Surprise: Catching bugs in rocks!

X-ray tomography is a powerful technique that allows us to see very tiny details inside a rock. However, the image acquisition is usually just a starting point for the image analysis. In order to get quantifiable information, one has to develop specific image processing algorithms. In the porous medium research, one of the most important processing step is the development of the task oriented image segmentation algorithm.

While trying our segmentation algorithm on a 3D image of a sedimentary rock, we found some curious piece of a former life! The “worm” you can see in the video is an orthoceras — an ancient mollusk that is often found in sediments.

This carbonate rock has been cored in the Miocene carbonate platform of Llucmajor, in Majorca. The rock has suffered a re-equilibration from aragonite to calcite (dissolution of aragonite and crystallization of calcite). This reaction led to the formation of porosity (grey parts of the picture). In this case the spatial distribution of the pores has been controlled  by the pre-existing structure of the rock. This process allowed the preservation of the shape of the fossil, even after re-equilibration and recrystallization into calcite. That is why we can see the orthoceras, although its skeleton has undergone chemical alteration.

Figure 1. This video is a series of 2D slices of a 3D volume. No orthoceras is actually swimming here

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One day of hard X-ray radiation

Most people understand geology as a science that deals mainly with large scale objects and processes, such as subduction zones and sedimentary basins. Nonetheless even the largest scale event can sometimes only be understood by looking at its tiny components. In fact, small scale processes such as dissolution and precipitation of rock-forming minerals together with other chemical reactions control what happens on a large scale.

There are many instrumental techniques to investigate objects at a small scale: different types of microscopy, spectroscopy and so on. One of the relatively new techniques developed in the 1970s is X-ray tomography. It is a nondestructive method, that allows reconstruction of 3D-structure of  an object.

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Fig 1. Radiogram of a hand. Bones are brighter because of higher X-ray absorption level.

How does this work? Perhaps you know how radiography works: X-rays emitted by a certain source penetrate the object of interest, for example your body, and interact with its matter. During the interaction, part of the X-rays are absorbed while another part reaches the photo-detector. Roughly speaking, the fraction of X-rays being absorbed depends on the density of the matter, for example bones absorb more X-rays than organs and skin. The part of the X-rays that reach the  detector produces a 2D projection image of the object — a radiogram.

Tomography uses a series of radiograms of the object, made from different view angles, and produces not a 2D but a 3D density map of the object. Both X-ray radiography and tomography are well known to the general public by their medical applications: radiography is used for detection of broken bones, and computed tomography (CT) is widely used for detection of tumors, but is also highly useful when geologists are looking at rocks.

In practice, tomography of rock samples can be done with lab-scale equipment (like in Karins post), which has a comparable size to the medical CT-scan. However, in order to see the tiniest details, a long exposition time is needed to produce a radiographic projection with high spatial resolution. It could take a whole day or even several days to make a full tomogram of a sample. Luckily, there is a way to shorten tomography acquisition time — to use more powerful X-ray sources!

The best X-ray sources available today are provided by synchrotrons. Usually it is hard to get working time on a synchrotron: there is a special application procedure (for which you have to write smart projects) and high competition between research groups. This summer our group got lucky and we got 24 hours of synchrotron time at the ESRF (European Synchrotron Radiation Facility) in Grenoble, France (Fig. 2).

Fig 2. View on the ESRF synchrotron from above. X-rays are delivered in beamlines distributed all along this huge ring (see how small the cars are!)

In the evening of the 7th of July, after the working day, we went to Grenoble for image acquisition of our rock samples. On arrival we were accommodated in guest houses on the ESRF campus. It was around a 5 minutes walk from the guest houses to the tomography beamline ID19 where we were working. The campus of ESRF is cozy, green, and surrounded by alpine mountains from all sides. It is full of trees and green grass with rabbits pasturing on it. There are bike tracks and bike parkings everywhere to go from one place to the other (look at the ring size on Fig. 2).

Fig 3. In the control room of the beamline
Fig 4. In the hutch, where you place your rock sample for analysis (the hutch walls are made of lead to protect people against radiation when the X-rays are switched on!)

The next day at 8 am we started our 24 hours shift at the ID19 beamline. It is a very long (145 m) line because it takes huge distances to focus X-rays to a tiny spot for analysis at high spatial resolution. Hence the building with a hutch is  located aside of the main ring. There were two rooms at our disposal: the experimental hutch itself and the control room with computers and other control equipment (Figs. 3 and 4).

People working at ESRF have a peculiar sense of humor. Computers in the anteroom are named quite usually (so typical computer names): Lysithea, Ganymedes, Callisto, and Siegfrid, but monitors that showed what was going on in the experimental hutch (that is closed when X-rays are on) are “Big brother 1”, “Big brother 2”, “Big brother 3” and “Big sister”. By the way, Big brother 1 was looking at the sample stage, so we could see the step motors moving the sample to put it in focus, and turning the sample during tomography.

Fig 5. Big brother 1 is watching our sample

From Montpellier, where our lab is, we brought 12 samples (natural dunite and peridotite samples from Oman and experimental olivine samples), 5 of which were imaged with two different resolutions. Resolutions were chosen such that we can image the whole sample with medium (0.65 µm) resolution and a subvolume of the sample with high resolution (0.16 µm).  Imaging with high resolution allow us to see smaller pores, cracks and inclusions, but the imaged volume gets smaller.Depending on the sample size it needed 2 to 4 scans of subparts to get a view of the whole sample. And one scan takes around 20 minutes, that is quite fast for a 3D image with a 0.65 µm resolution! So our schedule for these 24 hours was really tight, but we succeeded to get images of almost all our test samples.

Fig 6. 2D tomogram slice of a natural dunite sample

The visit to the ESRF allowed us to obtain almost 1 terabyte of high resolution 3D-images in only 24 hours. Use of synchrotron radiation is the only way to get such a huge amount of data in a short period of time compared to a conventional CT scanner. We are grateful to high-energy physics for providing such a tool. And not only physics, but also other fields of science such as chemistry and mathematics contribute to achievements and developments of new methods in geology.

By the way, these linkages to other fields of science is one more argument that geology is a science.