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.