis which in turn enabled the characterization of its potential as a tool for in vivo imaging of inflammation in mice models. Furthermore, we use a zymosan-induced edema model in mice to substantiate the potential of Lip-Q in optical imaging of inflammation in vivo. Considering possible uptake due to inflammation-induced enhanced permeability and retention (EPR) effect, an always-on liposome formulation with low, non-quenched concentration of DY-676-COOH (termed Lip-dQ) and the free DY-676-COOH were compared with Lip-Q in animal trials.

Fluorescence-quenching of a Liposomal-encapsulated Near-infrared Fluorophore as a Tool for In Vivo Optical Imaging

The use of fluorophores for in vivo imaging can be greatly limited by opsonization, rapid clearance, low detection sensitivity and cytotoxic effects on the host. Encapsulation of fluorophores in liposomes by film hydration and extrusion leads to fluorescence quenching and protection which enables in vivo imaging with high detection sensitivity.

Optical imaging offers a wide range of diagnostic modalities and has attracted a lot of interest as a tool for biomedical imaging. Despite the enormous ...

Live Cell Imaging during Mechanical Stretch

There is currently a significant interest in understanding how cells and tissues respond to mechanical stimuli, but current approaches are limited in their capability for measuring responses in real time in live cells or viable tissue. A protocol was developed with the use of a cell actuator to distend live cells grown on or tissues attached to an elastic substrate while imaging with confocal and atomic force microscopy (AFM). Preliminary studies show that tonic stretching of human bronchial epithelial cells caused a significant increase in the production of mitochondrial superoxide. Moreover, using this protocol, alveolar epithelial cells were stretched and imaged, which showed direct damage to the epithelial cells by overdistention simulating one form of lung injury in vitro. A protocol to conduct AFM nano-indentation on stretched cells is also provided.

A novel imaging protocol was developed using a custom motor-driven mechanical actuator to allow the measurement of real time responses to mechanical strain in live cells. Relevant to mechanobiology, the system can apply strains up to 20% while allowing near real-time imaging with confocal or atomic force microscopy.

There is currently a significant interest in understanding how cells and tissues respond to mechanical stimuli, but current approaches are limited in ...

Rapid Subtractive Patterning of Live Cell Layers with a Microfluidic Probe

The microfluidic probe (MFP) facilitates performing local chemistry on biological substrates by confining nanoliter volumes of liquids. Using one particular implementation of the MFP, the hierarchical hydrodynamic flow confinement (hHFC), multiple liquids are simultaneously brought in contact with a substrate. Local chemical action and liquid shaping using the hHFC, is exploited to create cell patterns by locally lysing and removing cells. By utilizing the scanning ability of the MFP, user-defined patterns of cell monolayers are created. This protocol enables rapid, real-time and spatially controlled cell patterning, which can allow selective cell-cell and cell-matrix interaction studies.

We present a protocol to perform subtractive patterning of live cell monolayers on a surface. This is achieved by local and selective lysis of adherent cells using a microfluidic probe (MFP). The cell lysate retrieved from local regions can be used for downstream analysis, enabling molecular profiling studies.

The microfluidic probe (MFP) facilitates performing local chemistry on biological substrates by confining nanoliter volumes of liquids. Using one ...

Visualizing Adhesion Formation in Cells by Means of Advanced Spinning Disk-Total Internal Reflection Fluorescence Microscopy

In living cells, processes such as adhesion formation involve extensive structural changes in the plasma membrane and the cell interior. In order to visualize these highly dynamic events, two complementary light microscopy techniques that allow fast imaging of live samples were combined: spinning disk microscopy (SD) for fast and high-resolution volume recording and total internal reflection fluorescence (TIRF) microscopy for precise localization and visualization of the plasma membrane. A comprehensive and complete imaging protocol will be shown for guiding through sample preparation, microscope calibration, image formation and acquisition, resulting in multi-color SD-TIRF live imaging series with high spatio-temporal resolution. All necessary image post-processing steps to generate multi-dimensional live imaging datasets, i.e. registration and combination of the individual channels, are provided in a self-written macro for the open source software ImageJ. The imaging of fluorescent proteins during initiation and maturation of adhesion complexes, as well as the formation of the actin cytoskeletal network, was used as a proof of principle for this novel approach. The combination of high resolution 3D microscopy and TIRF provided a detailed description of these complex processes within the cellular environment and, at the same time, precise localization of the membrane-associated molecules detected with a high signal-to-background ratio.

An advanced microscope that permit fast and high-resolution imaging of both, the isolated plasma membrane and the surrounding intracellular volume, will be presented. The integration of spinning disk and total internal reflection fluorescence microscopy in one setup allows live imaging experiments at high acquisition rates up to 3.5 s per image stack.

In living cells, processes such as adhesion formation involve extensive structural changes in the plasma membrane and the cell interior. In order to ...

Continuous Measurement of Biological Noise in Escherichia Coli Using Time-lapse Microscopy

The protocol developed here offers a tool to enable computer tracking of Escherichia coli division and fluorescent levels over several hours. The process starts by screening for colonies that survive on minimal media, assuming that only Escherichia coli harboring the correct plasmid will be able to thrive in the specific conditions. Since the process of building large genetic circuits, requiring the assembly of many DNA parts, is challenging, circuit components are often distributed between multiple plasmids at different copy numbers requiring the use of several antibiotics. Mutations in the plasmid can destroy transcription of the antibiotic resistance genes and interject with resources management in the cell leading to necrosis. The selected colony is set on a glass-bottom Petri dish and a few focus planes are selected for microscopy tracking in both bright field and fluorescent domains. The protocol maintains the image focus for more than 12 hours under initial conditions that cannot be regulated, creating a few difficulties. For example, dead cells start to accumulate in the lenses' field of focus after a few hours of imaging, which causes toxins to buildup and the signal to blur and decay. Depletion of nutrients introduces new metabolic processes and hinder the desired response of the circuit. The experiment's temperature lowers the effectivity of inducers and antibiotics, which can further damage the reliability of the signal. The minimal media gel shrinks and dries, and as a result the optical focus changes over time. We developed this method to overcome these challenges in Escherichia coli, similar to previous works developing analogous methods for other micro-organisms. In addition, this method offers an algorithm to quantify the total stochastic noise in unaltered and altered cells, finding that the results are consistent with flow analyzer predictions as shown by a similar coefficient of variation (CV).

Continuous Measurement of Biological Noise in Escherichia Coli Using Time-lapse Microscopy

This work presents a microscopy method that allows live imaging of a single cell of Escherichia coli for analysis and quantification of the stochastic behavior of synthetic gene circuits.

The protocol developed here offers a tool to enable computer tracking of Escherichia coli division and fluorescent levels over several hours. The process ...