3D print of a biofilm from confocal microscopy data

Scott Chimileski animalcule 3D print

A 500x 3D print of a section of mature Haloferax volcanii biofilm

3D printers may soon be common household items. Or at least – hopefully  – common laboratory items. I recently converted confocal data from a biofilm into a 3D print.

The biofilm print features one of the larger tower structures I have observed for this archaeal species, Haloferax volcanii, which lives at high salt concentrations. A 3D reconstruction of the same image stack was recently published in an article in BMC Biology. The data was collected in 2012 at the Center for Biofilm Engineering at Montana State University.     

Scott Chimileski animalcule Leeuwenhoek biofilm 3D print

At 7.5 cm in height, the print is five hundred times larger than the actual size of the biofilm. This would be equivalent to making a print of a person taller than the empire state building.

I chose to print in sandstone because it is one of the more economical materials. It also has a nice natural feel, unlike plastic. My second choice was ceramic. However, each material comes with its own practical guidelines: ceramic is both more delicate (as you might expect) and preserves less detail.

Scott Chimileski Haloferax volcanii biofilm 3D print

Each 3D model build depends on the specific properties of the printed material.

There is a great potential for this sort of work. I think that any form of scientific data that has a three dimensional element can and should be 3D printed. 3D glasses allow a virtual sense of three dimensions by playing a kind of trick on human stereovision. But this is not an intuitive experience. Having something physical to see and touch is ultimately the best way to appreciate and understand anything in 3D – especially something invisible.


A video showing the model used to create the 3D print:




Into the swarm – a microbiologist on assignment in the world’s largest kayak raft

Resident Adirondack photographer Nancy Battaglia flew overhead in a floatplane to get this amazing shot.

A few weeks ago I headed up to the Adirondack mountains in New York on a Saturday to be part of the truly unique One Square Mile of Hope event: a Guinness World Record attempt to create the largest floating kayak complex.  When I heard about this event two days before it happened, I instantly knew I had to drop everything and go.

Why would I need to be one of thousands of kayaks during this seemingly bizarre event (on a rainy day, I might add)?  Well, I do like kayaking. And, I’ll definitely take any excuse to head up to the Adirondacks.  Beyond this, the event raised over $100,000 for breast cancer research – I was certainly happy to contribute.


The movement of E. coli cells within a swarm. Darnton et al. 2010. Dynamics of Bacterial Swarming. Biophysics Journal. Volume 98, Issue 10: 2082–2090. See also: Berg Lab at Harvard University, Rowland Institute.

However, none of these were the number one reason for my participation.  In reality, I was (I can only imagine), the only microbiologist-on-assignment in that swarm of kayaks that day.

One aspect of microbiology that particularly interests me is the development of collective behaviors. When I saw aerial photographs of similar events in the past, I knew that there is probably no better way on the planet to experience what it would be like to be inside a swarm of microbial cells. The kayaks themselves, long and rod-shaped, are like the cells. They aggregate and line-up in a way analogous to micrographs I have seen of swarming bacteria.

Scott Chimileski Swarming Animalcule

Feeling like an individual cell in a swarm of bacteria: the moment when we all raise our paddles as we (hoped at that time to) beat the record!

Like a swarm of bacteria, this kayak raft also moved together. As the assemblage gained in size towards the final count at noon, everyone within the swarm was concerned that we would run adrift into a nearby island. The rules state that every kayak must contact an adjacent boat via hand contact alone, a transient bond not unlike those between swarming bacteria, and that the raft cannot touch the bottom.

Once the count was finished, we could then all raise our paddles at once – creating a collective sail that further accentuated the movement of the swarm.

So, did we beat the record? Yes! Though it was steadily raining and quite cool, there were 3,150 kayaks in that swarm! People came from 31 states and from several foreign countries to surpass the previous record by quite a large margin.

Check out how it is that they counted all these kayaks as well. Someone literally had to sit with an enlarged photo and count them one by one, marking them with tacks! Excellent work by all from the Kiwanis Club of the Central Adirondacks and One Square Mile of Hope who organized the event!

One Square Mile of Hope

More kayak-mounted GoPro photos and time-lapse videos from inside the swarm to follow!

Trapped in a salt crystal

Scott Chimileski animalcule haloarchaea haloferax volcanii

A colossal salt temple among microbes.

While testing a new camera, I recently collected some photographs of the haloarchaeon Haloferax volcanii within salt crystals that had formed in a 6 well culture dish. These formations are halite or rock salt, a mineralized form of salt left behind as water evaporates.


High levels of salt are toxic to most forms of life. For example, seawater has a salt concentration between 3% and 4% and human blood contains just 0.9% salt. Many microbial species including some bacteria and algae live at elevated salt concentrations, within brines from 5% to about 15% salt. But there is only one microbial group that tolerates and in fact often thrives at very high salt concentrations: the haloarchaea.

Scott Chimileski animalcule haloarchaea haloferax volcanii

Haloferax volcanii cells become trapped as salt crystals precipitate within culture wells.

Haloarchaea are found in bodies of water like the Dead Sea and the Great Salt Lake, in sub-terrain salt deposits,  within evaporation ponds at sea salt production facilities, and at other sites where salt concentrations exceed 20% or even 30%.  Even when all of the water evaporates, leaving behind only precipitated halite, haloarchaeal cells often remain living, held up in fluid inclusions within the salt crystals themselves.  Remarkably, a recent culture-independent study supported earlier culture based isolation experiments suggesting that haloarchaeal species can be recovered from ancient halite deposits, persisting for thousands or even millions of years.


More of Hfx. volcanii with salt crystals:


Scott Chimileski animalcule haloarchaea haloferax volcanii


Haloferax haloarchaea halite animalcule Scott Chimileski


Experiments with photogrammetry

A stone bear from New Mexico with blue “life-lines.”

A Native American stone bear from New Mexico.

I have been experimenting with photogrammetry lately : a computational method for producing 3D models based on photographs taken from many angles.

Scott Chimileski bear

The blue lifelines are one of my favorite features.

This stone bear figure from New Mexico is about 2.5 inches long and is a great semi-complex small object to practice photogrammetry. I have been using a Canon 6D with a 50 mm macro lens to capture images. To begin, you simply need to take a series of photos from many angles and load them into the software. Overall, the software works really well automatically, but I have noticed that some optimization is definitely required to create a final accurate model.


The bear has been successfully converted into a 3D model, shown here in mesh format.

Beyond making sure you have covered all angles of the subject (and that all photos are similarly exposed, etc.), it is important to consider the surface the object rests on. Newspaper or something similar provides reference points that make it easier for the software to stitch all of the photographs together.  I was also able to make models of small objects by placing them across terrain lines on a map.

Scott Chimileski bear photogrammetry

The photogrammetry software (Autodesk 123D Catch) calculates where in space each photo was taken.

After loading your images, it takes a few minutes for the program to run and build the model. If all went well (it is possible to encounter errors if there is a problem with the photos), the model is loaded and can be manipulated and refined in 3D dimensions. If you find any obvious problems you can manually stitch points in the photos together at this point as well.

This is a fascinating technique. I have a feeling this bear is just the beginning of quite a bit of photogrammetry I will be doing in the future.

Hunting for microbes while exploring Block Island’s salt marsh ecosystems


Scott Chimileski Block Island Rose hip

Rose hip flowers can be found throughout Block Island’s dunes.

I have been going on vacation on Block Island every summer since I was a child. Block Island is small, only a few miles wide, and sits just 12 miles off of the coast of Rhode Island. Despite its size, the island is a robust habitat for many plants and animals, surrounded by a coastal marine ecosystem, dotted with over 300 freshwater ponds, and innervated by a system of brackish marshland.


Looking down at the bottom of the salt marsh.

I have spent over 6 months of my life here combined, but every time I get off the ferry, and I begin to explore the island’s various habitats, I have a renewed sense of wonder.  One of the first things you see and hear are the birds. The island is an oasis for rare birds and they are everywhere, ducking in and out of the dense shrub-filled landscape. They seem especially happy, most of the time blasting higher with 3 or 4 wing beats, and then free falling, over and over again as they hunt for bugs. There are also beautiful bright rose hip flowers, countless odd and colorful insect species, and of course purple starfish and marine creatures of all kinds.

Scott Chimleski Block Island

Underwater photography in the Great Salt Pond.

But this year I want to look into these ecosystems a bit further. I am intrigued by the unseen microbial layer at the base of every ecosystem. What do the microbes of Block Island soil, water and air look like?

Scott Chimileski

Colonies formed from salt marsh mud.

Well, here is a quick survey. These colonies appeared after two days at room temperature. The plate was inoculated with a sample of marsh mud I collected while kayaking with my sister along the edge of the salt marshes of Great Salt Pond. Beneath the kelp, the sediment at the bottom was dense and littered with seashells.

Scott Chimileski

An unseen universe of microbes. The side of a rock removed from the salt marsh mud. My camera is collecting an underwater time-lapse sequence in the background.

Of course, this is mere glimpse into the microbial diversity of this sample.  But it is beautiful nonetheless.  After every corner that we kayaked around there was a heron stalking through ankle deep water, appearing truly like the dinosaurs of this land.  I thought to myself, how large is this heron, and how small the millions of microbes that themselves stalk the mud beneath the heron’s feet. What amazing dimensions of life layer our visible world.

The colors of the microbial world: bright pink

Scott Chimileski

A pink Vibrio species.

This bright pink species was recently isolated by undergraduate student Stephanie Morgan of the Stage College of Florida for the Small World Initiative microbe hunting course. I talked to Stephanie at her poster at the 2014 ASM General Meeting (she did an excellent job!), and I had also seen some of her posts of this isolate on the Small World Initiative Facebook page.

Stephanie’s 16S rDNA data suggest this is a Vibrio species, and if you know about the Small World Initiative, you might guess that this isolate produces antimicrobials in addition to the stunning pink color, and it does! It is also important to keep in mind that in some pigment producing species, the pigment itself has antimicrobial properties. In other words, the observed color and antibiosis may be caused by the same chemical.

Scott Chimileski

All’s fair in love and war. Pink Vibrio species produces a potent antimicrobial compound.

In the above photo, also from Stephanie Morgan’s work, the pink Vibrio isolate on the left has produced an antimicrobial compound (or several compounds) effective against many bacterial species tested, including the Staphylococcus epidermidis overlay shown here.

The isolate on the far right is also interesting. It appears this isolate has an ability to spread across the agar surface, possibility by swarming.  Notice the finer structure at the leading edge of each branch.

Let the science draw your eye, the art exact wonder

Scott Chimileski Smithsonian great horned owl

In 1996 my dad was directing the move of the Library at the Smithsonian National Museum of Natural History in Washington, D.C. My dad would always talk about the moves his company was doing in terms of miles of books. The Smithsonian was merging their collections, and ten miles of books had to be carefully moved–a job that would require a six week business trip. I was twelve at the time, and my brother and sister were ten and nine. Luckily for us, it was summer and we would be going this time, at least for one long weekend. What could be more exciting? The three of us, let lose, hanging out in the museum while my dad was working.

After the drive down from Connecticut, my dad showed us the area he would be working out  of, introduced us to a bunch of people he was working with, and took us through the Natural History Museum. After that, we were on our own. We walked through the long hallways with high walls, in and out of exhibits, even sneaking into a back hallway or two, and would meet up with my dad at lunchtime.

One particular memory stands out in my mind: the “Eyes on Science, Illustrating Natural History” interactive exhibit that my sister and I went to one morning.  We spent hours, that seemed like days, in this one room with long tables, bright lights, and 3D models of animals, filled with paper and color pencils of all kinds. My sister and I drew bumble bee’s. Her and I remember working hard on the fuzzy legs.  These many hairs on the bee’s appendages you might never see as it flies by, but become a main feature under high magnification. We were completely focused, recreating these creatures on paper the best that we could.  At the end, we both won a poster with an illustrated owl for doing well in the workshop, something that we felt truly proud of, a big honor for a kid! My parents had them laminated on foam board, and to this day in every place that I live it is one of the first posters I hang.

Below a watercolor Great Horned Owl painted by an artist named J.C. Anderson, with intricate brush stokes, and the perfect amount oranges and yellows, is a four line phrase: “Let the science draw your eye, the art exact wonder.” For me, it is a memory not only of this childhood trip with my brother and sister, but of one of the first times I came to appreciate that art and science are complementary, mixable human endeavors–not ways of thinking that come from unconnected parts of the brain.

Smithsonian owl JC Anderson

As humans, we are tuned to perceive color and aesthetic beauty, to feel awe, to sense grandeur, to declare magnificence. Our minds are driven by pattern and visual information, just as a bear or bloodhound is driven by scent. Each and every time I look at the owl, I am drawn into the eyes. I know the owl’s eyes are stunning examples of evolved organs of vision–made of millions of specialized photoreceptor cells, developed in the embryo with unimaginable precision, arranged exquisitely to capture light . But I was not yet a scientist the first time these eyes captured my imagination. The true measure of art is that everyone can appreciate and feel it’s power. There is no greater medium to express and share science, to attract people young and old to see a part of the nature that unites every living organism on Earth.

A drop of seawater


I came across this image of single drop of seawater magnified twenty-five times from photographer David Littschwager.

This is a stunning example of Leeuwenhook’s world of animalcules. Visible within this one field of view are true animals such as crab larva, fish eggs and copepods, as well as diatom algae, and microbial species like cyanobacteria (orange spiral-shaped cells) and countless others too small to see.

This image certainly makes you rethink the word plankton. All of this endless diversity held within in a single familiar word.

David Littschwager was also the photographer for the National Geographic feature article “Within One Cubic Foot,” written by E.O. Wilison in 2010.

Biofilm simulation series: QS+ and EPS+ cells

Nadell et al. 2008D Nadell, Carey; B Xavier, João; A Levin, Simon; R Foster, Kevin (2008): The Evolution of Quorum Sensing in Bacterial Biofilms. Video_S1.mov.PLOS Biology. 10.1371/journal.pbio.0060014.sv001.

If biofilm formation is simulated beginning with a mixed population of quorum sensing  sensitive (QS+) and extracellular matrix producing (EPS+) cells, as autoducer levels rise (shown as blue gradations from below) above a critical threshold, QS+ cells stop producing matrix and shift their metabolism towards biomass production.  This leads to bursts of growth in cells exposed to maximum nutrient levels at the top of tower structures during the later stages of biofilm development.