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. 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 µm x 1,000 µm) 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 ≤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.
This protocol describes a workflow for the efficient targeting of high-resolution, three-dimensional electron microscopy (EM) to a specific region of interest (ROI). Since its beginnings in the 1930s, EM has been an essentially two-dimensional technique. The first published images were of whole tissues or cells but that soon gave way to sections that were cut by hand using an ultramicrotome and imaged using a transmission electron microscope (TEM). TEM produces very high-resolution micrographs where even the smallest of cellular structures are clearly discernable. However, the thinness of section necessary for the tissue to be imaged by the electron beam made information in the Z dimension minimal. Since cells are three-dimensional structures, interactions between cell structures and cell surfaces had to be inferred from limited data. This raised the potential for misinterpretation, especially in structures that were complex. Some microscopists managed to obtain more accurate 3D structures by serial-sectioning cells and tissues and then painstakingly reconstructing them from individual TEM images1. This was a very labor-intensive process and before the advent of digital imaging and computer rendering the results were also difficult to visualize. In recent years two techniques have been introduced which have become collectively known as volume electron microscopy (volume EM)2 that have made EM in three dimensions accessible to more laboratories.
The idea of obtaining a stack of images from an embedded block inside an electron microscope can be traced back to 1981 when Steve Leighton and Alan Kuzirian built a miniature microtome and placed it in the chamber of a scanning electron microscope3 (SBF-SEM). This prototype was eventually copied and improved 23 years later by Denk and Horstmann4 and subsequently commercialized. At roughly the same time biological scientists became aware of another technology used primarily in materials science, the focused ion beam. This technique uses an ion beam of some kind (Gallium, plasma) to remove a very small amount of surface material from a sample (FIB-SEM)5. Both techniques employ sectioning followed by imaging providing a series of images which can be combined into an X, Y, Z, stack. Both techniques provide 3D information but at different resolution scales. SBF-SEM is limited by the physical properties of the diamond knife to slices no thinner than 50 nm for long serial imaging runs; however the sample block size that can be sectioned is large, up to 1 mm x 1 mm x 1 mm. Due to the large digital acquisition format of the back scattered electron detector (32k x 32k pixels) that receives a signal from the block face, image pixel sizes can be as small as 1 nm. This results in non-isotropic voxels where the X,Y dimension is frequently smaller than the Z. Because of the precision of the ion beam, FIB-SEM has the ability to collect images with isotropic voxels ≤5 nm. However, the total area that can be imaged is quite small. A summary table of various samples and volumes imaged with the two techniques has been published previously3.
Tissue preparation for volume EM is more difficult than for standard TEM or SEM because samples must be stained to provide adequate signal generation in the SEM. Frequently, stainings need to be optimized not only for the particular tissue type but also for adding contrast to certain cellular structures to make identification and reconstruction easier. The protocol used here is based on the NCMIR standard6. Additional staining usually means additional protocol steps. Thus for volume EM, standard protocols need to be extended to ensure sufficient time for reagents to penetrate the sample. Microwave assisted processing can reduce the time needed for staining from hours to minutes and makes volume EM sample preparation more efficient7. This method is applicable to all cell and tissue types8 and to research questions where the inhomogeneity of the tissue makes sampling of a specific area essential9.
Once a data stack is obtained it can be aligned and the structures of interest segmented from the rest of the data and modeled in 3D. Although the automation of imaging many slices of tissue has made image acquisition relatively straightforward, the process of digitally reconstructing and visualizing the data is a time-consuming task. Software for this purpose is not yet integrated nor fully automated. Since much of the early work using volume EM was directed towards neuroscience, the techniques for staining and digitally segmenting structures such as axons is fairly far advanced compared to other cells and organelles. While the literature on other non-neuronal tissues is growing quickly, nonlinear or irregular structures require more manual input.
Using both SBF-SEM and FIB-SEM is a useful approach for targeting and imaging specific, nonhomogeneous, tissue structures at high resolution in 3D. Combining that with microwave assisted tissue processing that vastly decreases the time needed for sample preparation. Together this workflow will make generating high-resolution isotropic voxel image datasets of fine structures an efficient and more rapid process.
1. Sample fixation and processing for electron microscopy
2. Prepare embedded samples for imaging
3. Imaging in the SBF-SEM
4. SBF-SEM data processing
5. Imaging in the FIB-SEM
Images from the SBF-SEM provide an overview of the tissue, giving insight into the spatial orientation of cells and intercellular connections (Figure 4A). The subsequent FIB-SEM imaging on a new region, which is usually a region of interest determined after inspection of the SBF-SEM run, adds high-resolution detail of specific cells and/or structures (Figure 4B).
Figure 4C,D show the difference in rendering of the non-isotropic voxels of the SBF-SEM data (Figure 4C) and the isotropic voxel FIB-SEM data (Figure 4D). The z thickness used in SBF-SEM means that the rendering clearly shows the sections, resulting in a 'staircase' effect in on the surface. In the FIB-SEM data the 5 nm sections ensure that the rendering appears much smoother and individual sections blend into the surface completely.
Figure 1: Creation of the block face from a resin embedded sample. (A) A root-tip embedded in resin. (B) Using a razor blade the excess resin is trimmed away until a block of 0.5 mm2 remains. (C,D) The trimmed block is glued onto a metal pin and after a night in the oven, the sides of the block are trimmed and the surface smoothened with a diamond knife using an ultramicrotome. (E) Inside the SBF-SEM, the sample is oriented so that the blockface and ROI can be recognized, scale bar = 20 µm. Please click here to view a larger version of this figure.
Figure 2: Correlation between SBF-SEM and FIB-SEM. Overview images of the block-face using the SBF-SEM (A) and the FIB-SEM (B), scale bar = 5 µm. (C,D) Zoom on the ROI. Red box delineates the region to be imaged with FIB-SEM, scale bar = 5 µm. Please click here to view a larger version of this figure.
Figure 3: FIB-SEM scheme and preparation steps. (A) Scheme showing the orientation of the FIB beam, SEM beam and sample. The sample needs to be positioned to the coincidence point of the FIB and SEM beams to be able to mill and image on the same region. (B) Schematic drawing of the trench needed for SEM imaging of the sections removed by the FIB. (C) Image taken with the FIB beam showing Platinum deposition on the ROI, scale bar 5 µm. (D) Image taken with the FIB beam showing the lines used for auto-focus and 3D tracking. The lines in the middle are used for auto-focus and the outside lines provide 3D tracking. Carbon deposition on top of the lines provides the needed contrast (platinum vs carbon) to perform these tasks, scalebar 5 µm. (E) Image taken with the FIB beam after milling of the trench, scalebar 5 µm. (F) Image taken with the SEM beam showing the region of interest imaged during the FIB-SEM run, scale bar 2 µm. Please click here to view a larger version of this figure.
Figure 4: SBF-SEM and FIB-SEM results before and after segmentation. (A) 3D view of SBF-SEM dataset (100 x 100 x 40 µm, scale bar = 10 µm), (B) 3D view of FIB-SEM dataset (17 x 10 x 5.4 µm, scale bar = 2 µm), (C) Rendered vacuoles segmented from SBF-SEM data by thresholding, scale bar = 2 µm D. Rendered granules segmented from FIB-SEM data by thresholding, scale bar = 2 µm. Please click here to view a larger version of this figure.
Protocol for Microwave Processing | |||||||||
Program # | Description | User Prompt (on/off) | Time (hr:min:sec) | Power (Watts) | Temp (°C) | Load Cooler (off/auto/on) | Vacuum/Bubbler Pump (off/bubb/vac cycle/vac on/vap) | Steady Temp | |
Pump (on/off) | Temp (°C) | ||||||||
8 | TCH | OFF | 0:01:00 | 150 | 50 | OFF | VACUUM CYCLE | ON | 30 |
OFF | 0:01:00 | 0 | 50 | OFF | VACUUM CYCLE | ON | 30 | ||
OFF | 0:01:00 | 150 | 50 | OFF | VACUUM CYCLE | ON | 30 | ||
9 | OSMIUM | OFF | 0:02:00 | 100 | 50 | OFF | VACUUM CYCLE | ON | 30 |
OFF | 0:02:00 | 0 | 50 | OFF | VACUUM CYCLE | ON | 30 | ||
OFF | 0:02:00 | 100 | 50 | OFF | VACUUM CYCLE | ON | 30 | ||
OFF | 0:02:00 | 0 | 50 | OFF | VACUUM CYCLE | ON | 30 | ||
OFF | 0:02:00 | 100 | 50 | OFF | VACUUM CYCLE | ON | 30 | ||
10 | 50% EtOH | ON | 0:00:40 | 150 | 50 | OFF | OFF | ON | 30 |
70% EtOH | ON | 0:00:40 | 150 | 50 | OFF | OFF | ON | 30 | |
90% EtOH | ON | 0:00:40 | 150 | 50 | OFF | OFF | ON | 30 | |
100% EtOH | ON | 0:00:40 | 150 | 50 | OFF | OFF | ON | 30 | |
100% EtOH | ON | 0:00:40 | 150 | 50 | OFF | OFF | ON | 30 | |
15 | 0.1M CACODYLATE | ON | 0:00:40 | 250 | 50 | OFF | VACUUM CYCLE | ON | 30 |
0.1M CACODYLATE | ON | 0:00:40 | 250 | 50 | OFF | VACUUM CYCLE | ON | 30 | |
15 | ddH2O | ON | 0:00:40 | 250 | 50 | OFF | VACUUM CYCLE | ON | 30 |
ddH2O | ON | 0:00:40 | 250 | 50 | OFF | VACUUM CYCLE | ON | 30 | |
16 | Uranyl Acetate | OFF | 0:01:00 | 150 | 50 | OFF | VACUUM CYCLE | ON | 30 |
OFF | 0:01:00 | 0 | 50 | OFF | VACUUM CYCLE | ON | 30 | ||
OFF | 0:01:00 | 150 | 50 | OFF | VACUUM CYCLE | ON | 30 | ||
OFF | 0:01:00 | 0 | 50 | OFF | VACUUM CYCLE | ON | 30 | ||
OFF | 0:01:00 | 150 | 50 | OFF | VACUUM CYCLE | ON | 30 | ||
OFF | 0:01:00 | 0 | 50 | OFF | VACUUM CYCLE | ON | 30 | ||
OFF | 0:01:00 | 150 | 50 | OFF | VACUUM CYCLE | ON | 30 |
Table 1. Detailed protocol for microwave processing.
Step | Current | Estimated Time |
Deposition Platinum | 3n A | 10-15 minutes |
Milling Autotune and Tracking Marks | 50-100 pA | 4-6 minutes |
Deposition Carbon | 3 nA | 5-10 minutes |
Milling Coarse Trench | 15-30 nA | 30-50 minutes |
Polishing Surface | 1.5-3 nA | 15-20 minutes |
Imaging Run | 700 pA-1.5 nA | Hours-days |
Table 2. FIB milling currents used for sample preparation and imaging run
Volume electron microscopy is more challenging and time consuming than conventional SEM or TEM. Because of the need to stain tissues or cells en bloc, processing steps must be long enough to ensure penetration of reagents throughout the sample. Using microwave energy to facilitate penetration makes for shorter, more efficient processing and improves staining. Because preparation for EM is much more stringent than for light microscopy all solutions and reagents must be quality controlled strictly. Changes in pH, tonicity, the use of impure reagents, and introduction of contaminants due to poor technique can all have deleterious effects on the final image.
Volume EM also requires individually tailored protocols for each different sample type. Mammalian tissues of different types: plants, single cells such as yeast, trypanosomes, C. elegans, etc., all need their own variations to achieve optimal results. Fixation and staining must be designed so as to preserve structural integrity and keep the sample as close to its in vivo morphology as possible. Fixation of tissues at physiological temperature, pH and tonicity is critical to making the sample as life-like as it can be. High-pressure freezing (HPF) of samples may help to preserve a more life-like situation, (or perhaps just yield different artifacts), but for other than cells and very thin tissues HPF will fail as vitreous ice can only be generated in small volumes. Therefore for many questions chemical fixation is the only option. No matter if the fixation is HPF or chemical, in any EM experiment the structural results need to be carefully compared to similar results from live cell or tissue imaging to see if they are consistent. Staining must also be optimized while considering the specific question that needs to be answered and the protocol that will be used for visualization of the digital images.
Having both an SBF-SEM and FIB system in close proximity is a great advantage in many experiments. The large field of view and high X,Y resolution of SBF-SEM makes finding individual structures/cells/events straightforward and provides an overall spatial orientation of cells in tissues. In addition, its ability to allow imaging through a sample in Z is very powerful; however, reconstructions that require fine geometric detail can fail or produce artifacts using this technique due to the non-isotropic voxels it generates. The FIB is limited by the physics of the process to a smaller imaging field but its 3D resolution is sufficient for very accurate reconstructions. Combining the two techniques is straightforward as samples can move from SBF-SEM to FIB without further processing or preparation. We acknowledge that using the SBF-SEM for searching through a sample to find a particular area is a very expensive use of a much more capable tool. However, the ability to immediately see the new blockface and determine whether the ROI has been reached is a great advantage. Additionally, the alternatives of using serial semi-thin (0.5 µm) LM sections may remove small structures before they are detected, and inspecting a block using single TEM sections which have to be cut, put on a grid and then viewed in an equally expensive TEM is not as efficient as the method presented.
Because many programs exist to segment and render the data, and the needs of a given structure may not be best served by a single application, no standard workflow can be proposed. Some simple structures may be segmented with a thresholding algorithm if they fall within very narrow grey scale values. Neuronal structures can be semi-automatically segmented using a program such as Ilastik11 but it will be less useful on more random or complex shaped organelles such as ER. Microscopy Image Browser is a very flexible program that can align, segment, and render volume EM data, but requires significant user interaction12. As a general rule the amount of time needed to digitally visualize the results will greatly exceed the time for preparing the sample and imaging.
Volume EM techniques have opened up the third dimension to ultrastructural analysis. Other methods of obtaining 3D EM have limitations in their volume (TEM tomography), or their efficiency (serial section TEM). Although for the most part volume EM techniques are too complex and costly to be implemented in individual laboratories, the number of shared core facilities offering them has been growing and the number of sample types successfully imaged has increased rapidly. For those with a specific question and a particular tissue it is likely someone will be able to offer advice and instructions on its preparation and imaging. Volume EM equipment can be improved to include the capacity to handle larger samples in the SBF-SEM and the capability of milling larger ROIs with the FIB. Software which is able to segment out structures of interest in a more automated way will vastly simplify the process of analyzing the data and improvements in computing speed will reduce the time needed to do so. Despite its current limitations, volume EM is still a useful tool and combining SBF-SEM and FIB-SEM provides an efficient workflow for identifying rare events and imaging them at high resolution.
The equipment for volume EM was provided by a generous grant from the Government of Flanders.
Name | Company | Catalog Number | Comments |
3View 2XP | Gatan | NA | In chamber ultramicrotome for SBFI |
Cacodylate buffer 0.2M solution | EM Sciences | 11652 | |
Conductive epoxy resin (circuit works) | RS components | 496-265 | |
Diatome Histo 4.0mm diamond knife | EM Sciences | 40-HIS | |
Digitizing tablet | Wacom | DTV-1200W | No longer available |
Eppendorf tubes | Eppendorf | 0030 120.094 | |
Flat Embedding Mold | EM Sciences | 70900 | |
Gluteraldehyde 25% solution | EM Sciences | 16220 | |
High MW Weight Tannic Acid | EM Sciences | 21700 | |
Lead Citrate | Sigma-Aldrich | 22861 | |
NaCl | Sigma-Aldrich | 746398 | |
Osmium Tetroxide 4% solution | EM Sciences | 19170 | |
Paraformaldehyde | Sigma-Aldrich | P6148 | |
Pelco Biowave Pro + | Ted Pella | 36700 | |
Potassium Ferrocyanide | Sigma-Aldrich | P3289 | |
Quorum Q150T ES sputter coater | Quorum Technologies | 27645 | |
Reichert-Jung Ultracut ultramicrotome | NA | NA | No longer available |
Sodium Cacodylate 0.2M | EM Sciences | 11653 | |
Spurrs Resin kit | EM Sciences | 14300 | |
Uranyl Acetate | EM Sciences | 22400 |
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