Name: dynamic pore-scale reservoir-condition imaging of reaction in carbonates using synchrotron fast tomography
Uploaded: 2017-02-21T12:30:00.000+00:00
Duration: 10 min 18 s
Description: Watch this Scientific Journal Video about Dynamic Pore-scale Reservoir-condition Imaging of Reaction in Carbonates Using Synchrotron Fast Tomography at JoVE.com

We gratefully acknowledge funding from the Qatar Carbonates and Carbon Storage Research Centre (QCCSRC), provided jointly by Qatar Petroleum, Shell, and Qatar Science &amp; Technology Park. We also gratefully acknowledge the funding and support provided by Diamond Lightsource and Manchester University at the I13 Imaging Branch.

1. Imaging Strategy Design
<ol>
	<li>Calculate the X-ray spectra of the beamline at the highest pink beam energy and flux in order to predict imaging performance using the experimental tuning curve and measuring filter transmissions. An example of the X-ray spectra of the Diamond Lightsource I13-2 &#39;Pink Beam&#39; is shown in Figure 2.</li>
	<li>As the lower energy X-rays cause heating of the sample and do not add to imaging contrast, filter out the lower part of the X-ray spectrum such that only the highest energy X-rays are used in imaging the sample. Choose in line filters of materials that absorb at the desired low wavelengths of light suitable to the light source by calculating the theoretical filter transmission at the available light wavelengths31,32. Here, use aluminum and gold for the beam line at this light source.
	<ol>
		<li>Use a band-pass filter consisting of a combination of X-ray filters as high-pass and an X-ray mirror operating near the critical angle as low-pass filter. In this case, use a set of 0.2 mm pyrolytic carbon and 0.2 mm aluminum filters and for the mirror a platinum-coated strip under an incident angle of 1.15 mrad. The mirror reflects only light below 30 keV and additional inline filters have been installed of 2 mm Al and 0.1 &#181;m Au which have absorption peaks at 13 and 22 keV respectively to filter more of the lower energy X-rays. Figure 3 depicts the beamline imaging apparatus.</li>
	</ol>
	</li>
	<li>Choose a scintillator that scintillates abundantly at the beamlines available light frequencies and flux. In this case, the scintillation screen is made of 250 &#181;m-thick cadmium tungstenate (CdWO4), which is stacked with 750 &#181;m-thick lead tungstenate (PbWO4). Then choose an objective lens and camera that have an appropriate field of view and snapping time resolution for the experimental requirements. In this case, couple a 1.25X objective lens with an aperture of 0.04 with a PCO EDGE 5.5 CMOS camera and used to capture a 4-mm field of view with a frame rate of 0.001 s.</li>
	<li>Choose the &#39;flyscan&#39; technique for image acquisition as this method of stage rotation reduces sample vibration. Traditional acquisition requires that the stage stop at each angular increment, take a projection, and then move to the next angle. The image acquisition during these dynamic tomographies was done with a &#39;flyscan&#39;, which takes tomographic scan as the stage is moving and assumes an angular increment such that the difference between each successive projection is small. The &#39;flyscan&#39; method eliminates the small vibrational effects of the start-and-stop motion and provides higher quality image more quickly.</li>
</ol>
2. Assembly of Equipment and Cell
<ol>
	<li>Load the core into the cell in preparation for core flooding.
	<ol>
		<li>First, wrap the core in one layer of aluminum foil and insert into a sleeve (e.g., Viton) (Figure 4).</li>
		<li>Cut the sleeve to size so that it is 2 mm shorter than the combined length of core and interior end fittings. The end fittings are 1/16&#34; national pipe thread (NPT) to union fittings that have been machined to 5 mm in exterior diameter, while the sleeve is 4 mm in interior diameter.</li>
		<li>Stretch the sleeve over the 5 mm end fittings to create a tight seal. Ensure that there is not any space between the end fittings and the core to ensure that the confining pressure does not over compress the sleeve and pinch off flow.</li>
		<li>Wrap the fittings and sleeve in two additional layers of aluminum both to prevent gaseous CO2 from diffusing into the confining fluid and to keep the sleeve in place on the fittings and prevent a hydraulic pathway from connecting the confining and pore fluids.</li>
		<li>Put the core holder back together by sliding the tubing and seals back in place and seal the end caps and end fittings by replacing the bolts.</li>
	</ol>
	</li>
	<li>Mount the core holder on the stage and connect the flow and the electrical lines.</li>
	<li>Test the stage rotation and ensure that all flow and electrical lines are free to rotate from -90&#176; to 90&#176;.</li>
	<li>Take a dry scan of the entire core prior to beginning the experiment.
	<ol>
		<li>Scan the core in overlapping sections around 4 mm in width and length. Calibrate the scan exposure time to an average count value of around 15,000, which ensures a high signal to noise ratio without over-saturating the scintillator. Take each dry scan with at least 2,400 projections to maintain phase contrast and edge sharpness.</li>
		<li>Take flat and dark images of the scintillator so that any damage and external noise can be accounted for during reconstruction. Take flats by moving the core holder out of the field of view and taking an image of just the scintillator with the beam on. Take darks using the same method with the beam off.</li>
	</ol>
	</li>
</ol>
3. System Pressurization
<ol>
	<li>Load a 1% wt potassium chloride (KCl) 5% wt sodium chloride (NaCl) brine into the disassembled reactor by pouring fluid in through the top of the reactor vessel.
	<ol>
		<li>Add powdered carbonate rock to achieve the desired brine acidity. In this case no carbonate was added.</li>
		<li>Reassemble the reactor by tightening the bolts and rewrapping it with heating tape and inserting the temperature probe into the top.</li>
		<li>Load CO2 into the injection pump by opening valve 1 (V1 in Figure 1).</li>
		<li>Close Valve 1 and pressurize the injection pump to 100 bar.</li>
		<li>Open Valve 2 to flood the reactor with CO2. Heat the reactor to 50 &#176;C using a PID controlled heating wrap in combination with a temperature probe and continuously stir with an entrainment stirrer driven by an external electric motor. Equilibrate the brine with CO2 at 10 MPa and 50 &#176;C for between 2 and 6 h to ensure that the brine is completely saturated with CO2 and the carbonate is fully dissolved.</li>
	</ol>
	</li>
	<li>Prior to connecting the core holder, completely purge the system of air and possible precipitants in the lines from previous experiments. To do this, connect the lines above and below the core holder to bypass the core holder (U1 and U2).
	<ol>
		<li>Load deionized (DI) water into the receiving pump through valve 11 by setting the receiving pump to refill.</li>
		<li>Open valves 7, 4, and 3 and use the receiving pump on constant pressure mode to drive DI water backwards through the system and out of valve 3 below the reactor. Use approximately ten system volumes to ensure the lines are clear of air and rinsed clean.</li>
	</ol>
	</li>
	<li>Empty the receiving pump and then load a brine of 25% wt KI into the receiving pump through valve 11 and load DI water into the confining pump through valve 10.
	<ol>
		<li>Close valve 10 and open valves 8 and 6. Use the confining pump to confine the core at 2 MPa.</li>
		<li>Close Valve 11 and pressurize the receiving pump to 10 Bar.</li>
		<li>Open valves 9, 7, 4, &#38; 3 and use the resulting pressure drop to drive KI doped brine through the core.</li>
		<li>Step up the confining and pore pressures incrementally until a reasonable flow rate is established. Drive approximately two complete system volumes of brine through the core and drain the fluid through valve 3 below the reactor. In this way all air is purged from the system and the core is flooded with high contrast brine that makes the arrival of undoped reactive brine easy to observe.</li>
		<li>Close valve 3 and incrementally increase the confining and pore pressures until the core is confined at 12 MPa and the pore pressure is 10 MPa. Switch on the PID controller to bring the core to 50 &#176;C.</li>
		<li>Stop the receiving pump, close valve 3, and open valve 5 at the base of the reactor to connect the reactor system to the core.</li>
	</ol>
	</li>
</ol>
4. Fluid Flow and Image Acquisition
<ol>
	<li>Center the middle of the core in the field of view and take 2-D projections continuously as the core is flooded to track the core flooding progress. Take 2-D projections by turning on the pink beam and using the camera to take images without rotating the stage. Starting 2-D projections before reactive fluid injection gives a clear before brine image that will later be compared to subsequent brine filled images.</li>
	<li>Set the receiving pump to refill at the desired flow rate thus pulling fluid from the reactor through the core at the desired flow conditions while leaving the injection pump to regulate pressure from the front end.
	<ol>
		<li>Monitor the 2-D projections for changes in attenuation that signal the arrival of reactive brine. When reactive brine arrives, the transmission of the core will increase and the 2-D projections will brighten considerably as more light hits the scintillator and the doped brine is displaced by the highly X-ray transparent reactive fluid. If there is no attenuation difference between reactive and non-reactive brine then, depending on the beam line spectrum, restarting the experiment from step 2.1 with a higher salt concentration KI or using a different highly absorbing salt may be required.</li>
		<li>Stop the 2-D scans and 3-D take tomographies successively as fast as the imaging apparatus allows. Use approximately 1,000 projections per scan. Scan the core using only 180&#176; of rotation (as opposed to the traditional 360&#176;). While using fewer degrees of rotation decreases the signal to noise ratio, it is faster and helps to avoid stretching and tangling the flow and electrical lines. Take 3-D scans until either the time limit is reached or the core looks sufficiently dissolved that there is an imminent danger of internal structural collapse (and thus causing the loss of both the confining pressure and future whole core dry scan data).</li>
	</ol>
	</li>
	<li>After the last scan is taken, depressurize the system efficiently to avoid reacting the core any further.
	<ol>
		<li>First stop the receiving pump. Then close valve 5 connecting the reactor to the rest of the system.</li>
		<li>Step the system pressure down using the confining and receiving pumps keeping around 1MPa more pressure on the confining fluid.</li>
		<li>Once within 1 MPa of atmospheric pressure is reached, open the confining and receiving pumps using valves 10 and 11 and run in constant flow mode to drain any remaining fluid.</li>
		<li>Shut off the PID controller and open the 4-way union (U2) at the top of the core holder to release any remaining system pressure.</li>
		<li>Slowly loosen the confining line while catching excess DI confining water with absorbent paper. Close valves 6 and 7 and disconnect union 1 and the electric lines.</li>
		<li>Loosen the stage clamp and remove the core holder from the stage.</li>
	</ol>
	</li>
	<li>Carefully remove the core assembly from the core holder and then disconnect the sleeve from the interior end fittings. Do not remove the core from the sleeve because doing so may damage the fragile reacted core. Place the sleeve-covered core in a beaker full of DI water to dilute any potentially reactive brine and stop all reaction.</li>
	<li>Dry the entire core in a 60 &#176;C oven for at least 12 h. Then remount the core on the stage using a traditional sample mount, and scan it again at the same resolution and projections as the initial dry scan.</li>
</ol>
5. Image Processing
<ol>
	<li>Correct the reconstructed images for any beam hardening associated with using a polychromatic beam by assuming that any affects are radially symmetric Gaussian functions33.</li>
	<li>Filter the images using an edge-preserving filter such as non-localized means to increase signal to noise34,35 (see <a href="https://www.jove.com/files/ftp_upload/53763/5.2_Filtering.png" target="_blank">Supplemental File</a>).</li>
	<li>Segment the dry scan images using a watershed segmentation36 algorithm and define the seeds as rock and void (see <a href="https://www.jove.com/files/ftp_upload/53763/5.3_Segmentation.png" target="_blank">Supplemental File</a>).
	<ol>
		<li>Take the first image of the core with reactive brine and register each subsequent image to the first image and resample it using the Lanczos37 resampling method with the first image as a reference. As ongoing reaction tends to blur edges, watershed segmentation on the images is not sufficient for accurate segmentation.</li>
		<li>Subtract each reacted core image from the first image to get the difference image. Segment the difference images into change and no change. Register the segmented dry scan to the first reactive scan and then subtract the segmented change from the segmented dry scan to achieve the segmented reacted images38.</li>
	</ol>
	</li>
</ol>
6. Modeling
<ol>
	<li>Use the binarized images as inputs into a either a direct Navier-Stokes flow solver39,40, or a network extraction model41 (Figure 8) to characterize permeability changes and provide physical insights into the dynamics of dissolution.</li>
</ol>

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M., Averdunk, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Techniques+for+image+enhancement+and+segmentation+of+tomographic+images+of+porous+materials.">Techniques for image enhancement and segmentation of tomographic images of porous materials.</a> Physica A. 339, 145-151 (2004).</li><li>Lanczos, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> An iteration method for the solution of the eigenvalue problem of linear differential and integral operators. , (1950).</li><li>Andrew, M., Menke, H., Blunt, M. J., Bijeljic, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Imaging+of+Dynamic+Multiphase+Fluid+Flow+Using+Synchrotron-Based+X-ray+Microtomography+at+Reservoir+Conditions.">The Imaging of Dynamic Multiphase Fluid Flow Using Synchrotron-Based X-ray Microtomography at Reservoir Conditions.</a> Transport Porous Med. , 1-24 (2015).</li><li>Raeini, A. Q., Blunt, M. J., Bijeljic, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modelling+two-phase+flow+in+porous+media+at+the+pore+scale+using+the+volume-of-fluid+method.">Modelling two-phase flow in porous media at the pore scale using the volume-of-fluid method.</a> J. Comput. Phys. 231, 5653-5668 (2012).</li><li>Bijeljic, B., Raeini, A., Mostaghimi, P., Blunt, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Predictions+of+non-Fickian+solute+transport+in+different+classes+of+porous+media+using+direct+simulation+on+pore-scale+images.">Predictions of non-Fickian solute transport in different classes of porous media using direct simulation on pore-scale images.</a> Phys Rev E. 87, 013011 (2013).</li><li>Dong, H., Blunt, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pore-network+extraction+from+micro-computerized-tomography+images.">Pore-network extraction from micro-computerized-tomography images.</a> Phys Rev E. 80, 036307 (2009).</li><li>Menke, H. P., Bijeljic, B., Andrew, M. G., Blunt, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dynamic+Pore-scale+Imaging+of+Reactive+Transport+in+Heterogeneous+Carbonates+at+Reservoir+Conditions.">Dynamic Pore-scale Imaging of Reactive Transport in Heterogeneous Carbonates at Reservoir Conditions.</a> Energy Procedia. 63, 5503-5511 (2014).</li><li>Bijeljic, B., Mostaghimi, P., Blunt, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Signature+of+non-Fickian+solute+transport+in+complex+heterogeneous+porous+media.">Signature of non-Fickian solute transport in complex heterogeneous porous media.</a> Phys. Rev. Lett. 107, 204502 (2011).</li><li>Ott, H., Oedai, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Wormhole+formation+and+compact+dissolution+in+single-and+two-phase+CO2-brine+injections.">Wormhole formation and compact dissolution in single-and two-phase CO2-brine injections.</a> Geophys. Res. Lett. 42, 2270-2276 (2015).</li></ol>

The authors have nothing to disclose.

The most critical steps for dynamic imaging of reaction in heterogeneous pore structures at reservoir conditions are: 1) accurate temperature control of the cell inside the pink beam; 2) successful core holder stability on a fast moving stage; 3) efficient data processing and storage techniques; and 4) effective segmentation of time-resolved images.
Temperature control is essential for reservoir condition imaging using a Pink Beam. If the temperature rises above the reactor temperature, CO2 will exsolve in the pore space and both change the pH of the brine and create ganglia of supercritical CO2 in the pore space that could change the nature of dissolution44. The use of filters to absorb the lower energy X-rays is critical for removing this additional temperature stress which allows the thermocouple and heating wrap to effectively control temperature externally. However, filters lower the total energy throughput of the beam and thus must be used sparingly so as not to significantly increase total acquisition time. Moreover, filter type and thickness must be tailored to the specific energy wavelengths and throughput of the beam line.
The core holder undergoes rotational and vibration stresses during tomography acquisition that can cause the carbon fiber sleeve to shake during stage rotation and blur the projections. To minimize this potential, the core holder is designed as a short 6 cm sleeve for use at synchrotrons. This sleeve would not be favorable for use with bench top scanners, as the steel end fittings would inhibit minimization of source-sample distance and geometric magnification. However, with a parallel light source these are not concerns.
Each tomographic scan taken in a series can have a size of over 20 GB meaning that a series of 100 scans will be 2 TB in size. When taking many scans in a row very quickly both the instrument bandwidth and storage options provide substantial data management challenges. The experimental imaging apparatus must be designed with these constraints in mind so as to fully realize the dynamic imaging potential of fast tomography. Data transfer bottlenecks must be identified before starting the experiment and the technology infrastructure adapted so that issues such as camera read off speed, transfer bandwidth, and storage write speed do not inhibit acquisition speed potential.
Effective segmentation of the time-resolved images of dissolution provides a challenge. When a tomographic scan is taken in a changing system the edges of the solid-liquid boundary can become blurred. This blurring makes traditional segmentation techniques such as watershed, which works on the assumption that the boundaries will be the regions with the highest attenuation gradient, much less successful. To circumvent this, the difference image of the unreacted and reacted images is calculated which provides an image of only regions of change. This method allows for successful segmentation of the continuously changing pore structure.
Synchrotron fast tomography coupled with a reservoir scale apparatus is a powerful experimental method that can be adapted to explore a range of applications including multiphase flow processes, advection-dispersion, and transport in chemically heterogeneous mediums. However, the current apparatus is limited to a time resolution on the order of seconds, single-phase experiments, and small sample sizes. Future design upgrades may include additional pumps for three-phase capabilities, increasing flux to be able to penetrate larger mediums, better reconstruction techniques that allow for fewer projections to be taken per scan, and multivariate approaches to image acquisition and segmentation that can further improve information depth, breadth, and accuracy.

A major concern of carbon capture and storage (CCS) is long-term storage security1,2. Carbon dioxide, CO2, injected into the subsurface will dissolve in the host brine and form carbonic acid3,4,5. This acidic brine has the potential to react with and dissolve the surrounding rock, particularly if the host rock is limestone6. Dissolution can be favorable and allow for continued formation permeability7 and greater storage permanence8. However, geologic seal integrity may be compromised by this dissolution and allow CO2 to migrate to the surface9. Accurate predictive modeling of storage permanence is thus dependent on fully understanding dissolution in the brine-rock system and the distribution and the rate of fluid movement in the subsurface10,11,12.
However, the nature and the rate of dissolution in carbonates is dependent on both the properties of the brine13,14,15,16 and the host rock17. The dissolution rates are also strongly dependent on brine temperature and pressure6, making the development of experimental techniques for measuring complex time-dependent processes at representative reservoir conditions vital.
Previous experiments have observed that field-scale reaction rates are typically orders of magnitude lower than experimental batch reactor measurements18,19. Weathering, mineral heterogeneity, and incomplete mixing in a heterogeneous flow field are possible explanations for this phenomenon. However, it is not possible to assess the most significant factors without direct observation of the evolving pore space during reaction. Thus, dynamic pore-scale experiments are required to provide both the insights into the interplay between transport and reaction and to validate predictive models.
An established experimental method for studying pore-scale processes in carbon storage applications is X-ray microtomography (&#181;CT)20,21. &#181;-CT has several benefits: it achieves high spatial resolutions of down to around 1 &#181;m, it is non-invasive, and provides three-dimensional images. Limestone dissolution has been studied at the core (~cm) scale22 and it was found that rock-brine reaction increases physical heterogeneity. To advance understanding of how different transport and reaction conditions alter the complex solid and pore structures it is necessary to measure reaction-induced changes in pore-space geometry, topology and flow in subsurface rock systems at reservoir temperatures and pressures and at a higher resolution, to investigating in detail pore-scale processes. This paper describes a method of studying reactive dissolution processes in rock with complex pore structures and focus on measuring the time and spatially dependent reaction rate between a CO2-acidified brine and limestone rock at reservoir conditions.
There have been several studies that have looked at reaction in complex carbonates23,24,25,26,27, but due to experimental or imaging constraints they have been either limited to pre and post reaction images or were not completed at representative subsurface conditions. Menke et al.28 has performed dynamic in situ imaging of reaction between a CO2-acidified brine and Ketton limestone at the pore scale over a period of several hours and at a temperature and pressure representative of an aquifer at approximately 1 km in depth. However, Ketton is a relatively homogenous rock with large grains that is easy to image in very little time (~17 min) and with few projections (~400). Most carbonate rocks have complex pore structures that require many projections to accurately resolve which can be a very time intensive process using traditional &#181;-CT &#8212; either with a monochromatic beam at a synchrotron source or with bench-top X-ray scanners. Thus, a fast method of tomography is needed to see reaction-induced changes in heterogeneous carbonates dynamically.
The amount of time it takes to image a sample is controlled by the flux of the X-ray source. One method of scanning quickly is to use the polychromatic beam of a synchrotron source20. This so-called &#39;Pink Beam&#39; provides orders of magnitude more intense light than bench-top sources and therefore images can be taken on the tens-of-second rather than hour time scales. An undulator that consists of a periodic structure of dipole magnets produces the Pink Beam. The electron beam is forced to undergo oscillations as it traverses the magnets and as a consequence radiates energy. The energy produced is concentrated to narrow wavelength bands and is very intense. Mirrors and filters are then used to narrow the spectrum of light to suit experimental needs. Mirrors absorb the high-energy spectrum while filters absorb the lower energies. It is therefore possible to narrow the spectrum to the desired band of radiation using only these tools.
However, using this intense X-ray flux is not without its challenges. The lower energy X-rays of the Pink Beam spectrum are absorbed by the sample as heat. This can interfere with the temperature control of the in situ apparatus and cause CO2 to exsolve from solution20. CO2-saturated brine is very sensitive to both heat and pressure and therefore a small change in thermal equilibrium can significantly change the pH of the in situ fluid5. Thus, careful design and control elements for the X-ray spectrum must be incorporated into the beam line equipment prior to imaging.
Fast tomography also produces a vast amount of data at a high rate. The limitations of data read out from the camera and subsequent storage provide a substantial technological challenge. Some have overcome this by taking several consecutive scans and storing them on the camera memory before reading them to external data servers. However, this requires that the experiment be relatively short as the camera memory can only hold a finite volume of data. Binning the data on the camera also reduces transfer time as it reduces the volume of data needing to be transferred, but it has the potential to reduce the quality of the images. Alternatively, the data can be transferred off the camera after each scan before starting the next, which will increase the total time between scans. This study used the latter method with each image acquisition taking ~45 seconds and data read off taking an additional ~30 s.
When taking scans at a high rate, the sample stage must spin much faster than with traditional scanning and therefore the potential angular stress on the core holder is great. Carbon fiber, while X-ray transparent, is flexible when stressed. If the sample moves during image acquisition image blurring can occur. The core holder sleeve was designed to be as short as possible to mitigate these potential stresses. Additionally, flexible polyether ether ketone (PEEK) tubing was used on all elements of the experimental apparatus close to the stage so that the stage was free to rotate. One drawback of using PEEK tubes is that it is permeable to CO2 on diffusive timescales. Fluid residing in the lines for long periods will gradually become desaturated over a period of about 24 h. All lines that were not near the core holder were made of stainless steel and the fluid was pre-equilibrated in a vigorously mixed Hastelloy reactor heated and pressurized to experimental conditions23,29,30.
The experimental apparatus is depicted in Figure 1. Reservoir temperature is maintained in the core holder by wrapping the exterior of the sleeve in an X-ray transparent heating tape and inserting a thermocouple through the radial port of the cell and into the confining fluid. A Proportional Integral Derivative (PID) controller then regulated temperature to within 1 &#176;C. Pressure and flow conditions were maintained using three high-pressure syringe pumps that are accurate to a flow rate of 0.001 mL/min. Two salts were used for the experiment, a highly absorbing 25% wt KI unreactive brine and a low absorbing 1% wt KCl, 5% wt NaCl reactive brine. The difference in attenuation made it easy to see the arrival of reactive brine in the core making dead volume calculations unnecessary.

<table><tbody><tr><td>NaCl salt</td><td>Sigma Aldrich</td><td>S7653-1KG</td><td></td></tr><tr><td>KCl salt</td><td>Sigma Aldrich</td><td>P9333-1KG</td><td></td></tr><tr><td>KI salt</td><td>Sigma Aldrich</td><td>30315-1KG</td><td></td></tr><tr><td>Core holder</td><td>Airbourne Composites</td><td>110 mm Core holder</td><td>Constructed in conjunction with Imperial College</td></tr><tr><td>PEEK tubing</td><td>Kinesis</td><td>1560xL</td><td></td></tr><tr><td>Thermocouple</td><td>Omega Engineering</td><td>KMTSS-IM300U-150</td><td></td></tr><tr><td>Flexible Heating Tape</td><td>Omega Engineering</td><td>KH-112/10-P</td><td></td></tr><tr><td>1/16&quot; Needle Valve</td><td>Hydrasun Ltd</td><td>MVE1002</td><td></td></tr><tr><td>High Pressure Syringe Pump</td><td>Teledyne ISCO</td><td>1000D</td><td></td></tr><tr><td>600 mL Parr Reactor</td><td>Parr Instrument Company</td><td>4547A - hastelloy</td><td></td></tr><tr><td>CO&lt;sub&gt;2&lt;/sub&gt; Cylinder</td><td>BOC</td><td>CO2 - size E</td><td></td></tr><tr><td>Viton</td><td>Fisher Scientific</td><td>11572583</td><td></td></tr><tr><td>Aluminium Foil</td><td>Coroplast</td><td>1510AWX</td><td></td></tr><tr><td>ImageJ - image processing</td><td>NIH</td><td>ImageJ</td><td></td></tr><tr><td>Matlab</td><td>Mathworks</td><td>Matlab</td><td>Used for data analysis</td></tr><tr><td>Avizo</td><td>FEI</td><td>Avizo</td><td></td></tr><tr><td>Snoop Leak Detector</td><td>Swagelok</td><td>MS-SNOOP-8OZ</td><td></td></tr></tbody></table>

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.

The reaction was imaged between calcite and unbuffered scCO2 saturated brine in 4 mm-diameter 1.2 cm-long Portland carbonate core42. Portland carbonate is a relatively pure (&#60;99%) calcite oolite with a complex heterogeneous pore structure43. The low energy X-rays were filtered by passing the beam through 2 mm of Al and 0.1 &#181;m of Au. A CdWO4 scintillator with a 1.25X objective lens and a PCO EDGE camera were used in the detector assembly. The dry scans were acquired with 4,000 projections while the dynamic scans had 1,000 projections each. Total acquisition time was ~1 minute 15 seconds per scan with ~100 scans taken over a period of 2 hours.
Reconstruction and artifact removal was completed using the Diamond Lightsource proprietary software. Each image consists of 20003 voxels, which were then binned to increase signal to noise resulting in an image of 10003 voxels at a resolution of 6.1 &#181;m (Figure 5). The images were then processed using the image processing modules in Avizo 8.1 and ImageJ programs (see Supplemental File). Each image required approximately 12 CPU hours and 3 GPU hours of processing on a computer with a 3.0 GHz CPU and a Tesla K20C GPU.
The segmented images were analyzed as a time series for porosity changes by counting the number of voxels of pore and rock. During dissolution porosity increases with time (Figure 6). Visual inspection of the segmented images (Figure 7) shows the presence of a channel in the direction of flow. When porosity is plotted as a function of both time and distance from the sample inlet it is clear that a channel is formed in the first hour and then widened as the experiment continues (Figure 8).
The segmented images were then used as input into a network extraction model to analyze permeability changes (Figure 9). It was found that there was a sharp increase in permeability during the initial hour, but then the permeability stabilized at later times.
<img alt="Figure 1" src="/files/ftp_upload/53763/53763fig1.jpg" /> 
Figure 1. The in situ experimental apparatus. CO2 is pressurized by the injection pump and used to equilibrate brine in the reactor. Reactive brine is pulled through core assembly by the receiving pump. The cell is confined by DI water in the confining pump and heated using heating tape controlled by a thermocouple in the confining fluid. The experimental system is connected together using tubing and fluid flow is directed using Valves (V) and Unions (U). <a href="https://www.jove.com/files/ftp_upload/53763/53763fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" src="/files/ftp_upload/53763/53763fig2.jpg" /> 
Figure 2. The X-ray spectra of the Diamond Lightsource I-13I pink beam calculated using both the experimental tuning curve and theoretical mirror reflectivity and filter transmission. Mirrors absorb energies above 30 keV; Al and Au filters absorb energies below 13 and 22 keV respectively. <a href="https://www.jove.com/files/ftp_upload/53763/53763fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" src="/files/ftp_upload/53763/53763fig3.jpg" /> 
Figure 3. The beam line imaging apparatus. The Al and Au sheets filter the pink beam and the remaining X-rays hit the core assembly. A portion of the X-rays are absorbed by the sample while the rest pass through the sample and hit the scintillator which fluoresces in the visible spectrum. This visible light is then focused by the objective onto the CCD, which translates that light into a pixelated digital image where the pixel intensity value is a function of the number of X-rays that are absorbed by the scintillator. <a href="https://www.jove.com/files/ftp_upload/53763/53763fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" src="/files/ftp_upload/53763/53763fig4.jpg" /> 
Figure 4. The core assembly inside the core holder. PEEK tubing is attached to the interior end fittings and threaded through the steel end caps. The core is wrapped in aluminum foil and inserted into the sleeve. The sleeve is then stretched over the end fittings to create a watertight seal and two additional layers of aluminum foil are added to hold everything in place and prevent gas diffusion. The thermocouple is secured to the outside of the core assembly with the outer layer of adhesive aluminum foil. Figure modified from Menke et al.42. <a href="https://www.jove.com/files/ftp_upload/53763/53763fig4large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" src="/files/ftp_upload/53763/53763fig5.jpg" /> 
Figure 5. A 2-D slice of the reconstructed image before (a) and after (b) dissolution. The lighter areas are grain and the darker areas are pore. Blurring at the edges of the grain/pore boundary can be seen in the reacted portion of the pore space (b). <a href="https://www.jove.com/files/ftp_upload/53763/53763fig5large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 6" src="/files/ftp_upload/53763/53763fig6.jpg" /> 
Figure 6. Porosity plotted with time. Porosity increases linearly with a small decrease in slope in the second hour of dissolution. Figure modified from Menke et al.42. <a href="https://www.jove.com/files/ftp_upload/53763/53763fig6large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 7" src="/files/ftp_upload/53763/53763fig7.jpg" /> 
Figure 7. A 3-D rendering of the change in porosity at 60 minutes into the experiment, where green represents the greatest change in porosity and red the least. A clear porous channel created by fluid-solid chemical reaction is seen in the center of the core where dissolution is greatest. Figure modified from Menke et al.42. <a href="https://www.jove.com/files/ftp_upload/53763/53763fig7large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 8" src="/files/ftp_upload/53763/53763fig8.jpg" /> 
Figure 8. Profiles of porosity as a function of distance from the sample inlet. Porosity is uniform along the axis of dissolution, but the rate of dissolution changes as a function of time. Figure modified from Menke et al.42. <a href="https://www.jove.com/files/ftp_upload/53763/53763fig8large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 9" src="/files/ftp_upload/53763/53763fig9.jpg" /> 
Figure 9. (A) A network extraction performed on the segmented images is shown at 60 minutes, showing large pore spaces (balls) and their connections (tubes). (B) The computed permeability is shown to increase with time with a sharp rise between 40 and 60 minutes as a wide dissolution channel is established. Figure modified from Menke et al.42. <a href="https://www.jove.com/files/ftp_upload/53763/53763fig9large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

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

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 ...

dynamic-pore-scale-reservoir-condition-imaging-reaction-carbonates

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8.5K Views.  Imperial College London. 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 µm resolution over a period of 2 h.

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

Revealing Dynamic Processes of Materials in Liquids Using Liquid Cell Transmission Electron Microscopy

The recent development for in situ transmission electron microscopy, which allows imaging through liquids with high spatial resolution, has attracted significant interests across the research fields of materials science, physics, chemistry and biology. The key enabling technology is a liquid cell. We fabricate liquid cells with thin viewing windows through a sequential microfabrication process, including silicon nitride membrane deposition, photolithographic patterning, wafer etching, cell bonding, etc. A liquid cell with the dimensions of a regular TEM grid can fit in any standard TEM sample holder. About 100 nanoliters reaction solution is loaded into the reservoirs and about 30 picoliters liquid is drawn into the viewing windows by capillary force. Subsequently, the cell is sealed and loaded into a microscope for in situ imaging. Inside the TEM, the electron beam goes through the thin liquid layer sandwiched between two silicon nitride membranes. Dynamic processes of nanoparticles in liquids, such as nucleation and growth of nanocrystals, diffusion and assembly of nanoparticles, etc., have been imaged in real time with sub-nanometer resolution. We have also applied this method to other research areas, e.g., imaging proteins in water. Liquid cell TEM is poised to play a major role in revealing dynamic processes of materials in their working environments. It may also bring high impact in the study of biological processes in their native environment.

We have developed a self-contained liquid cell, which allows imaging through liquids using a transmission electron microscope. Dynamic processes of nanoparticles in liquids can be revealed in real time with sub-nanometer resolution.

The recent development for in situ transmission electron microscopy, which allows imaging through liquids with high spatial resolution, has attracted ...

Characterization of Electrode Materials for Lithium Ion and Sodium Ion Batteries Using Synchrotron Radiation Techniques

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We describe the use of synchrotron X-ray absorption spectroscopy (XAS) and X-ray diffraction (XRD) techniques to probe details of intercalation/deintercalation processes in electrode materials for Li-ion and Na-ion batteries. Both in situ and ex situ experiments are used to understand structural behavior relevant to the operation of devices

Intercalation compounds such as transition metal oxides or phosphates are the most commonly used electrode materials in Li-ion and Na-ion batteries. ...

Reservoir Condition Pore-scale Imaging of Multiple Fluid Phases Using X-ray Microtomography

X-ray microtomography was used to image, at a resolution of 6.6 &#181;m, the pore-scale arrangement of residual carbon dioxide ganglia in the pore-space of a carbonate rock at pressures and temperatures representative of typical formations used for CO2 storage. Chemical equilibrium between the CO2, brine and rock phases was maintained using a high pressure high temperature reactor, replicating conditions far away from the injection site. Fluid flow was controlled using high pressure high temperature syringe pumps. To maintain representative in-situ conditions within the micro-CT scanner a carbon fiber high pressure micro-CT coreholder was used. Diffusive CO2 exchange across the confining sleeve from the pore-space of the rock to the confining fluid was prevented by surrounding the core with a triple wrap of aluminum foil. Reconstructed brine contrast was modeled using a polychromatic x-ray source, and brine composition was chosen to maximize the three phase contrast between the two fluids and the rock. Flexible flow lines were used to reduce forces on the sample during image acquisition, potentially causing unwanted sample motion, a major shortcoming in previous techniques. An internal thermocouple, placed directly adjacent to the rock core, coupled with an external flexible heating wrap and a PID controller was used to maintain a constant temperature within the flow cell. Substantial amounts of CO2 were trapped, with a residual saturation of 0.203 &#177; 0.013, and the sizes of larger volume ganglia obey power law distributions, consistent with percolation theory.

We present a methodology for the imaging of multiple fluid phases at reservoir conditions by the use of x-ray microtomography. We show some representative results of capillary trapping in a carbonate rock sample.

X-ray microtomography was used to image, at a resolution of 6.6 &#181;m, the pore-scale arrangement of residual carbon dioxide ganglia in the pore-space ...

Non-invasive 3D-Visualization with Sub-micron Resolution Using Synchrotron-X-ray-tomography

Little is known about the internal organization of many micro-arthropods with body sizes below 1 mm. The reasons for that are the small size and the hard cuticle which makes it difficult to use protocols of classical histology. In addition, histological sectioning destroys the sample and can therefore not be used for unique material. Hence, a non-destructive method is desirable which allows to view inside small samples without the need of sectioning.
We used synchrotron X-ray tomography at the European Synchrotron Radiation Facility (ESRF) in Grenoble (France) to non-invasively produce 3D tomographic datasets with a pixel-resolution of 0.7&micro;m. Using volume rendering software, this allows us to reconstruct the internal organization in its natural state without the artefacts produced by histological sectioning. These date can be used for quantitative morphology, landmarks, or for the visualization of animated movies to understand the structure of hidden body parts and to follow complete organ systems or tissues through the samples.

We used synchrotron X-ray tomography at the European Synchrotron Radiation Facility (ESRF) to non-invasively produce 3D tomographic datasets with a pixel-resolution of 0.7&micro;m. Using volume rendering software, this allows the reconstruction of internal structures in their natural state without the artefacts produced by histological sectioning.

Little is known about the internal organization of many micro-arthropods with body sizes below 1 mm. The reasons for that are the small size and the hard ...

Biology

Stress Distribution During Cold Compression of Rocks and Mineral Aggregates Using Synchrotron-based X-Ray Diffraction

We report detailed procedures for performing compression experiments on rocks and mineral aggregates within a multi-anvil deformation apparatus (D-DIA) coupled with synchrotron X-radiation. A cube-shaped sample assembly is prepared and compressed, at room temperature, by a set of four X-ray transparent sintered diamond anvils and two tungsten carbide anvils, in the lateral and the vertical planes, respectively. All six anvils are housed within a 250-ton hydraulic press and driven inward simultaneously by two wedged guide blocks. A horizontal energy dispersive X-ray beam is projected through and diffracted by the sample assembly. The beam is commonly in the mode of either white or monochromatic X-ray. In the case of white X-ray, the diffracted X-rays are detected by a solid-state detector array that collects the resulting energy dispersive diffraction pattern. In the case of monochromatic X-ray, the diffracted pattern is recorded using a two-dimensional (2-D) detector, such as an imaging plate or a charge-coupled device (CCD) detector. The 2-D diffraction patterns are analyzed to derive lattice spacings. The elastic strains of the sample are derived from the atomic lattice spacing within grains. The stress is then calculated using the predetermined elastic modulus and the elastic strain. Furthermore, the stress distribution in two-dimensions allow for understanding how stress is distributed in different orientations. In addition, a scintillator in the X-ray path yields a visible light image of the sample environment, which allows for the precise measurement of sample length changes during the experiment, yielding a direct measurement of volume strain on the sample. This type of experiment can quantify the stress distribution within geomaterials, which can ultimately shed light on the mechanism responsible for compaction. Such knowledge has the potential to significantly improve our understanding of key processes in rock mechanics, geotechnical engineering, mineral physics, and material science applications where compactive processes are important.

We report detailed procedures for compression experiments on rocks and mineral aggregates within a multi-anvil deformation apparatus coupled with synchrotron X-radiation. Such experiments allow quantification of the stress distribution within samples, that ultimately sheds light on compaction processes in geomaterials.

We report detailed procedures for performing compression experiments on rocks and mineral aggregates within a multi-anvil deformation apparatus (D-DIA) ...

Environment

Atom Probe Tomography Analysis of Exsolved Mineral Phases

Element diffusion rates and temperature/pressure control a range of fundamental volcanic and metamorphic processes. Such processes are often recorded in lamellae exsolved from host mineral phases. Thus, the analysis of the orientation, size, morphology, composition and spacing of exsolution lamellae is an area of active research in the geosciences. The conventional study of these lamellae has been conducted by scanning electron microscopy (SEM) and transmission electron microscopy (TEM), and more recently with focused ion beam (FIB)-based nanotomography, yet with limited chemical information. Here, we explore the use of atom probe tomography (APT) for the nanoscale analysis of ilmenite exsolution lamellae in igneous titanomagnetite from ash deposits erupted from the active Soufri&#232;re Hills Volcano (Montserrat, British West Indies). APT allows the precise calculation of interlamellar spacings (14&#8211;29 &#177; 2 nm) and reveals smooth diffusion profiles with no sharp phase boundaries during the exchange of Fe and Ti/O between the exsolved lamellae and the host crystal. Our results suggest that this novel approach permits nanoscale measurements of lamellae composition and interlamellar spacing that may provide a means to estimate the lava dome temperatures necessary to model extrusion rates and lava dome failure, both of which play a key role in volcanic hazard mitigation efforts.

Analysis of the morphology, composition, and spacing of exsolution lamellae can provide essential information to understand geological processes related to volcanism and metamorphism. We present a novel application of APT for the characterization of such lamellae and compare this approach to the conventional use of electron microscopy and FIB-based nanotomography.

Element diffusion rates and temperature/pressure control a range of fundamental volcanic and metamorphic processes. Such processes are often recorded in ...

Pore-scale Imaging and Characterization of Hydrocarbon Reservoir Rock Wettability at Subsurface Conditions Using X-ray Microtomography

In situ wettability measurements in hydrocarbon reservoir rocks have only been possible recently. The purpose of this work is to present a protocol to characterize the complex wetting conditions of hydrocarbon reservoir rock using pore-scale three-dimensional X-ray imaging at subsurface conditions. In this work, heterogeneous carbonate reservoir rocks, extracted from a very large producing oil field, have been used to demonstrate the protocol. The rocks are saturated with brine and oil and aged over three weeks at subsurface conditions to replicate the wettability conditions that typically exist in hydrocarbon reservoirs (known as mixed-wettability). After the brine injection, high-resolution three-dimensional images (2 &#181;m/voxel) are acquired and then processed and segmented. To calculate the distribution of the contact angle, which defines the wettability, the following steps are performed. First, fluid-fluid and fluid-rock surfaces are meshed. The surfaces are smoothed to remove voxel artefacts, and in situ contact angles are measured at the three-phase contact line throughout the whole image. The main advantage of this method is its ability to characterize in situ wettability accounting for pore-scale rock properties, such as rock surface roughness, rock chemical composition, and pore size. The in situ wettability is determined rapidly at hundreds of thousands of points. 
The method is limited by the segmentation accuracy and X-ray image resolution. This protocol could be used to characterize the wettability of other complex rocks saturated with different fluids and at different conditions for a variety of applications. For example, it could help in determining the optimal wettability that could yield an extra oil recovery (i.e., designing brine salinity accordingly to obtain higher oil recovery) and to find the most efficient wetting conditions to trap more CO2 in subsurface formations.

This protocol is presented to characterize the complex wetting conditions of an opaque porous medium (hydrocarbon reservoir rock) using three-dimensional images obtained by X-ray microtomography at subsurface conditions.

In situ wettability measurements in hydrocarbon reservoir rocks have only been possible recently. The purpose of this work is to present a protocol to ...

Visualization of Failure and the Associated Grain-Scale Mechanical Behavior of Granular Soils under Shear using Synchrotron X-Ray Micro-Tomography

The rapid development of X-ray imaging techniques with image processing and analysis skills has enabled the acquisition of CT images of granular soils with high-spatial resolutions. Based on such CT images, grain-scale mechanical behavior such as particle kinematics (i.e., particle translations and particle rotations), strain localization and inter-particle contact evolution of granular soils can be quantitatively investigated. However, this is inaccessible using conventional experimental methods. This study demonstrates the exploration of the grain-scale mechanical behavior of a granular soil sample under triaxial compression using synchrotron X-ray micro-tomography (&#956;CT). With this method, a specially fabricated miniature loading apparatus is used to apply confining and axial stresses to the sample during the triaxial test. The apparatus is fitted into a synchrotron X-ray tomography setup so that high-spatial resolution CT images of the sample can be collected at different loading stages of the test without any disturbance to the sample. With the capability of extracting information at the macro scale (e.g., sample boundary stresses and strains from the triaxial apparatus setup) and the grain scale (e.g., grain movements and contact interactions from the CT images), this procedure provides an effective methodology to investigate the multi-scale mechanics of granular soils.

The protocol describes procedures to acquire high-spatial resolution computed tomography (CT) images of a granular soil during triaxial compression, and to apply image processing techniques to these CT images to explore the grain-scale mechanical behavior of the soil under loading.

The rapid development of X-ray imaging techniques with image processing and analysis skills has enabled the acquisition of CT images of granular soils ...

Visualization of ATP Synthase Dimers in Mitochondria by Electron Cryo-tomography

Electron cryo-tomography is a powerful tool in structural biology, capable of visualizing the three-dimensional structure of biological samples, such as cells, organelles, membrane vesicles, or viruses at molecular detail. To achieve this, the aqueous sample is rapidly vitrified in liquid ethane, which preserves it in a close-to-native, frozen-hydrated state. In the electron microscope, tilt series are recorded at liquid nitrogen temperature, from which 3D tomograms are reconstructed. The signal-to-noise ratio of the tomographic volume is inherently low. Recognizable, recurring features are enhanced by subtomogram averaging, by which individual subvolumes are cut out, aligned and averaged to reduce noise. In this way, 3D maps with a resolution of 2 nm or better can be obtained. A fit of available high-resolution structures to the 3D volume then produces atomic models of protein complexes in their native environment. Here we show how we use electron cryo-tomography to study the in situ organization of large membrane protein complexes in mitochondria. We find that ATP synthases are organized in rows of dimers along highly curved apices of the inner membrane cristae, whereas complex I is randomly distributed in the membrane regions on either side of the rows. By subtomogram averaging we obtained a structure of the mitochondrial ATP synthase dimer within the cristae membrane.

We present a protocol of how to collect and process electron cryo-tomograms of whole mitochondria. The technique provides detailed insights into the structure, function, and organization of large membrane protein complexes in native biological membranes.

Electron cryo-tomography is a powerful tool in structural biology, capable of visualizing the three-dimensional structure of biological samples, such as ...

A 3D Cartographic Description of the Cell by Cryo Soft X-ray Tomography

Imaging techniques are fundamental in order to understand cell organization and machinery in biological research and the related fields. Among these techniques, cryo soft X-ray tomography (SXT) allows imaging whole cryo-preserved cells in the water window X-ray energy range (284-543 eV), in which carbon structures have intrinsically higher absorption than water, allowing the 3D reconstruction of the linear absorption coefficient of the material contained in each voxel. Quantitative structural information at the level of whole cells up to 10 &#181;m thick is then achievable this way, with high throughput and spatial resolution down to 25-30 nm half-pitch. Cryo-SXT has proven itself relevant to current biomedical research, providing 3D information on cellular infection processes (virus, bacteria, or parasites), morphological changes due to diseases (such as recessive genetic diseases) and helping us understand drug action at the cellular level, or locating specific structures in the 3D cellular environment. In addition, by taking advantage of the tunable wavelength at synchrotron facilities, spectro-microscopy or its 3D counterpart, spectro-tomography, can also be used to image and quantify specific elements in the cell, such as calcium in biomineralization processes. Cryo-SXT provides complementary information to other biological imaging techniques such as electron microscopy, X-ray fluorescence or visible light fluorescence, and is generally used as a partner method for 2D or 3D correlative imaging at cryogenic conditions in order to link function, location, and morphology.

Here, a protocol describing the sample preparation and data collection steps required in cryo soft X-ray tomography (SXT) to image the ultrastructure of whole cryo-preserved cells at a resolution of 25 nm half pitch, is presented.

Imaging techniques are fundamental in order to understand cell organization and machinery in biological research and the related fields. Among these ...