Coffee under the microscope 3.

Electron microscopy, plant cells and porosity

So far we have looked at coffee through optical microscopes, which has allowed us to appreciate grind size, shape and even helped to calculate grind size distribution.

Electron microscopy is designed to take us to a real close-up with the material of interest. Instead of light beams, it uses electron beams to create an image which can reveal details down to the nanometer (nm) range. Just to appreciate how small a nanometer is, think of these few examples: a nanometer is how much your nails grow in just one second. It’s a million times smaller than a millimetre, getting pretty close to the size of atoms: an atom is about a tenth of a nanometer across.

This means that an electron microscope can easily reveal the plant cell structure inside a coffee bean: plant cells are 10-100 micrometers in size, much bigger than the smallest features these amazing microscopes are capable of resolving.

This level of magnification gives us a sensational view of the bean’s internal structure; revealing its intricate porosity, and how this structure changes during roasting. For example, we'll look at a series of scanning electron microscopy (SEM) images that reveal the dramatic structural changes during both first and second crack.

Here’s an SEM image showing an extreme close-up of a green coffee bean:

SEM image of a green coffee bean (cryocut, cross section). Taken from Schenker et al1

The first thing you might notice are the three large circular holes or craters, each about 10 micrometer across. And if you look closely, you’ll see each of these holes is surrounded by a thick border line.

To understand what these features are, let’s take a step back and take a quick look at what a plant cell looks like in general. In many ways they are similar to an animal cell, with a couple of important differences. 

Animal cell vs. plant cell. Image from Wikipedia.

Both plant and animal cells have a cell membrane, where most of the lipids (oils) are found within the cell. On top of this plant cells have a rigid cell wall, made of cellulose and a couple of other carbohydrates. The cell walls serve as a “plant skeleton”, forming a very solid structure that can hold up even a tall tree.  We can also notice that the plant cell has a big empty “bag” in the middle, called a permanent vacuole. There is usually one very large vacuole, which can take up more than half of the cell's volume. The vacuole holds water or nutrients such as proteins, fats and carbohydrates—which, from our point of view, are key flavour compounds.

These are beautifully visible in the SEM image of the green coffee bean we have seen above.1.  The bean has been frozen and sliced in half to show it in cross-section. 

SEM image of a green coffee bean (cryocut, cross section). Modified from Schenker et al1. The red border shows the cell wall, the blue circle outlines the vacuole.

In the case of the green coffee bean, the cell wall is about 10 µm thick, the cell itself is approx. 20-30 µm in cross section, and the vacuole indeed takes up about half the cell volume. The presence of vacuoles gives the bean a structure a bit like swiss-cheese, and already indicates that we are dealing with a porous material. We'l see even more evidence of porosity later on.

What happens to the plant cell structure during roasting?

This has been a subject of a number of scientific studies, so we have some knowledge of what happens at a structural level.

For example, a Masters thesis by Niya Wang from the University of Guelph, Canada, shows a series of SEM images during the roasting process.2

SEM images tracking the progress of a  roast. Modified from Wang2

Here we can quite clearly see how the pores expand during first crack, then open up even more at second crack. The pressure increase inside the pores (caused by the build-up of gases such as CO2, steam and volatile organics) causes the cells to expand a bit like blowing up a balloon. This causes the cell walls to compress against each other, and eventually rupture. This breaking down of barriers between cells has obvious importance for how water infiltrates through the bean while brewing.

Redgwell et al3 also found that roasting breaks down about 12-40% of the structural carbohydrates. While cellulose is remarkably stable and shows almost no degradation, other polysaccharides become soluble as they degrade, contributing to the taste and viscosity of the coffee beverage.

Besides the micron-scale porosity, plants also contain an extensive network of nano-scale pores called plamodesmata between cells (just like there’s usually a series of narrow alleyways connecting two city blocks).  Neighbouring cells use these tiny channels to communicate with each other and share nutrients. And, as Schenker et al showed, this network of tiny pores also affects the aging of the roasted bean.

First, they measured the size of these pores (using a fascinating technique caller mercury porosimetry, though we won’t go into that now)—finding that most of the pores were about 24 nm wide.

Next they showed how this nano-scale network affects oil transport within the bean.

The below picture shows an SEM image of the outside of a coffee bean a day after roasting. Tiny, often sub-micron sized oil beads cover the surface, indicating the presence of an extended pore network through which the oil starts to emigrate to the surface of the roasted bean. 

Oil beads show on the surface of a roasted coffee bean, indicating a fine network of nanopores. Capillary forces help the oil migrate to the surface of the roasted bean. Image modified from Schenker et al1


Now, one last thing: what does grinding do to the cell structure?

Here are two SEM images I took using coffee ground on a BUNN (left, setting 10) and an EK43 (right, setting 11.5) grinder. The instrument was a benchtop SEM operated in BSE (backscattered electron) mode at 15 kV, and without coating the sample with any metal. The samples were not frozen or cross-sectioned as in some of the above images, and so reveal the grinds in their natural state. 

SEM images of  roasted coffee groud on a BUNN (left) and an EK43 grinder (right). Scale bar is 100 µm in both cases. 

The cell structure is mostly shattered to sharp shreds in the grinder, but in some images, such as these I’ve chosen to show here, the cell wall structure is still visible. Breaking up these walls exposes the inside of the cells, where many of the soluble materials are stored.

As we learnt from looking at the plant cell structure, many flavour compounds (such as amino acids, sugars and fats) are stored in the vacuoles, or in the cell membrane (such as oils). With the cell wall broken, we can extract these materials more easily and enjoy their contribution to the overall taste experience!

This SEM instrument is housed at LaTrobe University, and was operated in collaboration with the Australian Coffee Science Lab. Interested in getting your own samples imaged and analysed? Just give us a call, we would be excited to work with you!



1 S. SCHENKER, S. HANDSCHIN, B. FREY, R. PERREN, AND F. E SCHER: Pore Structure of Coffee Beans Affected by Roasting Conditions, Journal of Food Science,2000, 65(3):452 - 457

2 N. WANG: Physicochemical Changes of Coffee Beans During Roasting. Thesis presented to the University of Guelph, Ontario, Canada, 2012, p76

3 RJ REDGWELL, V TROVATO,D CURTI AND M FISCHER: Effect of roasting on degradation and structural features of polysaccharides in Arabica coffee beans. Carbohydr Res. 2002, 1;337(5):421-31.

Coffee pros have said…

Monika is a coffee professionals’ dream come true – finally there’s a scientist who understands us! With an inquisitive mindset paired with the scientific methodology and knowledge to back it up, Monika is an invaluable resource to anyone looking to dig a little deeper into their coffee.

Ben Bicknell, Five Senses Coffee
Ben Bicknell, Five Senses Coffee

Monika brings a wealth of coffee knowledge all backed by sound, solid, scientific principles. Having worked with her in the past, she’s an innovative scientist with a deep understanding of coffee from ‘bean to cup’.

Joseph Rivera, Coffee Scientist, creator of
Joseph Rivera, Coffee Scientist, creator of

I belive knowing the science behind why coffee taste so good is so important because it gives us the tools to not only make it taste better but more consistently. Monika helps us do this by ensuring the consistentcy of coffee through the Mythos and EK43 at The Bench Projects. She has also been vital in creating the perfect water and trials for my 2016 World Brewers Cup in Dublin, Ireland.

Devin Loong, 2014 Australian Brewers Cup Champion barista
Devin Loong, 2014 Australian Brewers Cup Champion barista

Register now for a free Consultation!

Register now
for a free Consultation!

Did you know?
Check our blog

As many baristas have noticed, soy milk is often harder to work with then dairy milk – it tends to curdle more in coffee, especially when steaming hot. With some coffees it behaves well, with some it doesn’t. Why does this happen? Is there anything...