We want to thank the members of the EM facility of the University of Lausanne for their support during this development of different steps of the AT procedure. We would like to thank Gareth Griffiths, Marta Rodrigues, Urska Repnik, Christel Genoud, Helmut Gnaegi, Einat Zelinger, Paola Moreno-Roman, Lucy O&#39;Brien and Lindsay Lewellyn for discussions during the preparation of the manuscript and critical reading. We want to acknowledge the groups that contributed the samples used to demonstrate the different scenarios: Matthias Lutolf, Michail Nikolaev, Devanjali Dutta, Till Matzat, and Fanny Langlet.

NOTE: Sample preparation methods are described elsewhere14,30,31, and are not covered in this publication. In short, the examples shown were chemically fixed with glutaraldehyde, post-fixed with 1% OsO4, then treated with 1% aqueous uranyl acetate before embedding in the embed resin. Alternatively, samples can be prepared using high-pressure freezing, freeze substituted with 0.1% uranyl acetate in acetone, and embedded in acrylic resin. Sample blocks were prepared using a flat embedding method that permits a clear view of the sample, facilitating its orientation for the sectioning (Figure 1B).
1. Array generation procedure
<ol>
	<li>Embedded sample orientation and trimming
	<ol>
		<li>Using the binocular/microscope, identify and mark the ROI on the embedded block surface by lightly scratching the block&#39;s surface with a razor blade. This will help to orient the sample inside the ultramicrotome and will reduce the sectioning surface.</li>
		<li>Clamp the sample on the ultramicrotome holder (Figure 2A).</li>
		<li>Trim the resin around the sample, first with the razor blade (rough trimming) and continue with the diamond trimming tool (fine trimming; Figure 2A). Use knives with 20&#176; or 90&#176; edge inclination to ensure that the top and bottom surfaces of the block are parallel to the knife&#39;s cutting edge. 
		&#8203;NOTE: This step is critical for serial sectioning and acquisition of straight ribbons.</li>
		<li>Mix xylene and glue in 3:1 proportion. With an eyelash attached to a toothpick, apply this mixture to the top and the bottom edges of the trimmed block. Let it dry thoroughly.</li>
	</ol>
	</li>
	<li>Prepare the array mounting support A (i.e., silicon wafers).
	<ol>
		<li>Cut the wafer piece using a wafer cleaving tool (EMS), adjusting its size to the project goal. 2 cm x 4 cm is convenient for both light and electron microscopy observations.</li>
		<li>Clean the wafer in distilled water to get rid of the debris.</li>
		<li>Glow discharge/plasma clean the surface using standard equipment. The precise parameters will depend on the machine used. Start with the parameters for the grids discharge and empirically adjust the time. This step is crucial for a good spread of the sections on the support while sections are drying and should not be omitted.</li>
	</ol>
	</li>
	<li>Prepare the arrays mounting support B (i.e., glass coverslip)
	<ol>
		<li>If planning multiplex immuno-labeling experiments, transfer the samples on a coverslip to better detect the fluorescence signal. To improve coverslip adhesiveness, use a detailed gelatin-coating procedure is described previously9.</li>
		<li>Increase the conductivity by coating the slides with the indium-tin-oxide (ITO) or gold by evaporation. Keep the prepared coverslips in a clean environment. Glow discharge the samples as described in 1.2.3.</li>
	</ol>
	</li>
</ol>
2. Sectioning of the sample
<ol>
	<li>AT knife preparation 
	NOTE: To generate the arrays, use a modified knife (ATS), designed to facilitate the acquisition of long ribbons. Histo-Jumbo knives&#160;or similar knives conceived for the generation of the sections on large supports can serve for AT sectioning as well.
	<ol>
		<li>Attach the needle to the bottom of the knife using the foamy sticky tape and pierce it (Figure 2B). Place the ATS knife in the ultramicrotome holder at 0&#176;. Adjust the edge of the knife parallel to the block surface using the standard procedure.</li>
		<li>Bring the trimmed block to the edge of the knife in a position ready for sectioning.</li>
		<li>Place the wafer/coverslip inside the knife basin and fill it with water to the same level as the knife edge. Let the diamond edge of the knife humidify properly and, if necessary, withdraw water using the attached syringe (Figure 2C).</li>
	</ol>
	</li>
	<li>Array sectioning and transfer
	<ol>
		<li>Set the microtome to the desired cutting parameters. With the ATS knife, the range of 50-100 nm and a cutting speed of 0.6-1 mm/s are advisable. Start sectioning (Figure 2Di).</li>
		<li>Obtain a ribbon of the length that will cover a targeted z-volume and stop the collection. Depending on the block size, homogeneity of the tissue, and type of resin, the ribbon will be relatively straight (Figure 2D-ii). Many samples will not produce straight ribbons, despite the invested effort and the type of knife is used.</li>
		<li>Depending on the final goal, make one long or several short ribbons aligned side by side. A 2 cm x 4 cm support can conveniently hold 100 to 1,000 sections. The arrangement of the ribbon on the support step is a step that requires dexterity and steady hands. However, the learning curve for this skill is rapidly acquired.</li>
		<li>Detach the ribbon from the knife-edge using a clean, non-sticky tip of an eyelash glued on the toothpick (Figure 2Diii).</li>
		<li>Using the eyelash, gently move the ribbon above the center of the support medium. At this point, use chloroform or heating pen for stretching of the sections if needed. However, remember that this manipulation may induce ribbon breaking and deformation.</li>
		<li>Start draining the water by pulling the syringe. For more delicate ribbons or a slower water retraction, let water drip by detaching the syringe from the hose. When the water level is lowering to the wafer level, control the ribbon and reposition it if necessary, by gently pushing the ribbon to the center. After settling the ribbons on the wafer surface, continue draining until the remaining water is completely retracted from the basin. 
		NOTE: If not using the bottom water retraction ATS knife, carefully reduce the water from the sides of the ATS knife to not induce turbulence.</li>
		<li>Leave the sections on the support inside the bath to let dry completely. Depending on the hydrophobicity of the support and environmental humidity level, water will evaporate at a different rate (Figure 2Div). It is important to let the sample dry slowly to diminish or altogether avoid all folds on the sample.</li>
		<li>Transfer the dry sample to a tightly closed box to protect from dirt contamination and place it to a 60 &#176;C oven for at least 30 min. If required, counterstain sections using heavy metals to enhance the overall contrast.</li>
		<li>At the end of the procedure, cautiously clean the knife following the manufacturer&#39;s instructions 
		NOTE: The transfer of multiple or serial sections on a wafer (Figure 2E) compared to the transfer on a slot grid (Figure 2F) change the EM preparation experience entirely. The uninterrupted sectioning and collection of the sections on single support reduces the amount of sectioning and section collection related mistakes frequent in serial sectioning. The equivalent of 100 sections of 1000 &#181;m x 500 &#181;m collected on one wafer corresponds to 33 slot grids (Figure 2G).</li>
	</ol>
	</li>
</ol>
3. Sample observation
NOTE: This section describes the workflow steps as implemented using a commercially available software (see Table of Materials). Any image acquisition software on any SEM equipped with the correct detectors can be used, however, the specific user actions will differ and will often be more manual.
<ol>
	<li>Acquire an overview map of SEM images that reveals section locations on the wafer. A built-in optical camera image helps with defining an SEM image mosaic that covers a ribbon of sections or all sections. Create the mosaic by click-drag with the mouse right on the camera image of the sample and start the Automatic Acquisition. 
	NOTE: Very coarse imaging settings, i.e., 1-2 &#181;m pixel size and 1 &#181;s dwell time suffice. This process is illustrated in Supplementary Material (pages 2-7).</li>
	<li>Locate sections with the Section Finder Auto Detection function or locate them manually. Section positions and outlines are retrieved automatically with this software based on image matching. For illustration of this process, see Supplementary Material (pages 8 - 15).</li>
	<li>In case the overview images do not show ROIs clearly, acquire higher resolution images of sections. Use the Section Preview function to create and acquire images automatically. This process is illustrated in Supplementary Material, pages 16-18. Imaging settings must be chosen according to the nature and size of the ROI that the user searches for.
	<ol>
		<li>To find optimal settings, activate the Live Imaging in the microscope control software and navigate to one ROI. Alter imaging settings until the images show ROIs clearly, but image acquisition is not excessively long.&#160;</li>
	</ol>
	</li>
	<li>Define imaging regions 
	&#8203;NOTE: Several different strategies are proposed.
	<ol>
		<li>If only a few sections need to be imaged, use the images of sections created so far for navigating to the relevant sections and use the Zoomable Viewer that shows all acquired images in their original relative locations to look at all sections. Once a section is found that should be imaged at high resolution, create an imaging region with click-drag. Choose high resolution imaging settings and store the settings in a template. Re-use this template for further sections.</li>
		<li>To find particularly small or hard to detect rare events, use the Lateral Screening approach. Manually create an imaging region with high resolution imaging settings on every tenth section or on one section per ribbon and acquire the images. Review the images and mark sections that contain the ROI in the software or take a note.
		<ol>
			<li>Starting from sections that contain the ROI, navigate forward and backward through the section set and create high resolution imaging regions in the same relative locations for as long as the structure is still visible in the section. This can be done manually or by using the procedure described in the next steps.</li>
		</ol>
		</li>
		<li>Acquire images in more than ten consecutive sections. Click Start Position Refinement after zooming the image to increase the precision of registered section locations as described in the manual. Doing so decreases the position variability of image series. The procedure is illustrated and explained in Supplementary Material pages 19-21.</li>
		<li>Click-drag on any section to define an imaging region while holding down the Alt key and select Create Tile Set Array from the context menu that opens when the mouse button is released. The software then creates imaging regions in the same relative location in all sections that have been found or marked previously. It is possible to limit imaging to a specific range of sections with the Section Span slider. 
		NOTE: This procedure can be repeated with any number of imaging regions and therefore allows recording many small high-resolution images instead of recording a single larger image on each section.</li>
		<li>Once created, set up pixel count, pixel size, tiling layout, pixel dwell time, etc. in each image series as needed. Once imaging series are created and set up, they are all listed in a job cue.</li>
	</ol>
	</li>
	<li>Configure auto functions and start image acquisition
	<ol>
		<li>Create a separate image series for auto functions using the same method as describe in the previous step. Move the image series to a position on the section that contains high-contrast structures.</li>
		<li>Set the image series to 1024 x 884 pixels and choose a pixel size corresponding to the highest resolution used in the image series set up in the previous steps. In the list of auto functions, check Auto Focus and Auto Stigmator.</li>
		<li>Select By Section in the acquisition sequence controls and make sure the auto functions image is the first item in the list. Start the image acquisition by clicking the Run button next to the job cue. These procedures are illustrated in Supplementary Material, pages 22-23. 
		&#8203;NOTE: It is not necessary to manually pre-focus on each section. During the recording session, whenever the microscope advances to a new section, the auto functions will be executed before all other images are recorded in this section.</li>
	</ol>
	</li>
</ol>
4. Data alignment and analysis
<ol>
	<li>Data export
	<ol>
		<li>Ensure that data is saved in .tif format, so there is no need for a dedicated export function. Sort data into a folder structure that corresponds directly to the layers and elements in the Layer Tree.</li>
		<li>Once image mosaics have been recorded, use the StitchAll function to automatically stitch all tiles.</li>
	</ol>
	</li>
	<li>Stack alignment and cropping in Fiji 
	&#8203;NOTE. Many software packages (free and commercial) can be used to work with Array Tomography data. The steps below are shown with open-source program Fiji32&#160;because it is widely available and contains all the required functions.
	<ol>
		<li>Import a stack of images (or stitched images) into Fiji as a virtual stack.</li>
		<li>If contrast/brightness needs to be normalized, choose Enhanced Contrast&#8230; from the Process menu. Set Saturated Pixels to 0.1 or less, and check Process all Slices.</li>
		<li>From the Plugins menu, choose Registration | Linear Stack Alignment with SIFT.</li>
		<li>Choose Rigid or Affine from the Expected Transformation drop-down menu. Otherwise, keep the default settings. Start the alignment by clicking OK. 
		NOTE: Loading the data as Virtual Stack allows Fiji to handle stacks of any size. The output of the alignment is created in RAM; however, this can limit the maximum size of stacks that can be processed. In that case, use Register Virtual Stack Slices, which is a folder-to-folder implementation of the same registration algorithm. Once registration is complete, load the output data as a virtual stack.</li>
		<li>Crop the image stack by clicking Crop so that it contains only the ROI.</li>
		<li>Save the stack as a single .tif image or series of .tif images. 
		NOTE: Critical steps of Array Tomography are shown in Figure 3.</li>
	</ol>
	</li>
</ol>

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W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Extrasynaptic+acetylcholine+signaling+through+a+muscarinic+receptor+regulates+cell+migration.">Extrasynaptic acetylcholine signaling through a muscarinic receptor regulates cell migration.</a> Proceedings of the National Academy of Sciences. 118 (1), e1904338118 (2021).</li><li>Schindelin, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fiji:+An+open-source+platform+for+biological-image+analysis.">Fiji: An open-source platform for biological-image analysis.</a> Nature Methods. 9 (7), 676-682 (2012).</li><li>Miguel-Aliaga, I., Jasper, H., Lemaitre, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Anatomy+and+physiology+of+the+digestive+tract+of+Drosophila+melanogaster.">Anatomy and physiology of the digestive tract of Drosophila melanogaster.</a> Genetics. 210 (2), 357-396 (2018).</li><li>Nikolaev, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Homeostatic+mini-intestines+through+scaffold-guided+organoid+morphogenesis.">Homeostatic mini-intestines through scaffold-guided organoid morphogenesis.</a> Nature. 585 (7826), 574-578 (2020).</li><li>Knoblich, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanisms+of+asymmetric+stem+cell+division.">Mechanisms of asymmetric stem cell division.</a> Cell. 132 (4), 583-597 (2008).</li><li>Daniel, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coordination+of+septate+junctions+assembly+and+completion+of+cytokinesis+in+proliferative+epithelial+tissues.">Coordination of septate junctions assembly and completion of cytokinesis in proliferative epithelial tissues.</a> Current Biology. 28 (9), 1380-1391 (2018).</li><li>Pasquettaz, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Peculiar+protrusions+along+tanycyte+processes+face+diverse+neural+and+non-neural+cell+types+in+the+hypothalamic+parenchyma.">Peculiar protrusions along tanycyte processes face diverse neural and non-neural cell types in the hypothalamic parenchyma.</a> Journal of Comparative Neurology. , (2020).</li><li>Kremer, J. R., Mastronarde, D. N., McIntosh, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Computer+visualization+of+three-dimensional+image+data+using+IMOD.">Computer visualization of three-dimensional image data using IMOD.</a> Journal of Structural Biology. 116 (1), 71-76 (1996).</li><li>Cardona, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=TrakEM2+software+for+neural+circuit+reconstruction.">TrakEM2 software for neural circuit reconstruction.</a> PLoS One. 7 (6), 38011 (2012).</li><li>Belevich, I., Joensuu, M., Kumar, D., Vihinen, H., Jokitalo, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microscopy+image+browser:+A+platform+for+segmentation+and+analysis+of+multidimensional+datasets.">Microscopy image browser: A platform for segmentation and analysis of multidimensional datasets.</a> PLoS Biology. 14 (1), 1002340 (2016).</li></ol>

The author Tilman Franke is an employee of Thermo Fisher that manufactures electron microscopes and piloting programs that are used in the article.

Electron microscopy gives insight into the ultrastructure of the cells and organisms, for which it is often desirable to image structures of interest in their 3-dimensional context. Despite numerous EM tactics for ultrastructural analysis, there is still no &#34;gold standard&#34; solution. The main reason is the wide variety of samples, many biological questions, which frequently require a tailored approach. The proposed AT workflow is designed to minimize the time necessary for sample processing, data acquisition, evaluation, and storage. Furthermore, the modified knife provides a helpful tool to simplify array acquisition. The compact layout of sections on wafers is convenient, both for the observation and the subsequent storage of the samples. This arrangement enables &#34;Lateral Screening&#34; of samples by horizontally moving from ribbon to ribbon and scanning only one section on each, significantly reducing the time required to localize an ROI. Proposed data acquisition scenarios facilitate the targeting of small and randomly distributed areas. Once found, AT/SEM restricts high-resolution imaging precisely to the volume of interest, whether performed manually or with the help of automatic function. AT for limited volumes can be completed manually, with the operator navigating through the sample and defining imaging regions one by one. The automated module of the software provides a flexible image acquisition strategy for imaging of small areas on large sections. The automation in this software allows recording large high-resolution images on hundreds of sections, achieving similar volumes as SBFI. Recording overview images of all sections simplifies the ROI localization and reduces the time spent at the microscope. Since the sections are not harmed during the recording of overviews and higher resolution Previews, AT/SEM permits reusing the sample to collect further data of other ROIs or at a higher resolution.
Image acquisition time is one of the most important (and most expensive) aspects of 3D EM and should therefore be considered in the experiment design. While it is unsurprising that imaging large areas takes longer than imaging small areas, it is easy to under-estimate the impact: Depending on the imaging parameters selected, the acquisition time on each section can vary from seconds to hours. Critical imaging parameters include the size of the field of view, resolution, and dwell time. Assuming a target resolution of 10nm per pixel and 1 &#181;s dwell time, imaging a field of 20 &#181;m x 20 &#181;m, 100 &#181;m x100 &#181;m, or 500 &#181;m x500 &#181;m takes 4 seconds, 100 seconds, or 2,500 s to record. We can multiply these per-section imaging times by the number of sections to estimate the time required for the complete imaging job. Long per-section imaging times can be acceptable if the number of sections is small or if microscope tool time is of no concern.
However, it is necessary to limit the recording time to an overnight job or a weekend job in most cases. An equally critical aspect of 3D EM that should be considered, is the amount and structure of the resulting image data. Recording the abovementioned imaging fields in 100 sections generates 400 mb, 10 gb, or 250 gb of image data, respectively; the 500 &#181;m x 500 &#181;m images pose the additional issue of being larger than 2 gb each. Many of the software programs used for data evaluation cannot open images of this size.
To reduce imaging time, it is important to choose pixel dwell time to meet the signal-to-noise ratio requirements for the subsequent data evaluation (e.g., reconstruction, tracing), and limit the recordings to defined ROIs. The AT extension of the software facilitates image acquisition in small areas in serial sections. The software supports manual and automatic workflows and many semi-automatic variants: imaging areas can be manually positioned and focused on each section, or the user can use the automatic section finder and position alignment features. Depending on the level of automation chosen and supported by the sample type or imaging goals, the time required for setting up image acquisition in hundreds of sections can take an entire workday (done manually) or only a few minutes. In principle, Array Tomography makes it more challenging than other 3D EM methods to acquire small ROIs; imprecise region placement on consecutive sections must be compensated by acquiring larger areas. For example, if the ROI is 20 &#181;m x 20 &#181;m in size and the section-to-section position variability of imaging fields is 10&#181;m, one needs to acquire 40 &#181;m x 40 &#181;m images in order to be sure that the ROI is fully captured in each image, on every section. Real-world image position variability ranges from 100 &#181;m to &#60;10 &#181;m depending on the availability or quality of software features for position alignment or user&#39;s patience. With this software, 10 &#181;m can be achieved without too much manual intervention in most samples.
Like any technique, the AT has several weak points that can influence successful data acquisition, and many are similar to other sectioning-based methods.Lack of homogenous distribution of empty resin versus tissue can result in curved or broken arrays. In extreme cases, sections can detach from the support (Figure 6A). Variable compression or stretching during the cutting process can create folds that can disrupt the sample in variable regions on subsequent sections (Figure 6B). Knife marks can appear on the surface of the collected sections using a damaged knife (Figure 6C). Differences in sectioning conditions can induce occasional section compression and thickness differences. Dust or dirt particles can land on a section and partially obscure the zone of interest (Figure 6D). Image acquisition can fail due to imperfect auto-contrast, auto-focus, and auto-stigmator functions. The positioning of automatically created imaging areas can be variable and may fail to capture the ROI in all sections.
Several problems can arise at the stage of stitching and alignment. The automatic stitching of mosaic tiles acquisitions can fail, for example, because of the large empty space inside the sample. Due to a drastic change in shape in 3D, image stacks can be challenging to register. Specially developed programs (e.g., IMOD, Fiji, TrackEM2, MIB, or MAPS-AT) can facilitate semi-automatic alignment32,38,39,40. More challenging sections can be manually aligned using photo editing software. Unfortunately, some datasets may be impossible to align correctly.
Large samples are challenging for TEM serial sections fitting onto grids; on the other hand, many projects do not justify long automatic acquisition using FIB/SEM or SBF-SEM. The AT is a straightforward alternative to a tedious serial section TEM where collection and manipulation of serial sections on a wafer are more straightforward than with the slot grids. Several strategies were developed to facilitate the collection of the arrays, and we share our method to expand the existing toolkit. In cases where the identification of the ROI is challenging, AT-SEM provides a fundamental advantage, with the efficient screening of the samples where organelle-scale resolution across 50 to 500 sections is required. For larger volumes, the automatic collection AT strategies can be efficiently collected if more sections are required. AT samples can be re-imaged multiple times, facilitating targeted imaging of high-resolution areas based on previously-acquired overview images. We believe that the targeted analysis and reduced oversampling by AT/SEM proposed here decreases the labor and data storage requirements. Ultimately, libraries of sections can be collected and maintained for later reuse and consultation. For volume acquisition, FIB or SBF-SEM approaches offer an excellent solution whenever the ROI is easy to identify on the block face or if large 3D volumes are needed for the analysis. However, FIB/SBF-SEM are less efficient when the high-resolution stack image has to be collected from a defined ROI in a targeted manner. To conclude, the proposed methods for screening of AT samples and the use of medium resolution overview images allow limiting image acquisition to the relevant parts of the section array. Precise aiming of imaging regions speeds up time-to-data and simplifies data evaluation.
In summary, although the concept of AT/SEM is not novel, its use is still not as widespread as its merits would suggest. Overall, it provides a complementary procedure to other existing EM methods. AT/SEM is compatible with the broadest range of sample preparation protocols and imaging workflows and can be done on any FIB/SEM or SBF-SEM microscope as an accompanying technique. In this paper, we have concentrated on AT for recording ultrastructural data from samples that are less likely to be successfully addressed by other methods. We hope that the described procedure for convenient collection of sections and considerably automated acquisition strategies will aid in the first attempts for those who have never encountered the method and will help to perfect it for those who already have some experience.

Despite the importance of EM-related techniques, the effort required to master them keeps the entire field restricted to a small number of specialists. One significant difficulty is the identification and retrieval of a Region of Interest (ROI) in the samples preserved for EM. The appearance of the same sample considerably differs when analyzed by optic microscopy and after processing for EM observation. The changes for chemically prepared samples include the anisotropic sample shrinkage after the dehydration steps (~10% in each dimension) and the loss of fluorescence when using osmium in the fixation and staining protocol (Figure 1A). For the ultrathin sectioning, the samples are embedded in epoxy or acrylic resins using different strategies (Figure 1B). For successful results of this preparation, the entire sample must be fractionated into pieces that do not exceed 1 mm x 1 mm. To meet standard Transmission Electron Microscopy (TEM) observation conditions&#39; requirements, this tiny portion of the sample is further sectioned to 50-150 nm thick slices. The resulting grayscale images show tissue organization and organelle structure of a minute fraction of the entire sample at greater detail than any other microscopy technique (Figure 1C). A typical TEM dataset provides 2D information, theoretically extrapolated to understand the processes naturally occurring in a 3D space in cells and tissues. Figure 1D presents the challenge of ultrastructural volumes acquisition: if a cube of side 1,000 &#181;m is sectioned at 50 nm thickness, 20,000 sections will be required to cover the entire volume; for a 500 &#181;m side cube, it will be 10,000 sections. To cover a 50 &#181;m x 50 &#181;m x 50 &#181;m volume, 1,000 sections &#34;only&#34; might be necessary. Obtaining this volume manually is practically impossible and extremely challenging to perform with automation. If, in addition to sample depth, we need to cover the entire surface of such hypothetical cubes, the coverage of 1 &#181;m2 surface at reasonable resolution becomes a serious logistic issue (Figure 1E). While for the extraordinary large-scale projects, such as connectomics approaches, the large number of sections is crucial, for the majority of the &#34;mundane&#34; EM projects, generating more sections required for the observation presents a significant disadvantage.
There are several methods to acquire 3D ultrastructural information: serial sectioning Transmission Electron Microscopy (TEM), TEM tomography, Array Tomography (AT), Serial Block Face Imaging Scanning Electron Microscopy (SBF-SEM), and Focused Ion Beam Scanning Electron Microscopy (FIB-SEM). Principal differences between these methods are the sectioning strategy and whether the image acquisition is coupled to section generation1. In serial sectioning TEM, sequential sections are collected on slot grids, TEM images are generated from these sequences and aligned2,3,4,5. In TEM tomography, tilt series from 150-300 nm sections on a grid, and when coupled to serial sectioning, provide a very high resolution, though relatively small volumes6,7,8. The AT approach uses physical sectioning with diverse manual and semi-automatic manners of sections collection on relatively large support, such as glass coverslip, silicon wafers or a special tape. For image acquisition, the support is analyzed in SEM, with diverse image acquisition strategies are available9,10,11,12,13,14,15 . For SBF-SEM, physical sectioning is achieved using a mini-microtome with a diamond knife set directly inside the SEM chamber, with the SEM image generated from the surface of the resin block16,17,18,19. For FIB-SEM, ion source removes thin layers of the sample, followed by automatic imaging of the exposed surface by the SEM20,21. TEM-tomography and the AT generate physical sections, which can be re-imaged if necessary, while FSBF-SEM and FIB-SEM eliminate the section after imaging. A recent combination of physical sections imaged by a multi-beam SEM provides a combination of methods that solves the &#34;bottleneck&#34; issue of the speed of image acquisition22. Each of these techniques has revolutionized the way EM data can be obtained and analyzed, and each approach has its practical impacts related to a given research question.
Given the nature of the preparation and the scale of the ultrastructural dimensions, it is not straightforward to predict where a specific target structure is located in the sample block (Figure1D,E). One solution for the ROI localization is recording the images from the entire block at the desired resolution from the beginning. The structures of interest can be in the acquired data volume when away from the microscope. Acquisition time and data handling associated with this strategy are problematic. It is desirable to reduce the amount of recorded data, especially if the ROIs are much smaller than the tissue block, i.e., if the objects of interest are specific types of cells (not whole organs). Different correlative light and electron microscopy techniques (CLEM) can be successful when the fluorescence is preserved and localized before or after preparation within the same sample23,24,25,26,27,28,29. Nevertheless, many cellular structures are recognizable even without fluorescence correlation, only based on the known ultrastructure. For these cases, we believe that lateral screening Array Tomography provides a balance tradeoff between the effort invested in ROI localization and the ultrastructural information quality. Using this strategy, a sub-set of sections on the wafer are screened within regular intervals, which can be established based on the ROI&#39;s size and nature. Once ROIs are found, data acquisition is set up in a continuous series of sections starting before and ending after the anchor section, collecting the relevant information in a targeted manner.
We present protocols for AT that simplify and accelerate the acquisition of regions or events of interest in numerous sections and yield better-aligned image volumes. Lateral screening and multistep acquisition produce data with very high resolution in precisely targeted regions. The procedure we describe addresses several challenges of 3D EM data acquisition, as it provides for: compatibility with a broad range of specimens without fundamentally changing the sample preparation workflow; targeted localization for sectioning and SEM acquisitions; reduced time and effort during setup; imaging of regions in multiple sections with better alignment of the resulting volumes; and a smooth stitching and alignment procedure to compile different images into a stitched mosaic picture. We chose to demonstrate the strength of our method with several samples from published and ongoing projects. We believe that this approach can significantly facilitate the generation and acquisition of targeted EM data, even for investigators with limited EM experience.

<table><tbody><tr><td>&lt;em&gt;&lt;strong&gt;Cutting&lt;/strong&gt;&lt;/em&gt;</td><td></td><td></td><td></td></tr><tr><td>AT sectioning knife</td><td>Diatome</td><td>DUATS3530</td><td>Diatome Jumbo knife</td></tr><tr><td>Diamond knife for trimming 90&amp;deg;</td><td>Diatome</td><td>DTB90</td><td>Diatome trimming 20&amp;deg;&lt;br/&gt; Glass knife</td></tr><tr><td>Pattex contact adhesive</td><td>Pattex</td><td>PCL3C</td><td></td></tr><tr><td>Silicon wafer</td><td>Ted Pella</td><td>16015</td><td>Resistance: 1-30 Ohms&lt;br/&gt; Type P: (Boron) (1 primary flat)&lt;br/&gt; Roughness: 2 nm&lt;br/&gt; No SiO2 top coating&lt;br/&gt; TTV: = &amp;lt;20 &amp;micro;m&lt;br/&gt; Wafer is polished on one side</td></tr><tr><td>Ultramicrotome</td><td>Leica UC6</td><td></td><td>Alternative: Leica UC7</td></tr><tr><td>Wafer cleaving kit</td><td>EMS</td><td>7642</td><td>EMF, Small Sample Cleaver, CatNo. 7652</td></tr><tr><td>&lt;em&gt;&lt;strong&gt;Image acquisition&lt;/strong&gt;&lt;/em&gt;</td><td></td><td></td><td></td></tr><tr><td>FESEM</td><td>Thermo Fischer Helios</td><td>1072419</td><td>Alternatives: Zeiss, Jeol, Hitachi, TESCAN</td></tr><tr><td>Maps 3 for SEM with Correlative Workflow &amp;amp; Array Tomography</td><td>Thermo Fisher Scientific</td><td>1135932</td><td>Maps provides automation of SEM imaging workflows and allows importing of 3rd party data for CLEM and navigation.</td></tr><tr><td>&lt;em&gt;&lt;strong&gt;Image analysis&lt;/strong&gt;&lt;/em&gt;</td><td></td><td></td><td></td></tr><tr><td>Amira x.y</td><td>Thermo Fisher Scientific</td><td>1131599</td><td>Amira is a 3D data visualization and analysis software with several practical functions for Array Tomography data reconstruction.</td></tr><tr><td>Image processing</td><td>Open source</td><td>Fiji (http://fiji.sc/#download)</td><td>IMOD, MIB (See text for refferences)</td></tr></tbody></table>

array tomography workflow for the targeted acquisition of volume information using scanning electron microscopy

Electron microscopy is applied in biology and medicine for imaging of cellular and structural details at nanometer resolution. Historically, Transmission Electron Microscopy (TEM) provided insight into cell ultrastructure, but in the recent decade, the development of modern Scanning Electron Microscopes (SEM) has changed the way of looking inside the cells. Even though the resolution of TEM is superior when protein-level structural details are needed, SEM-resolution is sufficient for the majority of the organelle-level cell biology-related questions. The advancement in technology enabled automatic volume acquisition solutions such as Serial block-face imaging (SBF-SEM) and Focused ion beam SEM (FIB-SEM). Nevertheless, to this day, these methods remain inefficient when the identification and navigation to areas of interest are crucial. Without the means for precise localization of target areas before imaging, operators need to acquire much more data than they need (in SBF-SEM), or, even worse, prepare many grids and image them all (in TEM). We propose the strategy of "lateral screening" using Array Tomography in SEM, which facilitates the localization of areas of interest, followed by automated imaging of the relevant fraction of the total sample volume. Array tomography samples are conserved during imaging, and they can be arranged into section libraries ready for repeated imaging. Several examples are shown in which lateral screening enables us to analyze structural details that are incredibly challenging to access with any other method.

Watch this Scientific Journal Video about Array Tomography Workflow for the Targeted Acquisition of Volume Information using Scanning Electron Microscopy at JoVE.com

Array Tomography Workflow for the Targeted Acquisition of Volume Information using Scanning Electron Microscopy

We describe the preparation of ribbons of serial sections and their collection on large transfer support for use as Array Tomography samples, along with automated imaging procedures in a scanning electron microscope. The protocol allows screening, retrieval, and targeted imaging of local, rare events, and the acquisition of large data volumes.

Electron microscopy is applied in biology and medicine for imaging of cellular and structural details at nanometer resolution. Historically, Transmission ...

array-tomography-workflow-for-targeted-acquisition-volume-information

Universidad San Sebastian

Research

JoVE Journal

Biology

4.7K Views.  Thermo Fisher. We describe the preparation of ribbons of serial sections and their collection on large transfer support for use as Array Tomography samples, along with automated imaging procedures in a scanning electron microscope. The protocol allows screening, retrieval, and targeted imaging of local, rare events, and the acquisition of large data volumes. 

Video: Array Tomography Workflow for the Targeted Acquisition of Volume Information using Scanning Electron Microscopy

Energy Dispersive X-ray Tomography for 3D Elemental Mapping of Individual Nanoparticles

Energy dispersive X-ray spectroscopy within the scanning transmission electron microscope (STEM) provides accurate elemental analysis with high spatial resolution, and is even capable of providing atomically resolved elemental maps. In this technique, a highly focused electron beam is incident upon a thin sample and the energy of emitted X-rays is measured in order to determine the atomic species of material within the beam path. This elementally sensitive spectroscopy technique can be extended to three dimensional tomographic imaging by acquiring multiple spectrum images with the sample tilted along an axis perpendicular to the electron beam direction.
Elemental distributions within single nanoparticles are often important for determining their optical, catalytic and magnetic properties. Techniques such as X-ray tomography and slice and view energy dispersive X-ray mapping in the scanning electron microscope provide elementally sensitive three dimensional imaging but are typically limited to spatial resolutions of &gt; 20 nm. Atom probe tomography provides near atomic resolution but preparing nanoparticle samples for atom probe analysis is often challenging. Thus, elementally sensitive techniques applied within the scanning transmission electron microscope are uniquely placed to study elemental distributions within nanoparticles of dimensions 10-100 nm.
Here, energy dispersive X-ray (EDX) spectroscopy within the STEM is applied to investigate the distribution of elements in single AgAu nanoparticles. The surface segregation of both Ag and Au, at different nanoparticle compositions, has been observed.

The use of energy dispersive X-ray tomography in the scanning transmission electron microscope to characterize elemental distributions within single nanoparticles in three dimensions is described.

Energy dispersive X-ray spectroscopy within the scanning transmission electron microscope (STEM) provides accurate elemental analysis with high spatial ...

Engineering

Obtaining 3D Chemical Maps by Energy Filtered Transmission Electron Microscopy Tomography

Energy filtered transmission electron microscopy tomography (EFTEM tomography) can provide three-dimensional (3D) chemical maps of materials at a nanometric scale. EFTEM tomography can separate chemical elements that are very difficult to distinguish using other imaging techniques. The experimental protocol described here shows how to create 3D chemical maps to understand the chemical distribution and morphology of a material. Sample preparation steps for data segmentation are presented. This protocol permits the 3D distribution analysis of chemical elements in a nanometric sample. However, it should be noted that currently, the 3D chemical maps can only be generated for samples that are not beam sensitive, since the recording of filtered images requires long exposure times to an intense electron beam. The protocol was applied to quantify the chemical distribution of the components of two different heterogeneous catalyst supports. In the first study, the chemical distribution of aluminum and titanium in titania-alumina supports was analyzed. The samples were prepared using the swing-pH method. In the second, the chemical distribution of aluminum and silicon in silica-alumina supports that were prepared using the sol-powder and mechanical mixture methods was examined.

This paper describes a protocol to achieve 3D chemical maps combining energy filtered imaging and electron tomography. The chemical distribution of two catalyst supports formed by elements that are difficult to distinguish by other imaging techniques was studied. Each application consists of mapping overlapped chemical elements - respectively spaced-ionization edges.

Energy filtered transmission electron microscopy tomography (EFTEM tomography) can provide three-dimensional (3D) chemical maps of materials at a ...

Chemistry

Using Tomoauto: A Protocol for High-throughput Automated Cryo-electron Tomography

Cryo-electron tomography (Cryo-ET) is a powerful three-dimensional (3-D) imaging technique for visualizing macromolecular complexes in their native context at a molecular level. The technique involves initially preserving the sample in its native state by rapidly freezing the specimen in vitreous ice, then collecting a series of micrographs from different angles at high magnification, and finally computationally reconstructing a 3-D density map. The frozen-hydrated specimen is extremely sensitive to the electron beam and so micrographs are collected at very low electron doses to limit the radiation damage. As a result, the raw cryo-tomogram has a very low signal to noise ratio characterized by an intrinsically noisy image. To better visualize subjects of interest, conventional imaging analysis and sub-tomogram averaging in which sub-tomograms of the subject are extracted from the initial tomogram and aligned and averaged are utilized to improve both contrast and resolution. Large datasets of tilt-series are essential to understanding and resolving the complexes at different states, conditions, or mutations as well as obtaining a large enough collection of sub-tomograms for averaging and classification. Collecting and processing this data can be a major obstacle preventing further analysis. Here we describe a high-throughput cryo-ET protocol based on a computer-controlled 300kV cryo-electron microscope, a direct detection device (DDD) camera and a highly effective, semi-automated image-processing pipeline software wrapper library tomoauto developed in-house. This protocol has been effectively utilized to visualize the intact type III secretion system (T3SS) in Shigella flexneri minicells. It can be applicable to any project suitable for cryo-ET.

We present a protocol on how to utilize high-throughput cryo-electron tomography to determine high resolution in situ structures of molecular machines. The protocol permits large amounts of data to be processed, avoids common bottlenecks and reduces resource downtime, allowing the user to focus on important biological questions.

Cryo-electron tomography (Cryo-ET) is a powerful three-dimensional (3-D) imaging technique for visualizing macromolecular complexes in their native ...

Bioengineering

Preparing Lamellae from Vitreous Biological Samples Using a Dual-Beam Scanning Electron Microscope for Cryo-Electron Tomography

Presented here is a protocol for preparing cryo-lamellae from plunge-frozen grids of Plasmodium falciparum-infected&#160;human erythrocytes, which could easily be adapted for other biological samples. The basic principles for preparing samples, milling, and viewing lamellae are common to all instruments and the protocol can be followed as a general guide to on-grid cryo-lamella preparation for cryo-electron microscopy (cryoEM) and cryo-electron tomography (cryoET). Electron microscopy grids supporting the cells are plunge-frozen into liquid nitrogen-cooled liquid ethane using a manual or automated plunge freezer, then screened on a light microscope equipped with a cryo-stage. Frozen grids are transferred into a cryo-scanning electron microscope equipped with a focused ion beam (cryoFIB-SEM). Grids are routinely sputter coated prior to milling, which aids dispersal of charge build-up during milling. Alternatively, an e-beam rotary coater can be used to apply a layer of carbon-platinum to the grids, the exact thickness of which can be more precisely controlled. Once inside the cryoFIB-SEM an additional coating of an organoplatinum compound is applied to the surface of the grid via a gas injection system (GIS). This layer protects the front edge of the lamella as it is milled, the integrity of which is critical for achieving uniformly thin lamellae. Regions of interest are identified via SEM and milling is carried out in a step-wise fashion, reducing the current of the ion beam as the lamella reaches electron transparency, in order to avoid excessive heat generation. A grid with multiple lamellae is then transferred to a transmission electron microscope (TEM) under cryogenic conditions for tilt-series acquisition. A robust and contamination-free workflow for lamella preparation is an essential step for downstream techniques, including cellular cryoEM, cryoET, and sub-tomogram averaging. Development of these techniques, especially for lift-out and milling of high-pressure frozen samples, is of high-priority in the field.

Using focused ion beam milling to produce vitreous on-grid lamellae from plunge frozen biological samples for cryo-electron tomography.

Presented here is a protocol for preparing cryo-lamellae from plunge-frozen grids of Plasmodium falciparum-infected&#160;human erythrocytes, which could ...

Biochemistry

Preparation and Observation of Thick Biological Samples by Scanning Transmission Electron Tomography

This report describes a protocol for preparing thick biological specimens for further observation using a scanning transmission electron microscope. It also describes an imaging method for studying the 3D structure of thick biological specimens by scanning transmission electron tomography. The sample preparation protocol is based on conventional methods in which the sample is fixed using chemical agents, treated with a heavy atom salt contrasting agent, dehydrated in a series of ethanol baths, and embedded in resin. The specific imaging conditions for observing thick samples by scanning transmission electron microscopy are then described. Sections of the sample are observed using a through-focus method involving the collection of several images at various focal planes. This enables the recovery of in-focus information at various heights throughout the sample. This particular collection pattern is performed at each tilt angle during tomography data collection. A single image is then generated, merging the in-focus information from all the different focal planes. A classic tilt-series dataset is then generated. The advantage of the method is that the tilt-series alignment and reconstruction can be performed using standard tools. The collection of through-focal images allows the reconstruction of a 3D volume that contains all of the structural details of the sample in focus.

This report describes a sample preparation protocol and specific imaging conditions for performing scanning transmission electron tomography of thick biological specimens.

This report describes a protocol for preparing thick biological specimens for further observation using a scanning transmission electron microscope. It ...

Targeted Studies Using Serial Block Face and Focused Ion Beam Scan Electron Microscopy

This protocol allows for the efficient and effective imaging of cell or tissue samples in three dimensions at the resolution level of electron microscopy. For many years electron microscopy (EM) has remained an inherently two-dimensional technique. With the advent of serial scanning electron microscope imaging techniques (volume EM), using either an integrated microtome or focused ion beam to slice then view embedded tissues, the third dimension becomes easily accessible. Serial block face scanning electron microscopy (SBF-SEM) uses an ultramicrotome enclosed in the SEM chamber. It has the capability to handle large specimens (1,000 &#181;m x 1,000 &#181;m) and image large fields of view at small X,Y pixel size, but is limited in the Z dimension by the diamond knife. Focused ion beam SEM (FIB-SEM) is not limited in 3D resolution, (isotropic voxels of &#8804;5 nm are achievable), but the field of view is much more limited. This protocol demonstrates a workflow for combining the two techniques to allow for finding individual regions of interest (ROIs) in a large field and then imaging the subsequent targeted volume at high isotropic voxel resolution. Preparing fixed cells or tissues is more demanding for volume EM techniques due to the extra contrasting needed for efficient signal generation in SEM imaging. Such protocols are time consuming and labor intensive. This protocol also incorporates microwave assisted tissue processing facilitating the penetration of reagents, which reduces the time needed for the processing protocol from days to hours.

Here, we present a protocol for efficiently combining serial block face and focused ion beam scanning electron microscopy to target an area of interest. This allows for efficient searching, in three dimensions, and locating rare events in a large field of view.

This protocol allows for the efficient and effective imaging of cell or tissue samples in three dimensions at the resolution level of electron microscopy. ...

Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition

Cryogenic electron tomography (cryoET) is a powerful method to study the 3D structure of biological samples in a close-to-native state. Current state-of-the-art cryoET combined with subtomogram averaging analysis enables the high-resolution structural determination of macromolecular complexes that are present in multiple copies within tomographic reconstructions. Tomographic experiments usually require a vast amount of tilt series to be acquired by means of high-end transmission electron microscopes with important operational running-costs. Although the throughput and reliability of automated data acquisition routines have constantly improved over the recent years, the process of selecting regions of interest at which a tilt series will be acquired cannot be easily automated and it still relies on the user's manual input. Therefore, the set-up of a large-scale data collection session is a time-consuming procedure that can considerably reduce the remaining microscope time available for tilt series acquisition. Here, the protocol describes the recently developed implementations based on the SerialEM package and the PyEM software that significantly improve the time-efficiency of grid screening and large-scale tilt series data collection. The presented protocol illustrates how to use SerialEM scripting functionalities to fully automate grid mapping, grid square mapping, and tilt series acquisition. Furthermore, the protocol describes how to use PyEM to select additional acquisition targets in off-line mode after automated data collection is initiated. To illustrate this protocol, its application in the context of high-end data collection of Sars-Cov-2 tilt series is described. The presented pipeline is particularly suited to maximizing the time-efficiency of tomography experiments that require a careful selection of acquisition targets and at the same time a large amount of tilt series to be collected.

The increasing demand for large-scale data collection in cryogenic electron tomography requires high-throughput image acquisition routines. Described here is a protocol that implements the recent developments of advanced acquisition strategies aimed at maximizing the time-efficiency and throughput of tomographic data collection.

Cryogenic electron tomography (cryoET) is a powerful method to study the 3D structure of biological samples in a close-to-native state. Current ...

Imaging Replicative Domains in Ultrastructurally Preserved Chromatin by Electron Tomography

Principles of DNA folding in the cell nucleus and its dynamic transformations that occur during the fulfillment of basic genetic functions (transcription, replication, segregation, etc.) remain poorly understood, partially due to the lack of experimental approaches to high-resolution visualization of specific chromatin loci in structurally preserved nuclei. Here we present a protocol for the visualization of replicative domains in monolayer cell culture in situ,&#160;by combining EdU labeling of newly synthesized DNA with subsequent label detection with Ag-amplification of Nanogold particles and ChromEM staining of chromatin. This protocol allows for the high-contrast, high-efficiency pre-embedding labeling, compatible with traditional glutaraldehyde fixation that provides the best structural preservation of chromatin for room-temperature sample processing. Another advantage of pre-embedding labeling is the possibility to pre-select cells of interest for sectioning. This is especially important for the analysis of heterogeneous cell populations, as well as compatibility with electron tomography approaches to high-resolution 3D analysis of chromatin organization at sites of replication, and the analysis of post-replicative chromatin rearrangement and sister chromatid segregation in the interphase.

This protocol presents a technique for high-resolution mapping of replication sites in structurally preserved chromatin in situ that employs a combination of pre-embedding EdU-streptavidin-Nanogold labeling and ChromEMT.

Principles of DNA folding in the cell nucleus and its dynamic transformations that occur during the fulfillment of basic genetic functions (transcription, ...

Cryo-Electron Tomography Remote Data Collection and Subtomogram Averaging

Cryo-electron tomography (cryo-ET) has been gaining momentum in recent years, especially since the introduction of direct electron detectors, improved automated acquisition strategies, preparative techniques that expand the possibilities of what the electron microscope can image at high-resolution using cryo-ET and new subtomogram averaging software. Additionally, data acquisition has become increasingly streamlined, making it more accessible to many users. The SARS-CoV-2 pandemic has further accelerated remote cryo-electron microscopy (cryo-EM) data collection, especially for single-particle cryo-EM, in many facilities globally, providing uninterrupted user access to state-of-the-art instruments during the pandemic. With the recent advances in Tomo5 (software for 3D electron tomography), remote cryo-ET data collection has become robust and easy to handle from anywhere in the world. This article aims to provide a detailed walk-through, starting from the data collection setup in the tomography software for the process of a (remote) cryo-ET data collection session with detailed troubleshooting. The (remote) data collection protocol is further complemented with the workflow for structure determination at near-atomic resolution by subtomogram averaging with emClarity, using apoferritin as an example.

The present protocol describes high-resolution cryo-electron tomography remote data acquisition using Tomo5 and subsequent data processing and subtomogram averaging using emClarity. Apoferritin is used as an example to illustrate detailed step-by-step processes to achieve a cryo-ET structure at 2.86 &#197; resolution.

Cryo-electron tomography (cryo-ET) has been gaining momentum in recent years, especially since the introduction of direct electron detectors, improved ...

Visualization of Organelles In Situ by Cryo-STEM Tomography

Cryogenic electron microscopy (cryo-EM) relies on the imaging of biological or organic specimens embedded in their native aqueous medium; water is solidified into a glass (i.e., vitrified) without crystallization. The cryo-EM method is widely used to determine the structure of biological macromolecules recently at a near-atomic resolution. The approach has been extended to the study of organelles and cells using tomography, but the conventional mode of wide-field transmission EM imaging suffers a severe limitation in the specimen thickness. This has led to a practice of milling thin lamellae using a focused ion beam; the high resolution is obtained by subtomogram averaging from the reconstructions, but three-dimensional relations outside the remaining layer are lost. The thickness limitation can be circumvented by scanned probe imaging, similar to the scanning EM or the confocal laser scanning microscope. While scanning transmission electron microscopy (STEM) in materials science provides atomic resolution in single images, the sensitivity of cryogenic biological specimens to electron irradiation requires special considerations. This protocol presents a setup for cryo-tomography using STEM. The basic topical configuration of the microscope is described for both two- and three-condenser systems, while automation is provided by the non-commercial SerialEM software. Enhancements for batch acquisition and correlative alignment to previously-acquired fluorescence maps are also described. As an example, we show the reconstruction of a mitochondrion, pointing out the inner and outer membrane and calcium phosphate granules, as well as surrounding microtubules, actin filaments, and ribosomes. Cryo-STEM tomography excels in revealing the theater of organelles in the cytoplasm and, in some cases, even the nuclear periphery of adherent cells in culture.

Visualization of Organelles In Situ by Cryo-STEM Tomography

Cryo-STEM tomography provides a means to visualize organelles of intact cells without embedding, sectioning, or other invasive preparations. The 3D resolution obtained is currently in the range of a few nanometers, with a field of view of several micrometers and an accessible thickness in the order of 1 &#181;m.

Array Tomography Workflow for the Targeted Acquisition of Volume Information using Scanning Electron Microscopy

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Using Tomoauto: A Protocol for High-throughput Automated Cryo-electron Tomography

Preparing Lamellae from Vitreous Biological Samples Using a Dual-Beam Scanning Electron Microscope for Cryo-Electron Tomography

Preparation and Observation of Thick Biological Samples by Scanning Transmission Electron Tomography

Targeted Studies Using Serial Block Face and Focused Ion Beam Scan Electron Microscopy

Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition

Imaging Replicative Domains in Ultrastructurally Preserved Chromatin by Electron Tomography

Cryo-Electron Tomography Remote Data Collection and Subtomogram Averaging

Visualization of Organelles In Situ by Cryo-STEM Tomography