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!

 

Biology resources

There have been many changes in science curricula since I was in school. Most of the stuff back then was descriptive. Physics was more structural mechanics. Now there's a lot more subatomic stuff and cosmology. Chemistry was more about how the elements and their compounds looked and behaved. Now, there's a lot more mathematics....calculating yields and such, and more about what happens at the atomic level.

Biology.....they used to talk about cells, organization of bodies, cell division, and the tree of life (organization of species) but now the tree of life is a different tree. It used to be based on observable similarities between different plants and animals ( and there were only two kingdoms.....plants and animals) but now it's based on similarities between their DNA which reflects how living things are related through evolutionary development.

I'm watching the lectures from the MIT introductory course in biology. They start with molecular chemistry then briefly touch on cellular organization. Then they spend a lot of time on how genetic materials translate into proteins. They end up with considerable amounts of medical biology....stem cells, immunology, cancer...

If you want a deep introduction, the MIT course is at https://ocw.mit.edu/courses/7-016-introductory-biology-fall-2018 .

As usual, there's a lot out there. Let's see. What's in my tool chest? It's nice to have all my tools in one place so I try to consolidate as much as I can on my phone. Beside the general purpose apps I've been using (the calculators, sensor apps, and general purpose tools) there are some useful programs specifically oriented toward biology.

A major emphasis on biology is imaging. Biological entities range from submicroscopic viruses (we won't be looking at them since it would take some very expensive and very non-portable equipment, like electron microscopes. We might do some Internet safaris, though ) to whole forests of Aspen trees (an Aspen Grove may well be a single organism.) The parts of organisms are important also, from the molecules that power them (again, too small for us to actually see) to individual cells, to whole ecosystems.

I walked down to Dry Creek Park the other day to take some pictures. I was a bit disappointed. We're in a period of cooling and frequent storms and everything was quiet......no birds or squirrels in sight. The creek was flowing so that microorganisms are washing downstream.....no stagnant water there to play with and the cold water encourages them to go dormant. Still, I got a few pictures.

This ash tree was still green. The grass in my lawn looks like it's getting ready for fall but the trees haven't quite caught on yet 

I have some identification books stored in my phone but I used Google Lens to check my identification. Once you have an image in Google Pictures, a poke at the Lens button  will search the Internet for a similar image. There are similar apps available for different phones and computers.

I can zoom in with my phone camera to about eight times (8x) but notice that, in the photos of an ash leaf above, the more I zoom, the blurrier the picture is. In an electronic camera, the number of light sensitive elements (pixels) there are in the CCD (charge-coupled device chip...the part of the electronic camera that replaced the film in older cameras and changes patterns of light into electrical signals)  is constant. Since the picture resolution is determined by the number of pixels available, that's constant, too. Resolution is usually specified as the number of pixels on the CCD. In my phone, the front camera ( the one on the same side as the user....the "selfie camera") has 16 mega pixels ("mega"="million") and the back camera (the one I usually use) has 50 megapixels. My phone actually has three lenses that focus the light on different sections of the CCD.

Imaging is important in biology because there is so much detail that matters that is hard or impossible to see. You probably got to use laboratory microscopes in school that magnified to over a thousand times. Field microscopes are usually lower powered for a couple of reasons. Portability is an obvious virtue in a microscope that will be in the field. Often, though, samples are brought back to the laboratory for examination. Most laboratory microscopes used to look at field samples trade resolution for field of view. They're usually bulkier than laboratory microscopes and have two eyepieces ("stereoscopic microscopes") to enhance the dimensionality of the image.

I determined the optical characteristics of my camera here:

http://adventuringbcc.blogspot.com/2021/05/i-am-camera.html

I have a very portable clip-on microscope for my phone that is quite serviceable in the field. It's rated at 60x magnification with more magnification possible with zoom.

That's sorta an advertising misinformation. You can get larger pictures with electronic zoom but the resolution remains the same so a zoomed picture will be blurry. Still, you have to zoom to get rid of the "tunnel" effect in the top picture above. I can get a fairly reasonable image at around 80 or 90x. The maximum around 120x is pretty poor.

There are ways to improve a blurry image. Most phone cameras have editing features that allow you to play around with a photo image. "Sharpen" is one that can improve an enlarged image. It senses borders in the image and averages the values of the pixels around the border, replacing the pixels on the border with the averages. It's an illusory improvement that can miss some important details, but with some skill, a photographer can get some decent photomicrographs like that. There are also "magnifying glass" apps that have the sharpen feature built in.

The bottom line is that if you want really good photomicrographs, use optical magnification instead of electronic (zoom) magnification.

I also have a clip-on front camera microscope that has a stage like laboratory microscopes and uses transmitted light (my other clip-on has a built in light that reflects light off the sample). Actually, I got that microscope with the "Cells" Science Wiz kit. 

Here is some stuff I found in Little Dry Creek. It's not very impressive since the water flow was pretty high and the water was cold. All the little beasties were hiding for the autumn. The magnification is about the same - around 60x.

Big things and distance views are important in biology field work also. My Carson telephoto lens will give me a moderate field, zoomable, magnification of six times. That's about perfect for wildlife photography. You want to be far enough from wildlife to avoid spooking them or from being mauled or trampled by them.

At telephoto distances, tiny movements of the camera can blur the image so a camera tripod with a phone adapter is necessary. For wildlife photography the tripod needs to be set up in a location that's as obsured as possible and a portable blind is useful. On the day I was taking photos for this blog, everyone was at home asleep. Winter does that sometimes. Anyway ....leaves.

And, of course, phone cameras usually have a video mode that lets you take movies of, say, wildlife behavior.

Microscopy requires things like stains, slides, droppers, knives to slice samples. There are good kits that aren't expensive. I have a couple from Home Science Tools and the Cells kit from Science Wiz.

A particularly useful tool is a microtome that lets you make very thin slices of materials to put on microscope slides. You can pay as much as you want for one. Mine:

an economy model, cost less than $20 and came with a razor blade. It's basically a flat plate with a screw piston that pushes the sample by tiny increments up through the center of the plate so it can be sliced off. Table models can run to four figures but you don't want a table models in your backpack, anyway.

I won't be doing any high powered microscopy but it can be pretty fascinating. You can equip yourself for considerably less than a thousand dollars (or more) and a good source is American Science and Surplus. Avoid the cheap kiddie microscopes. The affordable ones have poor, plastic optics and are not worth the savings. A good option, around $100 is the Celestron line of digital microscopes. 

There's life out there (even in the winter.) so go out and study it!