Coffee Beans

Rebeckah Burke

University of Rochester, Department of Chemistry

1. Introduction

From farm to cup, coffee undergoes an amazing transformation. In fact, most of us are only familiar with a single part of coffee: the bean. Coffee begins as a fruit, fondly referred to as the coffee cherry. However, most of the coffee fruit is stripped away in the processing steps, leaving only the coffee bean (endosperm) and sometimes silver skin behind.

Figure 1: This diagram illustrates the anatomy of coffee (left). All the layers of the fruit are stripped away, leaving only the green bean and residual silver skin prior to roasting (right).

Coffee beans are often sold as blends. While blends contain beans of the same species (Arabica), they often contains different sub-species, or varietals, of coffee from places all over the world. In contrast, single origin coffees are sourced by geological location and contain a single varietal of coffee. Single origin coffees typically have distinct flavor notes that arise from different factors in their growing environment, like elevation, climate, and soil. In addition, coffee can be processed in a variety of ways, and this, too, impacts the flavor.

Figure 2: The coffee cherry significantly varies between different varietals of Arabica coffee.

Additionally, coffee beans must be roasted before they can be used to create a delicious cup of coffee, as the raw, green beans have a bland and upleasant flavor. Physical and chemical changes that occur during roasting transform the coffee seed into the bean we know and love. In addition to the chemical reactions that take place during roasting, the beans lose water content. This evaporation of water creates a build up of internal pressure and an evolution of gases. As this changes the volume of the coffee bean, the pore structure in the coffee bean is expected to undergo physical changes.

For this project, two single origin coffees were explored using microscopy: Brazil and Papua New Guinea (PNG). Green and roasted coffee beans of the same origin were compared to study the change in microstructure as a result of the roasting process. Additionally, two different varietals were examined to see if the growing conditions that impact the chemical composition and flavor of the coffee beans also corresponded to changes in coffee microstructure.

Table 1: This table offers a comparison of the growing enviroments and processing of the coffees used for this project.

The two coffees studied were deliberately chosen to be of different varietals, grown at different elevations and processed with two different techniques. The varietals are both sub-species of Arabica coffee. Typica is the original variety, and all other varieties are mutations or genetic selections of typica, including yellow bourbon. The coffee cherries for these two varietals are shown in figure 2. In addition to different growing environments, these coffees were processed differently after harvest. Natural processes, like the Brazil, is a dry method of processing, and the coffee cherries are thinly spread on brick or drying tables and left to dry in the sun. Once dried, the residual skin and fruit are mechanically removed. Washed processes, like the PNG, remove the skin and sticky flesh of the coffee cherry by machine prior to drying.

Several techniques were used in the process of studying these samples. Two important sample preparation techniques were used to prepare the beans for electron microscopy: critical point drying and sputter coating. The beans themselves were imaged using both light microscopy and secondary electron imaging. Interaction modeling was used to better understand the interaction volume for the coffee. Finally, some of the obtained images were colorized using Adobe Photoshop.

2. Sample Preparation

Prior to any electron imaging, the coffee samples required some preparation. Because green coffee beans do contain some water, these samples were fractured with The Chopper and dehydrated with solutions of 95% and 100% ethanol. Then, the slivers were dried using critical point drying (CPD). In CPD, samples are placed in a high-pressure chamber filled with ethanol. Once all the ethanol is replaced with liquid carbon dioxide, the temperature and pressure in the chamber are increased until they pass the critical point for carbon dioxide. This method allows samples to be dried with minimal disruption of surfaces.

Figure 3: The green bean samples were dehydrated with ethanol (left), and then dried using the Samdri-PVT-3B critical point drying apparatus. Conductive coating was applied using the Denton Vacuum Sputter coater.

As the roasted beans contain far less water than the green beans, these samples were fractured and then soaked in acetone for several hours. Then, they were left to dry in air. In preparation for SEM imaging, the samples were mounted on stubs using carbon tape and graphite adhesive glue. Once secured on the stub, the samples were sputter coated with 160-200 Angstroms of gold. As coffee beans are completely insulating, coating and grounding the samples was important for counteracting the effects of charge buildup in the sample and increasing the number of secondary electrons emitted from the sample.

Figure 4: Green and roasted coffee samples were mounted on stubs and coated with gold. They're ready for some SEM imaging!

3. Scanning Electron Microscopy

Scanning electron microscopy (SEM) is a tool used for imaging specimens using an electron beam. The image is formed as a result of the interaction of the specimen with the beam. One of the most common imaging modes used in SEM is secondary electron (SE) imaging. Secondary electrons are generated from an inelastic scattering event. These types of electrons are emitted from the upper portion of the interaction volume. They are commonly used for imaging the surface structure of materials and can provide excellent resolution. All images were collected on a Zeiss Auriga CrossBeam SEM-FIB

The SE2 detector was used to collect secondary electron images of both the green and roasted beans from the Brazil and PNG samples.

Figure 5: Comparison of green coffee beans from Brazil (left two micrographs) and PNG (right two micrographs) at two different magnifications.

Figure 6: Roasted coffee beans from Brazil (left two micrographs) and PNG (right two micrographs) were compared at two magnifications.

From the micrographs, a significant difference could be seen between the green and roasted beans. The green beans have a very tight, knotty structure, and pores are not visible. In contrast, the roasted beans are significantly less dense with a very webby structure of pores. However, no real structural difference can be discerned between the Brazil and PNG beans. For the roasted beans, the Measure tool in ImageJ was used to the provide an approximate diameter for the pores in the roasted beans. For each type of bean, the diameter of the roasted pores were measured in the longest direction (n=55). Though this was a rudimentary analysis, it still demonstrates that there is no significant difference between the structure of the two roasted beans.

Table 2: The diameters of pores in roasted Brazil and PNG coffee beans are compared.

Though the Brazil and PNG beans demonstrated no significant structural differences, the beans sure still look cool! A smattering of SE2 images are highlighted below.

Figure 7: Different angles of Brazil beans.

Figure 8: Some neat micrographs of PNG beans.


Figure 9: One of the coolest features of coffee beans is the silver skin. It has awesome textures.

4. Light Microscopy

Light microscopy was another technique used to look at the coffee beans. One advantage of light microscopy is the inherent colorization of the images. Unlike secondary electron imaging, light microscopy does not provide much depth of field, and unfortunately, because coffee beans have significant curvature, obtaining an image without blury spots was extremely difficult.

Figure 10: Light microscopy was used to investigate both Brazil and PNG coffee in two different modes: DIC (left, middle left) and bright field (middle right, right). (Left to right: green PNG, green Brazil, green Brazil, roasted PNG)

Two different imaging modes were used for light microscopy. Differential interference contrast (DIC) mode uses plane polarized light, which is spatially separated, or sheared, at the objective lens and recombined before observation. The interference between these two waves upon recombination creates contrast due to the optical path differences. In contrast, bright field imaging uses the transmitted beam, and contrast is created by absorbance of light by the sample.

Though obtaining focused images was a challenge, light microscopy provided an interesting perspective for studying these beans, as the images maintined color. These images highlight some interesting textures in DIC mode (left and middle left). For these samples, the surface of the coffee bean was fractured with a razor blade, so the portion of the beans just below the surface could be imaged. The middle right bright field image highlights the delicate texture of the silverskin within a green bean, and the rightmost image reveals the unique patterning on the outside of a roasted coffee bean, a characteristic not seen with electron microscopy.

5. Interaction Modeling

To better understand the interaction volume for these samples, a modeling program was used to simulate electron flight using software owned by the Institue of Optics at the University of Rochester. Using 2000 trajectories and 0 degree tilt, the interaction volume was modeled at several different accelrating voltages for bulk organic material, as an approximation for the composition of coffee beans. Simulations revealed a penetration depths of 0.55 microns at 5 kV and 2.00 microns at 10 kV. By decreasing the accelerating voltage from 5 kV to 4 kV, the penetration depth decreases by almost 0.2 microns. As organic material is composed low atomic number elements, so the interaction volume should be fairly deep, even at lower accelerating voltages.

Figure 11: Electron flight simulations were performed at 5 kV, 10 kV, and 4 kV to model the interaction volume of bulk organic material.

6. Colorization

Adobe Photoshop was used to colorize a few cool coffee bean photos.

Figure 12: The colorization of these SEM images adds a bit of fun to the SEM images.

7. Conclusions

Studying coffee beans with various microscopic techniques revealed very different microstructures of green and roasted beans. Unfortunately, no significant difference was observed between the two different single origin coffees. Nonetheless, coffee is comprised of a variety of interesting textures, which were highlighted with electron and light microscopy. Next time you enjoy a cup of coffee, I hope you can appreciate how cool those beans look up close. I know I will!


Thank you to Fuego Coffee Roasters for providing me with coffee bean samples for my project!

I would also like to thank Brian McIntyre for answering endless questions and always being available to help and my TA, Rakan, for helping me with the SEM labs. Thanks to my family for inspiring my love of coffee and to my husband, Josh, for always being excited about new coffee discoveries and for his many coffee connections!


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Hoffmann, J. The World Atlas of coffee; Firefly Books: Buffalo, NY, 2014.

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