Cells and extending perception: some tools of biology - 2

 Both field work and laboratory exercises involve imaging, especially if there's a blog involved. Fortunately, modern smartphones provide several camera options.

My smartphone is a Motorola Moto g Power with three cameras. There are two back cameras (the ones on the side opposite the screen), and one front camera (the one used for selfies).

My field kit (fits nicely into my backpack)

Life happens across all scales of a biome and imaging has to keep up with the scale 

The molecules that make up the basis of life are just regular compounds like salt (sodium chloride) and water extending up to huge molecules like proteins and genetic molecules. They exist at the nanometer scale. A nanometer is a thousandth of a micrometer, which is a thousandth of a millimeter, which is a thousandth of a meter. It's smaller than the wavelength of visible light, so we can't use a light microscope to see it. 

Electron wavelengths are on the order of 20 nanometers down to (under acceleration) picometers (a picometer is a thousandth of a nanometer). We can use electrons in electron microscopes to see molecules.

Pleolipoviral virion (HRPV-6)

Tatiana A. Demina, Hanna M. Oksanen

From Electron Microscope, Wikipedia article 

But electron microscopes are expensive and absolutely not portable so any image at the nanoscale here will be from public domain images.

I catch up at the micrometer scale. 

My smartphone, a Motorola Moto g Power, has three built in cameras. For most of my past photography, point-and-shoot did pretty much what I wanted but biology is requiring a little more ... finesse. So I'm taking a course in photography, a series of lectures by Marc Levoy, professor emeritus of computer science at Stanford University. (Digital Photography )  Early on he recommends avoiding phone cameras but for reasons of expense and portability, I ain't gonna. 

Actually, I am very impressed with the advances in phone cameras from my last to my current phone. 

There are many (!) camera apps available to optimize the cameras in smartphones. They work some different from professional cameras. To approximate the same control over images, they have to use some advanced algorithms to simulate them.

In addition to the camera app that came with the phone, a fairly no frills point-and-shoot digital camera with options in the settings menu, I selected three other general purpose apps and two for managing exterior cameras like camcorders and a bore scope.

Why collect camera apps? Because they each have their own strengths and weaknesses. Don't feel limited by my selection, but the ones I use are:

OpenCamera. By Mark Harman. A fairly unassuming camera, with a lot under the hood including a choice of metadata to a display as stamps on the photographs.

Proton, by Hinnka. This is a strong simulation of a professional DSLR down to dial selectors. Both it and the next offer extensive control of exposure, color, special effects, and style with in-camera editing of images 

ProShot, by Rise Up Games, is also an excellent simulation of a pro DSLR camera  I used ProShot for most of the photo micrographs in the first part of this blog (this is part 2).

Microscopy and photomicroscopy operate in the micrometer range, perfectly doable for visible light. Most small organisms, bacteria, protozoa, many medical parasites, molds and yeasts, fall into that range.

The micrometer is such a common unit in biology that it's often just shortened to "micron" and the nanometer is sometimes called a "millimicron" (less so than in the past).

Single cells are usually colorless which makes them hard to see with visible light so stains and other tricks (polarized light, fluorescence, dark field microscopy, etc ) are used to make them visible. Stains are dyes that attach to or dissolve in or react with certain parts of cells. For instance, lipid soluble dyes will preferentially color the lipid membranes of cells while water soluble dyes will go to the watery interiors. The indicators commonly used in analytical chemistry may dye different parts of cells that have different chemical properties differently. For instance, a pH indicator will dye acid and base elements different colors 

Even food colors will bring out the nuclei in cells.

Cheek epithelium cells

I have two clip-on microscopes as featured in the last part of this blog. The more powerful one will resolve cells but isn't quite strong enough to clearly view structures within the cells smaller than a nucleus or large vacuole.

The less powerful microscope is more portable and easier to use in the field but is fine for tiny details like grains of sand, small crystals, tiny flowers, small insects and other invertebrates.

The camera apps have functions that can sharpen microscopic images and enhance contrast.

Macrophotography involves close up photographs of detail, and usually operates in the millimeter range. Most smartphones today have at least a standard back camera and a camera with a macro lens. Some have wide field cameras. Mine doesn't but I do have a clip-on wide field kens 

On one of my treks into town, I noticed a mossy looking (actually not a moss but a succulent) plant covered spot of the ground. Interested in the tiny white flecks, I switched to my micro camera, got close and took this photograph.

Rattlesnake weed (Euphorbia albomarginata)

These tiny, exquisite blossoms were barely a millimeter across.

The first exposure I had to the idea of "bellyflowers" was from a documentary long ago by the Moody Institute of Science about researchers in Death Valley. In the desert (like where I now live), it's often a good survival trait to be small and close to the ground, so many desert flowers are produced by ground covers and are tiny 

"Standard" photography is also important in biology because the centimeter to decameter range is where we live. I saw this fellow on a trip back from town one day and he stayed long enough for me to get a picture.

Osprey

 The advantage of "regular" photography is that I almost always have my smartphone with me but I only have my photographic paraphernalia if I plan to have it.

I'm also impressed by the stabilization offered by current phone cameras. The trick of waiting until the shutter button has been poked and the camera motion has settled down is good, but my newest phone has OIS, "optical image stabilization". If I twitch in one direction when I press the shitter release, the camera senses it and twitches the camera kens in the opposite direction, canceling the blur 

Telephotography carries my photography into the range from here to as far as my eyes can see. Capturing images of skittish or dangerous animals from afar or surveying ecosystems is valuable in ecology and conservation 

Jupiter

Grackle in the tree top

Clip-on telephoto lenses are not expensive and are of fairly good quality. Mine is a Pusokei 22x telephoto lens .

The bird came out great.....Jupiter, not so much. Telephoto can only go so far in capturing astronomical images. For that, you need a telescope and that is outside my range for this blog. Biology, in general, though, goes on to the stars in it's search for answers to the questions of where life on Earth came from and if there might be other life in other parts of the universe and what it might be like. That is the purview of exobiology.

I was excited when I noticed that my last phone had "night vision". I figured "infrared camera" but was a little disappointed when I found that it wasn't. On the other hand, I've started fooling around with it on my new camera and am changing my mind.

Night vision has to have some light to work. I tried it in our pitch black garage and couldn't see anything, but given half a chance, it can use what light is available to produce some pretty awesome images 

It's a software adaptation of digital cameras. They take several quick photographs, superimpose them, and then clean up blurry edges. 

As macular degeneration has pretty much destroyed my night vision, I have found that I can use my phone's night vision to navigate dark dates.

It seems that most phone cameras are now equipped with night vision.

The banner for this blog was hand stitched but modern digital cameras have a feature called "panorama". You stand in one spot and rotate and your camera will nicely stitch the whole scene together for you.

Bitter Lakes National Wildlife Refuge

The Chihuahuan desert 

The other side of the smartphone camera is the video. Most phone cameras are also video cameras and, what's more, they have video editors 

I went out on a stormy night to capture about 2 minutes of distant lightning. The result was too long to insert into a Blogger blog so I trimmed it down some to get this.

Now, it's difficult to catch action precisely in a photograph. You can use apps like motion detectors to trigger a camera. Some cameras even come with motion detectors, but there is an easier way ....just make a video and extract what you want.

When reviewing the video above, I spotted a strike that I wanted a photograph of so I cut the following out and cleaned it up some.

This is the extracted scene but I felt like the blue made details a little harder to see so I shifted it a little more to the red to get this.

The most common admonition I've seen in courses on photography is "take lots of pictures". Much of photography is feeling. Volume gives you a chance to learn the features of your camera and a feeling for composition and, generally, what works 

I don't have Professor Levoy's objection to smartphone cameras so, whether you have a film or digital camera or a smartphone, go out and take lots of pictures!