Home Biology Discover the facility and advantages of Quantity Electron Microscopy

Discover the facility and advantages of Quantity Electron Microscopy

Discover the facility and advantages of Quantity Electron Microscopy


Quantity electron microscopy (vEM) is a strong offshoot of electron microscopy. It supplies 3D reconstructions of samples at nanometer decision. vEM covers a group of strategies that contain taking a number of sections from a single pattern and imaging them to provide a complete 3D picture. Picture volumes can exceed ten cubic microns and make it attainable to review giant numbers of subcellular constructions and their connectivity.

What for those who may see intact constructions inside cells, in three dimensions, with the picture quantity exceeding tens of microns, at nanometer decision? 

All of these are attainable with quantity electron microscopy (vEM), a dazzlingly highly effective offshoot of electron microscopy (EM).

Learn on for an introduction to vEM, the way it works, the questions it will possibly deal with, and a few of its greatest challenges. 

What Is Quantity Electron Microscopy?

Merely put, vEM permits us to picture three-dimensional (3D) constructions of organic samples at excessive decision of their native setting. The time period describes a spread of electron microscopy strategies that present a 3D picture on the finish relatively than a single linear technique.

Such a abstract belies its energy, nonetheless. There’s a purpose Nature listed it amongst their applied sciences to look at in 2023, together with titans just like the James–Webb telescope and high-precision radiocarbon courting.

3D photos of huge chunks of cells and tissues permit us to see and interrogate networks of subcellular parts. Usually talking, the extra related subcellular parts (reminiscent of mitochondria and synapses) are, the more healthy the cells are. Plus, organelles and molecular complexes affiliate and dissociate with one another and their setting in accordance with their perform. 

The reverse can be prone to be true. Disconnection between subcellular parts may point out pathological states for a given pattern kind—and that is the realm vEM lets us discover!

Moreover connectedness, there are different advantages of vEM too. You possibly can analyze a a lot larger space than standard EM strategies however with out compromising on the decision of your information or processing extra samples. The elevated imaging space means you may picture a number of cells concurrently and select bigger areas of curiosity.

We’ll come to the analysis questions you may reply utilizing vEM later, however for now, observe vEM reveals pattern connectedness, texture, and spatial/mobile context.

The important thing phrase right here is connectedness.

vEM originated inside connectomics—finding out the mind’s intact structural and useful connections referred to as the connectome—which is difficult to review with conventional 2D imaging strategies.

Fluorescence microscopy precisely captures comparatively macroscopic properties, reminiscent of the placement of mobile parts, whereas electron microscopy captures the ultrastructural particulars of a pattern. Nevertheless, each these strategies are often restricted to the horizontal aircraft.

This rationalization is barely simplified—we’ve got confocal laser scanning microscopy, in spite of everything. However that requires getting your goal to fluoresce by conjugating it to dye or utilizing transgenics. The purpose is vEM is an extra 3D imaging approach that has its personal key advantages. 

Why Do We Want vEM? A Easy Illustration

So why do we want vEM? Sadly, 2D slices and cross-sections by way of 3D shapes can result in deceptive representations of their form. 

Try Determine 1 beneath to see what number of cross-sections a dice can generate—it will depend on the way you slice it!

What is Volume Electron Microscopy and Should You Use it?
Determine 1. Some attainable cross-sections of a dice. (Picture credit score: Thomas Warwick.)

Now think about that, relatively than a dice, you may have an organelle reminiscent of a vacuole or mitochondrion. The variety of attainable (and deceptive) cross-sections is sort of limitless.

Then think about that you’re taking a look at a construction that nobody has ever seen. How are you aware what’s correct? 

One answer is to get a 3D picture of the intact construction. And now, with vEM, you may!

How Does vEM Work?

Typical electron microscopy strategies often contain sectioning samples into single, ultra-thin slices sectioning samples into single, ultra-thin slices and imaging them.

With vEM, you purchase photos from a collection of slices by way of your pattern after which computationally mix them to create the ultimate 3D reconstruction. And what a reconstruction! Try this 3D rendering of a number of related neurites. [1]

There are three fundamental methods to generate a number of slices from a pattern for 3D imaging.

1. Array Tomography

Array tomography is the most cost effective strategy. 

You repair and part your pattern as you’d for another electron microscopy strategy, however you generate loads of sections. Then, you organize them right into a ribbon that serves as a ticker tape by way of your pattern.

When you’ve bought all of your sections, you picture them serially to create a 3D reconstruction.

Array tomography can be essentially the most labor-intensive strategy, but it surely’s non-destructive, which means you may retrieve the sections and picture them utilizing another modality. It’s additionally appropriate with scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Learn this text for a fast refresher on the variations between SEM and TEM for those who want it, and take a look at this text for a deeper dive into array tomography.

2. Serial Block-Face Scanning Electron Microscopy

The serial block-face (SBF) strategy is much like array tomography. Nevertheless, as a substitute of producing all of the sections at first and imaging all of them in collection, the sectioning and imaging are iterative. That’s to say, you part, then picture, part, picture, and so forth.

The wonderful thing about SBF is that you would be able to automate it. The Volumescope 2 SEM is a strong, modular vEM answer that comprises an ultramicrotome contained in the imaging chamber for automated information acquisition!

Nevertheless, not like array tomography, SBF is harmful, which means evaluation through different microscopy strategies should come beforehand. Plus, it’s solely appropriate with SEM.

3. Targeted Ion Beam Scanning Electron Microscopy

Targeted ion beam scanning electron microscopy (FIB-SEM) combines a targeted ion beam (often gallium ions) with scanning electron microscopy. In contrast to serial block-face imaging, FIB-SEM doesn’t contain eradicating sections sequentially. [2] 

As an alternative, it makes use of the targeted ion beam to erase pattern materials layer by layer to disclose a brand new, deeper floor for imaging at every step. Due to this, it’s harmful. 

On the plus facet, utilizing an ion beam to take away pattern materials affords a a lot larger decision within the z path when in comparison with utilizing an ultramicrotome. The z-direction decision may be as excessive as a number of nanometers.

The best way to Determine Whether or not to Use vEM

vEM is wonderful. However must you use it?

The very best factor to do is sit down along with your native analyst or core facility supervisor and converse to them concerning the objectives of your undertaking to determine whether it is acceptable. 

vEM takes a very long time (see beneath), and the services to do it are uncommon at current, so you need to formulate your analysis query nicely and have clear, particular objectives. 

There are two important standards:

  1. Your analysis query have to be involved with 3D ultrastructures. 
  2. This ultrastructure should confer a change in perform or phenotype.

Listed here are some examples of questions you may deal with utilizing vEM:

  • Are there adjustments in mobile/organellar form/group underneath totally different circumstances?
  • Are there adjustments in mobile/organellar connectedness underneath totally different circumstances?
  • Are there ultrastructural variations in tissues or cells underneath totally different circumstances?
  • The place do subcellular entities originate, how are they distributed, and the place do they go?

And, as a result of vEM allows you to find just about any subcellular part you need (offering you may stain it), you can begin to reply deep questions reminiscent of:

  • How a lot of X is there per cell?
  • What’s the complete quantity and mass of X per cell?
  • How do these values change underneath totally different circumstances?

Maybe the important thing level is apparent—the uncooked information you reply these questions with is a picture, not an summary illustration of your information. 

And vEM datasets are extremely wealthy. Plan for this and put together to take the time to investigate your information fastidiously. Keep in mind that there’ll in all probability be extra information than you may hope to interpret, and your photos will possible include constructions invaluable to another person’s undertaking. Sharing your information is subsequently inspired.

The Electron Microscopy Public Picture Archive is the first on-line repository for 3D photos and tomograms. Remember to have a look at a number of the unimaginable information on it.

The vEM Workflow

So, you may have determined to make the leap and embark on a vEM undertaking. What are you able to count on? 

Earlier than you do something, go to the amount electron microscopy group’s webpage. It hosts coaching movies, protocols, explanations, key individuals, information, a Twitter feed—every part!

Here’s a breakdown of the workflow, key concerns, and issues you may count on. When you’re in a rush, take a look at Determine 2 beneath.

What is Volume Electron Microscopy and Should You Use it?
Determine 2. A fundamental quantity electron microscopy workflow. (Picture credit score: Thomas Warwick.)

Pattern Preparation (1-2 Weeks)

Pattern prep for vEM has loads in frequent with different EM strategies. You repair your pattern, coat it with a heavy steel stain to supply distinction, then slice it up and picture it.

You’ll wish to determine your area of curiosity utilizing a smart strategy reminiscent of fluorescence microscopy or micro-computer tomography (micro-CT). Then you definately’ll transfer on to staining your pattern earlier than embedding it in resin and doing any guide trimming.

Take care along with your pattern prep, because it largely dictates whether or not your vEM imaging undertaking will succeed or fail. Now we have a superb information to EM pattern prep, and lots of the factors apply to vEM additionally.

And eventually, observe that vEM samples are sometimes embedded in a non-conductive resin, so one of many challenges is guaranteeing that your pattern prep ends in conductive samples for imaging.

Picture acquisition (1-7 Days)

As talked about earlier, a key know-how in vEM is SBF imaging, the place your pattern is lower into sections utilizing an ultramicrotome contained in the imaging chamber of the electron microscope.

In such instances, picture acquisition begins by fastidiously aligning the ultramicrotome to work harmoniously with the microscope optics. Then, you set the chopping window and imaging parameters earlier than buying your information.

Presently, vEM devices are giant and costly. The info acquisition doesn’t tolerate pattern motion, so they’re often on anti-vibration flooring and want shielding from electromagnetic interference from surrounding infrastructure (practice stations, trams, and so on.)

Knowledge Processing (Days, Weeks, or Months)

Upon getting information, you should course of and interpret it. How lengthy this and your hands-on time will take will depend on your analysis objectives. 

One step you’ll need to do, no matter your downstream intentions, is to align your slices to provide the 3D picture.

Past that, it relies upon, as I say, in your objectives. In concept, inspecting your closing 3D picture for a sure/no reply to your analysis query ought to be comparatively fast and easy.

However chances are you’ll must do one thing extra complicated, reminiscent of determine areas of curiosity to section to (say) generate coaching information for a man-made intelligence mannequin. Relying in your pattern kind, it could be exhausting to section utilizing automated strategies, which means you need to do it manually. When you’ve generated a whole lot of information, this might take years! 

Nevertheless, most tasks gained’t be at this excessive fringe of issues, and weeks to months might be a extra affordable estimate.

And keep in mind, vEM know-how is in its infancy. Technological progress, pushed by bold analysis and data-sharing initiatives, will probably cut back these time frames to one thing extra possible.

The Present Challenges of vEM 

So why isn’t all people doing it? vEM and the group surrounding it are comparatively new. A number of challenges forestall the approach from being mainstream (for now). 

Aside from pattern preparation, which is user-dependent, a number of the challenges are as follows. 

Knowledge Assortment Time

vEM tasks are intrinsically large-scale, and the info acquisition pace of electron microscopes limits the quantity of knowledge collected in a given interval. And unsurprisingly, there’s a trade-off between information acquisition pace and information decision. 

Inadequate {Hardware} Automation

And talking of large-scale tasks, electron microscopes of any variety are sophisticated. Arrange and monitoring require devoted personnel, which means the typical person can’t simply queue up a load of experiments and stroll away. The emergence of vEM could push electron microscope producers and services towards better automation. 

Dealing with Huge Portions of Knowledge

Knowledge dealing with and evaluation are additionally limiting steps as a result of vEM tasks can generate terabytes of knowledge. You possibly can’t simply slap it on a reminiscence stick and take it to the workplace. Such huge quantities of knowledge are difficult to switch, not to mention analyze and interpret. And also you’ve bought to again all of it up!

Knowledge Segmentation

Imaging bigger areas has two main penalties: there’s extra information to section, and the info are extra biologically complicated. Think about segmenting all of the mitochondria in a cell—you get the thought. Fortuitously, machine- and deep-learning strategies are always evolving, which means that we’re at all times heading in direction of extra correct, automated segmentation.

When you genuinely need to section a whole lot of mitochondria, take a look at the AI software MitoNet. [3]

Inadequate Knowledge Evaluation Automation and Streamlining

Equally, computerized picture annotation and segmentation strategies are nonetheless inadequate to annotate such wealthy and huge datasets precisely and reliably. Double-checking the outcomes of automated annotation additionally takes time. Assuredly information evaluation and software program pipelines will develop tremendously. 

3D Reconstruction is Arduous

Then there’s the apparent one—you need to precisely align all the photographs to get a 3D reconstruction, which may be very exhausting. Take into account all of the picture artifacts and pattern distortions that will come up throughout information acquisition, and it will get tougher nonetheless.

Into the Future: A Perspective on vEM

If these are challenges, what’s subsequent for vEM?

In a current interview with us on The Microscopists, Lucy Collinson, Head of Electron Microscopy on the Francis Crick Institute, places the way forward for quantity electron microscopy like this:

The connectome map of the Caenorhabditis elegans worm’s mind exists due to vEM. [4] Now the trouble of the connectomics group is directed towards offering the connectome of the fly mind. As soon as they’ve managed this, they’ll in all probability wish to map the mouse connectome.

If the problem of mapping the C. elegans thoughts is equal to 1 airline seat, then the fly mind is the equal of 4 Boeing 747 jumbo jets, and the mouse mind is the equal of the gap between Boston, MA, and Lisbon. 

Lucy has additionally co-authored a superb introduction to vEM [5] that goes into extra element than we do right here. 

The challenges in pattern preparation, information acquisition time, picture quantity, and information evaluation are monumental. Hopefully, the trouble expended in reaching them will usher within the subsequent technology of vEM know-how, making it extra accessible to each researcher.


  1. Motta A, Berning M, Boergens KM, et al. (2019) Dense connectomic reconstruction in layer 4 of the somatosensory cortex. Science 366:eaay3134 
  2. Xu CS, Hayworth KJ, Lu Z, et al. (2017) Enhanced FIB-SEM methods for large-volume 3D imaging. Elife 6:e25916
  3. Glancy B (2023) MitoNet: A generalizable mannequin for segmentation of particular person mitochondria inside electron microscopy datasets. Cell Syst 14(1):7–8 
  4. Mulcahy B, Witvliet D, Holmyard D, et al. (2018) A Pipeline for Quantity Electron Microscopy of the Caenorhabditis elegans Nervous System. Entrance Neural Circuits 12:94
  5. Collinson LM and Peddie CJ (2014) Exploring the third dimension: Quantity electron microscopy comes of age. Micron 61:9–19

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