Images of cells preserved in stone

As a child, petrified wood captured my imagination. However, as an adult, when someone taught me to look at the fossil wood at a microscopic level, I was in awe. At that moment, I like to think that I shared a joy similar to what the famous scientist, Robert Hooke, must have experienced when he examined fossil wood structure using his microscope, the first person ever to do so. The development of digital cameras and microscopes has catalysed my interest in using both technologies to zoom in on fossil wood specimens. In this respect, the purpose of this article is to stimulate this same interest among collectors.

The building blocks of life

In the last paragraph of The Origin of Species, Charles Darwin (1809-1882) eloquently reflects on the common ancestry of life on Earth.

There is a grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.” (Darwin, 1859, p. 490)

Darwin recognised that there exists a continuity to life on Earth through his theory of natural selection. This same continuity is echoed in the work of the German physician, Rudolf Virchow (1821-1902). In his 1858 classic work, Die Cellularpathologie, Virchow enunciates an idea that would add a critical component to cell theory. The framework for cell theory had been suggested just 19 years earlier.

Mattias Jackob Schleiden (1804-1881), a German botanist, established that all plants are composed of cells. Theodor Schwann (1810-1882), a German physiologist, combined Schleiden’s work on plants with his own observations that all animals are composed of cells, to set out a cell theory published in his 1839 book, Microscopical Researches into the Accordance in the Structure and Growth of Animals and Plants (Schwann, 1839/1847, pp 186-215). Schwann and Schleiden’s cell theory proposed that the cell is the basic unit of structure and function for all life. They suggested cells arise and grow through a process not unlike cystal growth. The crystallisation process was hypothesised to occur either within or on the outside surface of cells. It is this nature of how cells arise that Virchow revised and corrected. He realised that cell division could account for cell reproduction.

Fig. 1. Palmoxylon Vascular Bundle 150x. Catahoula Formation, Louisiana, USA. Field of view 2mm wide. (Photo by Mike Viney.)

As Virchow wrote, “Wo eine Zelle entsteht, da muss ein Zelle vorausgegangen sein (Omnis cellula e cellula)…” (Virchow, 1859, p. 25; “Where a cell arises, it must have been preceded by a cell”). With his emphases in Latin that all cells arise from cells, Virchow added an important tenet to Schleiden and Schwann’s earlier work completing what many high school biology students learn as the cell theory to this day: all living things are made of cells, cells are the units of structure and function for life, and cells come only from pre-existing cells (Miller and Levine, 2010, p.191).

The cell doctrine or cell theory is a cornerstone of modern biology. In the light of Darwinian evolution, cell theory indicates common ancestry through cell division. Christian de Duve, in his book Life Evolving: Molecules, Mind, and Meaning, uses a simple thought experiment, modified here, to contemplate how life is connected through deep time at the cellular level (deDuve, 2002, pp. 9-10). In adult humans, each of the more than 1013 cells can be traced back to the original unicellular zygote. The zygote itself was the product of a sperm fertilising an egg cell. The sperm and egg cell can be traced back to the zygotes from which they arose. This simple thought experiment takes us back from one generation to the next. There exists an unbroken continuity to life, such that we can trace all of our cells back to the very first cells that existed on Earth. Thus, we can infer from the cell doctrine that all organisms can trace their cells back to the very first cell from which all life arose some 3.5bya.

Amazingly, the first use of the term ‘cell’ and an account of the microscopic structure of fossil wood occurred over 200 years before Virchow’s work. Robert Hooke (1635-1703), the English natural philosopher referred to above, christened the term cell in his book Micrographia to desribe “little boxes” making up a pattern not unlike an empty “honey-comb” within a thin section of cork examined through his microscope (Hooke, 1665, p. 113). The cells that Hooke observed were empty and dead; he did not realise the importance that these structures have to life. In fact, it was Anton von Leeuwenhoek (1632-1723), a Dutch scientist, who was the first person to see and illustrate single living cells using his microscope.

Fig. 2. Titea singularis cross-section taken in sunlight with Cannon PowerShot SD770 IS Digital ELPH 10.0 Mega Pixels, cropped and resized in Adobe Photoshop Elements 2.0. Specimen measures 23cm in diameter. (Photo by Mike Viney.)

Interestingly, just four pages before naming the basic unit for all life, Hooke became the first person to hypothesise how wood might become mineralised. Hooke was asked by the Royal Society to examine petrified wood using his microscope (Hooke, p. 107). He came to the conclusion that petrified wood exhibits the same structure as living wood and suggested a process by which living wood might turn into the nature of stone:

That this petify’d Wood having lain in some place where it was well soak’d with petrifying water (that is such a water as is well impregnated with stony and earthy particles) did by degrees separate, either by straining and filtration, or perhaps, by precipitation, cohesion or coagulation, abundance of stony particles from the permeating water, which stony particles, being by means of the fluid vehicle convey’d, not onely into the Microscopical pores, and so perfectly stoping them up, but also into the pores or interstitia, which may, perhaps, be even in the texture or schematisme of that part of the Wood, which, through the Microscope, appears most solid, do thereby so augment the weight of the wood, as to make it above three times heavier than water, and perhaps, six times as heavie as it was when wood.” (Hooke,1665, p. 109).

At the time Hooke wrote this description, many people were unsure about the nature of fossils. Hooke came to the conclusion that once-living trees turn to stone when mineral ladened water permeates the buried wood. Modern studies of artificial and natural silicification of wood support the idea that multiple pathways can lead to the formation of mineralised wood. However, the idea that mineral laden water is part of the process is incorporated into every model (Mustoe 2015; Dietrich, Viney, and Lampke 2015).

Since Hooke’s observation of fossil wood, there have been important advances in the techinques used to observe fossil wood. Henry Witham (1779-1844) was an Englishman who pioneered the use of thin sections to study the internal microstructure of fossil plants. In his groundbreaking work, Observations of Fossil Vegetables, Witham describes how to make transverse and longitudinal thin sections of fossil wood to observe cell structure (Witham, pp. 187-189). To this day, making thin sections in transverse, radial and tangential orientations remains a standard practice for identifying fossil wood types. Scanning electron microscopy (SEM) was first used extensively by Peter Buurman to examine cell structure in mineralised wood (Buurman, 1972). Fossil wood specimens prepared for thin section slides or SEM studies must be altered by cutting, cleaving and fracturing. These techniques require skills and equipment that may not be available to the average person. However, cell structure that is visible along natural surfaces of fossil specimens or those prepared by lapidarists can be observed and enjoyed using equipment that requires very little training and which is accessible to the average person. The good news for a collector is that no alteration to their treasured fossil is required.

Fig. 3. Titea singularis close-up of cross-section taken in sunlight with Cannon PowerShot SD770 IS Digital ELPH 10.0 Mega Pixels, cropped and resized in Adobe Photoshop Elements 2.0. Field of view 2.2cm wide. (Photo by Mike Viney.)

Mineralised dinosaur bone and plant material that exhibits cell structure provide opportunities to photograph and contemplate lifes’ fundamental building blocks preserved in stone. Robert Hooke and Anton von Leeuwenhoek established and popularised the study of life at a microscopic level with their discoveries and carefully made drawings. Just as Hooke and his colleagues discovered a new world with the advent of microscopy, contemporary students of fossil wood and dinosaur bone can explore this same world using affordable digital cameras and microscopes. In fact, we can use macrophotography combined with microphotography in a non-distructive way to zoom in on a specific area revealing what the unadided eye cannot observe.

Fig. 4. Titea singularis close-up of adventitious roots near a vascular cylinder taken with a Dino-Lite AD7013 MT 5.0 Mega Pixels. The image was processed using Adobe Photoshop CS6. Field of view 7.7mm wide. (Photo by Mike Viney.)

Macro to micro photography

Our first specimen is the silicified tree fern, Titea singularis, from the Permian age Pedra de Fogo Formation in Bieland, in the Maranhao Province of Brazil (Figs. 2, 3, 4 and 5).

The cross-section of this fern tree exhibits a central vascular cylinder surrounded by a thick root mantle (Fig. 2). As we zoom in to see the boundary between the vascular cylinder and the inner root mantle, individual adventitious roots with star-shaped centres become visible (Fig. 3).

Fig. 5. Single Titea singularis adventitious root taken with a Dino-Lite AD7013 MT 5.0 Mega Pixels. The image was processed using Adobe Photoshop CS6. Field of view 3mm wide. (Photo by Mike Viney.)

We switch to using the Dino-Lite AD7013 MT 5.0 MP for the last two figures (Figs. 3 and 4). Fig. 3 zooms in at 60x on several adventitious roots near the central vascular bundle. Roots are organs made of specialised tissues that are, in turn, made of specialised cells.

Fig. 6. Palmoxylon cross-section taken in sunlight with Cannon PowerShot SD770 IS Digital ELPH 10.0 Mega Pixels, cropped and resized in Adobe Photoshop Elements 2.0. Field of view 5.5cm wide. (Photo by Mike Viney.)
Fig. 7. Palmoxylon cross-section close-up taken in sunlight with Cannon PowerShot SD770 IS Digital ELPH 10.0 Mega Pixels, cropped and resized in Adobe Photoshop Elements 2.0. Field of view 3.6cm wide. (Photo by Mike Viney.)
Fig. 8. Palmoxylon cross-section close-up taken in sunlight with Cannon PowerShot SD770 IS Digital ELPH 10.0 Mega Pixels, cropped and resized in Adobe Photoshop Elements 2.0. Field of view 1.1cm wide. (Photo by Mike Viney.)

In Fig. 4, we zoom in on the cross section of a single adventitous root magnified 105 times. The root measures 2mm by 2.5mm in cross-section. The star-shaped structure represents xylem, a tissue specialised for water transport in plants. The xylem of ferns is composed of tube-shaped water conducting cells called tracheids and vessel members. The largest xylem cells making up the star-shaped centre in this image measure just under 100μm in diameter.

Fig. 9. Palmoxylon cross-section magnified at 115x of two vascular bundles taken with a Dino-Lite AD7013 MT 5.0 MP. Images were resized in Adobe Photoshop CS6. Field of view 3.2mm wide. (Photo by Mike Viney.)

As the adventitious root developed, primary xylem grew from five to nine different points. Metaxylem was then produced towards the centre forming the arms of the star. Phloem is a tissue specialised for the transport of food made from the photosynthetic tissues of plants. In this fern root, the phloem tissue developed between the arms of the star and included tube-shaped cells called sieve elements. Cortical tissue composed of parenchyma cells and air spaces surround the xylem and phloem tissues. A sheath made of sclerenchyma cell layers encloses the cortex providing strength. The root epidermis and cortical cells proliferated to produce a dense mass of parenchyma tissue that held the root zone together (Fig. 4; Taylor, Taylor, and Kings, 2009, p. 422).

Fig. 10. Palmoxylon cross-section magnified at 200x of one vascular bundle taken with a Dino-Lite AD7013 MT 5.0 MP. Images were resized in Adobe Photoshop CS6. Field of view 1.1mm wide. (Photo by Mike Viney.)

Titea singularis is a tree fern in the order Marattiales. This was the first modern group of ferns to evolve a structure that we think of as a real tree fern. All arborescent or tree-like vegetation represents plants with true roots, stems and leaves. Arborescent plant life evolved several basic trunk structures that can be recognised by the arrangement of strengthening elements including: solid woody cylinders, reinforced tube-like cylinders with hollow centers, and fibrous cylinders composed of isolated, intertwined elements. The tree fern evolved this last strategy for constructing an arborescent form.

Our second series of photos zooms in on a Palmoxylon specimen from the Oligocene age Catahoula Formation of Louisiana in the USA (Figs. 6, 7, 8, 9 and 10).

Palmoxylon fibre is composed of scattered vascular bundles embedded in a ground mass of parenchyma tissue. The vascular bundles give a spotted appearance to palm fibre in transverse section, a pattern familiar to many collectors (Fig. 6). Figs. 7 and 8 zoom in closer to the vascular bundles.

We transition to using a digital microscope for Fig. 9 that magnifies two vascular bundles at 115x. To the upper right, a circular-shaped fibrous bundle can be seen.

Fig. 11. Grassy Mountain silicified hardwood limb cut at an angle to a true cross-section taken in sunlight with Cannon PowerShot SD770 IS Digital ELPH 10.0 Mega Pixels, cropped and resized in Adobe Photoshop CS6. Polished surface is 6cm in diameter. (Photo by Mike Viney.)

In the final image of this series, we use the digital microscope to magnify 200 times a single vascular bundle (fibrovascular bundle) in our Palmoxylon specimen. This owl-shaped fibrovascular bundle measures 1,364μm tall and 850μm at its widest point (Fig. 10). Fibrovascular bundles of palm fibre are composed of vascular tissue reinforced by a cap of thick-walled sclerenchyma cells. The large water conducting xylem vessels or ‘eyes’ of our owl-shaped structure measure a little over 203μm in diameter and are accompanied by much smaller water conducting tracheids. Air spaces are sometimes found in the vascular tissue area as well.

Fig. 12. Close-up of Grassy Mountain hardwood limb showing the first few annual rings surrounding the pith taken in sunlight with Cannon PowerShot SD770 IS Digital ELPH 10.0 Mega Pixels, cropped and resized in Adobe Photoshop CS6. Field of view is 3.3cm in wide. (Photo by Mike Viney.)

The food conducting phloem tissue is found between the vessels and bundle cap or “body” of the owl-shaped vascular bundle. Sieve tube members associated with companion cells make up the phloem tissue. Sieve tube members transport the products of photosynthesis from the leaves to the rest of the plant. Companion cells are parenchyma cells that develop from the same mother cell as the sieve tube member. The companion cell helps transport materials in and out of the seive tube member. The ‘mouth’ of our owl-shaped vascular bundle is the space once occupied by phloem tissue. The phloem was not preserved in this vascular bundle. Compare this same area in Fig. 10 with the photo in Fig. 1 in which the phloem is partially preserved. The right vessel of Fig. 1 also exhibits a ladder-like structure, called a scalariform perforation plate, that connects one vessel member to another forming one long, continuous, water conducting tube. Vessels are found primarily in the xylem of flowering plants. However, they also appear in many fern taxa and in gymnosperms belonging to the order Gnetales (Carlquist and Schneider, 2001; Ickert-Bond and Renne, 2016)). The ‘body’ of our own-shaped vascular bundle is made of schlerenchyma cells that provide structural support for the palm fibre.

Fig. 13. Grassy Mountain silicified hardwood 20o to cross-section magnified at 60x taken with a Dino- Lite AD7013 MT 5.0 MP. Images were resized in Adobe Photoshop CS6. Field of view is 4.8mm wide. (Photo by Mike Viney.)

Palm trees are monocot angiosperms (flowering plants) that produce a fibrous trunk from only primary growth, so, like tree ferns, they do not produce true wood or increase in girth. The scattered vascular bundles making up the palm fibre and adventitious roots form a fibrous composite trunk, a strategy for constructing a tree form not unlike tree ferns using isolated intertwined elements.

Our third and final series of photos zooms in on an ash-like, ring porous Miocene-age hardwood tree from the Grassy Mountain area in Malheur County, Oregon (Figs. 11, 12 and 13). Silicification of wood can result in a range of preservation from the obliteration of cell structure to the retention of subcellular anatomy. Single specimens from Grassy Mountain in Oregon often display a range of preservation.

Fig. 11 shows the polished surface of a limb cut at a 20° angle to the transverse. The unaided eye can clearly identify this specimen as a ring porous hardwood. Fig. 12 zooms in on the first few annual rings surrounding the pith. In the bottom right, we can see that the preservation is more complete. However, the rings in the central part of the picture offer only partial preservation that produces intriguing effects. The vessels seem to be somewhat preserved with the surrounding tissue largely absent.

We use the digital microscope to zoom in on the annual rings in the final image (Fig. 13). At this magnification, we can clearly see that the incomplete preservation of the wood surrounding the vessels has left them as very prominent structures. The vessels stand out as golden rod-shaped structures that reveal their former tube-like nature. The golden colouration is the result of iron minerals deposited in the open pores of the vessels (Mustoe and Acosta, 2016, p. 25). Here we have the ‘ghosts’ of former water conducting cells. The transparent chalcedony surrounding the vessels impregnated with iron minerals produces an amasing contrast that allows us to see the structure of the vessels in three diminsions.

The ring porous hardwood specimen is a dicot angiosperm. Arborescent dicots posses stems with a central pith surrounded by secondary wood and bark. This evolutionary strategy is a good example of using a solid woody cylinder design for constructing an arborescent form.


The work of Robert Hooke and Anton von Leeuwenhoek inspire us to explore the world that cannot be seen with the unaided senses. Hooke’s classic book, Micrographia, published in 1655, was the first book to illustrate living organisms through microscopes.

Over 350 years have passed since its publication. If we accept that a generation is the time from the birth of a parent to the birth of a child and use 25 years as an average for this time, then we are seperated by 14 generations. Important paradigms have been established in biology since this time including Schleiden, Schwann and Virchow’s cell theory (1839/1858), Darwin’s theory of evolution by natural selection (1859), Mendel’s laws of inheritance (1865) and comparitive biochemistry (1940).

Digital macro and micro photograph is available to the people today, but we can also explore the microscopic world with the benefit of knowledge gained by scientists over the past 14 generations. I encourage the reader to explore cells preserved in stone to contemplate their past function and to wonder at the knowledge that every living being on this planet can trace its ancestry back to the very beginning of life on Earth through the unbroken process of cell division.

Techniques for macro to micro digital photography

For readers who are intested in the steps I used to photograph the fossil wood specimens, here is a brief explanation. When looking for specimens, you can use a 10x or 20x loupe. You may even find yourself choosing and cherishing specimens based on that which is invisible to the naked eye.

Step 1: I like to photograph fossil wood specimens outdoors with my Cannon PowerShot SD770 IS Digital ELPH 10.0 Mega Pixels in a shaded area against a white foam board. Specimens with polished surfaces require special attention as it is easy to pick up unwanted reflections. Multiple photos should be taken and examined to ensure a selection representing the highest quality image. I use Adobe Photoshop CS6 to change the background, adjusted to true colour, and crop.

Step 2: I use the Dino-Lite MS36B rigid table top boom stand to secure my Dino-Lite AD7013 MT 5.0 MP (Fig. 14). I use the microscope for finding structure to study and photograph and take images at multiple magnifications. A microscope micrometer calibration glass slide can be used for calibrating the microscope measuring tool to determine structural dimensions. The digital microscope uses LED lighting, so colour adjustments using Adobe Photoshop are often necessary. I find gamma correction, levels, hue and saturation adjustments the most helpful.

Step 3: Once the microscopic images are taken, it is time to move back to the digital camera. I use the digital camera to take close-up images of the area in which the microscopic images were taken.

Step 4: You can now arrange your images to help the eye track a particular area on a fossil specimen from a macroscopic to microscopic view.

Fig. 14. Dino-Lite MS36B rigid table top boom stand used to secure the Dino-Lite AD7013 MT 5.0 MP. (Photo by Mike Viney.)


I would like to dedicate this paper to my father, Wayne Viney, who took me on wonderful excursions to petrified forests as a child. I would also like to thank George Mustoe, Don Viney, Jim Mills and Alex Brandl for their helpful comments.

About the author

Mike Viney enjoyed teaching science in the Ft. Collins, Colorado public school system for 30 years. He has published articles in the IAWA Journal, Geosciences, Rocks and Minerals, The American Biology Teacher and The Midwest Quarterly, with a special interest in petrified wood. He currently works as a teacher-in-residence in the College of Natural Sciences Education and Outreach Center at Colorado State Universityand maintains an onine museum dedicated to archiving information about petrified wood, which can be seen at:


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Carlquist, S. and E. L. Schneider  2001.  Vessels in Ferns:  Structural, ecological, and evolutionary significance.  American Journal of Botany 88(1): 1-13.

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De Duve, C. 2002. Life evolving: Molecules, mind, and meaning. New York: Oxford University Press.

Dietrich, D., M. Viney and T. Lampke 2015. Petrifactions and wood-templated ceramics: Comparisons between natural and artificial silicification. IAWA Journal 36 (2): 167-85.

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Mustoe, G. 2015. Late tertiary petrified wood from Nevada, USA: Evidence of multiple silicification pathways. Geosciences 5 (4): 286-309.

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Schwann, T. 1847. Microscopical researches into the accordance in the structure and growth of animals and plants (H. Smith, Trans.). London: Sydenham Society. (Original work published 1839).

Taylor, T. N., E. L. Taylor, and M. Krings 2009. Paleobotany: The biology and evolution of fossil plants [2nd Ed]. San Diego: Academic Press.

Virchow, R. 1859. Die cellularpathologie in ihrer begründug auf physiologische und pathologische gewebelehre [2nd Edition]. Zwanzig Vorlesungen, gehalten während der Monate Feruar, März und April 1858 im pathologischen Institute zu Berlin. Berlin: Verlag von August Hirschwald.

Witham, H. 1831. Observations of fossil vegetables, accompanied by representations of their interanal structure as seen through the microscope. The Edinburgh Journal of Science 8: pp 183-189.

 Mike Viney (UK)

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