Saturday, February 13, 2016

Paleontological Research Tips III: a complete idiot's guide to taking decent specimen photographs

Other posts in this series:

Paleontological Research Tips I: field notes for amateurs and professionals alike

Paleontological Research Tips II: field notes, continued 

Paleontological Research Tips IV: the art and science of maintaining a research notebook

Paleontological Research Tips V: manuscript writing, research productivity, peer review, and more

Here's the third installment of my series on paleontological research tips! This one is on specimen photography. It took me years to learn all this crap, picking up tips here and there from various sources, but the sheer majority of this was learned from my Ph.D. adviser R. Ewan Fordyce who is an unusually talented and skilled photographer. Ewan passes down much of his knowledge to his students, and we try to pick up as much of it as possible. Some paleontologists don't worry enough about taking and publishing good photographs, whereas others worry too much - photography can seem daunting, but it's OK - we're all here to repent and better ourselves through learning.

A very valuable skill to have as a paleontologist - and many scientists in general - is the ability to take high quality photographs that are acceptable for publication. Evidently, judging from the figures of many published papers I've read, I see that there is quite a lot of room for improvement. As per usual I won't name any names, and rather than pretend that I was born perfect and have not learned anything, I'll go ahead and make fun of some of my earlier published figures before I learned what I know about photography now. So, before I go into the nitty gritty, let's look at a couple of figures with several photographs each and critique what we can see.

Here's a shining example of a published figure I'm not very proud of - Boessenecker 2013: J. Paleo.

The two examples here are a figure I'm not so proud of, and another which I find to be one of my most visually satisfying figures. The first figure is from my J. Paleo paper on barnacle encrusted sea lion bones from Oregon, one of my first post-master's degree manuscripts which had a bit of a tortured review history, and I had taken all of the photos in fall of 2011. I started attempting (notice the word choice!) to publish the paper in summer 2012 when I was in NZ (northern, not austral summer) - which meant that I could not re-take the photos. I was beginning to learn at that point, and new that the photos weren't great, but had no idea when I'd be able to go back to UCMP at Berkeley where the fossils were. Even the reviewers complained about the photos. The lighting and contrast is a bit different, with the dorsal views having much higher contrast and being somewhat sharper; part 4 is washed out and mostly out of focus, and the same can be argued for part 3; parts 1 and 2 look fine. In part 5, the transverse processes are out of focus; part 6 is almost entirely in focus, but washed out. These photos were shot hand-held under direct sunlight, hence the 1) fine scale fuzziness and 2) extreme contrast.

And a figure with much, much better lighting, contrast, focus, and detail: the holotype periotic of Tohoraata raekohao. From Boessenecker and Fordyce 2015: Papers in Palaeontology.

The next figure is one I'm much more proud of - the periotic (inner ear bone) of the eomysticetid Tohoraata raekohao, derived from the first chapter of my Ph.D. thesis at University of Otago. This is not the published figure, but rather the super-dense and overly chaotic figure at the time of initial submission. Ignoring the anatomical labels written in the manner of a crazy person's living room wall manifesto, the photos are quite nice. All of them are consistent in lighting, contrast, lighting direction, and clarity. Everything is in focus - which is a bit of an impossibility for some lenses, but there is an advanced method to take care of that which I'll discuss below (see Advanced tips: focus stacking). In general, I can't point out anything glaringly obvious that's bad with this one, and am overall quite pleased. I did, after all, have to get my Ph.D. adviser R. Ewan Fordyce - well known in the field for painstakingly taking incredibly good photographs - to give me the OK to publish these images. These images were shot with 1) ammonium chloride coating, 2) focus-stacking for continuous focus, 3) soft lighting, 4) under manual setting with correct exposure set, and 5) on a camera stand.

My personal photography kit: yes, I bring all this crap with me to every museum visit. It's a pain, but it permits me maximum flexibility. Large camera tripod, medium tripod for LED lamp, tiny tripod, LED lamp, manual shutter release, camera body, short zoom, telephoto zoom lens, and of course a scale bar!

An example of my basic setup: camera tripod, fossil/scale bar on a white background, and the LED lamp positioned at upper left of photo.

Basic tips 1: the camera

I'll get this out of the way at the start: sure, you might be capable of taking decent photographs with a point and shoot or a smartphone, but for the purposes of this post I'm going to be talking about real cameras that have all sorts of scary knobs and dials with numbers on them. I'm talking about DSLR cameras - digital single lens reflex camera. I've met many people who buy these cameras, which often cost 400-500 us$ at the cheapest, and leave the camera setting on auto (the green box on the dial), and taking hundreds of crap photos for every good photo - wondering why they spent so damn much on the camera. You can treat an expensive DSLR like an overpriced point and shoot camera, but it's a bit like buying an armored humvee with a machine gun port on the roof to go grocery shopping and drop the girls off at soccer practice. So, if you want to take pictures with a smartphone or a crappy point and shoot, be my guest - but you won't be able to use many of the tips below, so go away.

Actually, that's not entirely true: smartphones and point and shoot cameras do have their uses, and owing to their smaller pricetag, are ideally suited towards field photography. Landscape photos out in nature (under regular daytime lighting) are easy to take and smartphones give you the option of panoramic panning photos. Because field photos are relatively easy, we're basically going to ignore them and mostly discuss close-up photographs of specimens.

DSLRs are pricey, but essentially anything where you can use a manual setting and change ISO, aperture (aka F-stop), and shutter speed is desirable. On smartphones/point and shoots only automatic settings are generally possible and the camera does it automatically for you. The camera is dumb; don't let it make decisions for you. I've got a relatively basic Canon Rebel EOS, but have used Nikon D1200, D700, and a D90 during my Ph.D. 

Basic tips 2: the lens

I'll admit I'm not that much of an expert on lenses, so this will be brief. Most cameras come with a standard 55-85 mm zoom lens; I've got a decent lens that came with an old film camera that took a swim in Monterey bay during fieldwork, which killed the camera but not the lens - and the lens is still happily clicking away on my current DSLR. Zoom lenses are great: the width of the photo can be modified, as can focus, but generally speaking the image quality is somewhat lower than a fixed focal length AKA prime lens. Prime lenses produce higher quality images, have a wider aperture (more on this below), and are generally lighter in weight as they have fewer internal lenses and working parts. The rub is that the focal length is fixed, meaning that if you are standing X feet away and cannot fit everything into frame, you cannot simply zoom out and either need to back away from the subject or swap with a different lens.

With prime lenses, the lower the number the shorter the lens and the wider the field of view; a standard prime lens is 50 mm, whereas a telephoto is 135mm, and a wide or extra wide angle lens is 34-14 mm (respectively). The shorter the prime lens, the greater the distortion (wide angle and extra wide approach a fish-eye lens), whereas minimal distortion is present in standard, telephoto, or super telephoto lenses. Here's the other rub: prime lenses are expensive, and if taking photos of a sporting event, it can be a pain in the ass to switch lenses. Luckily, fossils are not exactly fast-moving, so if well-funded, that's not really a problem.

Don't have a lot of money? Me neither! Zoom lenses work just fine and I've done a side-by-side comparison of photography using my cheap DSLR with a zoom lens, using the same lighting setup, and switching it out with a Nikon D90 with expensive prime lenses and the results are quite favorable. I still like the results with the expensive camera slightly more, but in general most would be hard-pressed to actually tell the difference. One last note: the limiting factor for taking good photos will be the lens, not the camera body. If you've got an expensive camera body with shit lenses, you will take photos that look crappier than an expensive high quality lens on a shit camera body.

A super handy chart showing what different aperture (f-stop), shutterspeed, and ISO settings mean for photos, put together by Daniel Peters.

 Basic tips 3: exposure

So you've got a DSLR and some kind of lens. Just put it on auto and click away, right? No! Please don't. You've got a state of the art piece of technology in your hands, and it is not that difficult to learn how to use it properly! The most important thing to learn is exposure - how to juggle different settings in order to take a photo that is at optimal exposure. First, when you look into the viewfinder you'll see a little bar with a zero in the middle and tick marks for -2, -1, +1, and +2. Exposure is essentially how much light is coming into the camera; the camera is set so that zero is optimal exposure, +1 or +2 is overexposed (too much light), and -1 or -2 is underexposed (too little light). "Ok great, let's just press a button to make exposure zero". Nope, doesn't work that way. Exposure is a function of three different settings on your camera: aperture, shutter speed, and ISO. All of these work with eachother to make great photos but if used at their extremes can produce shit.

When shooting in manual on a DSLR you can adjust shutter speed (upper left), aperture (upper middle), and ISO (upper right), the three of which should be adjusted to attain correct exposure using the little scale in the middle. Adjusting these three to get to zero, and maintaining quick enough shutterspeed to take a non-blurry photograph, is half the battle in photography. From

Aperture, known colloquially as F-stop, is a measure of how wide the mechanical aperture of the lens is. The lower the number, the wider the aperture - the higher the number, the smaller the aperture. My little zoom lens ranges from f/5.6 at the widest to f/32 at the smallest. At lower aperture, for god knows what reason (this isn't a post on optical science so read elsewhere if curious) the depth of field narrows - this is the band in which everything is in focus. Also, the closer an object is to the camera, generally speaking the depth of field scales so that it is narrower closer to you - hence the difficulty in focusing with your own eyes on objects close to your face. The higher the f-number, the broader the depth of field, and everything tends to be in focus. The flipside is that if you keep everything else constant, a lower f-number (wider aperture) will produce an overexposed image whereas a higher f-number (narrower aperture) will produce an underexposed image - because of the amount of light coming through the aperture (wider aperture = more light). A good strategy is to split the difference: f/16 is what I typically shoot with for small to medium sized specimens as it permits a decent amount of light but also has an intermediate depth of field.

 Which brings us to shutterspeed. This is literally how long the camera shutter is open for, and is fairly intuitive: the slower the shutter speed, the longer the shutter is open, the more light comes through; the faster the shutter speed, the shorter it is open, less light comes through. This compliments F-stop and the two can be used to balance each other: need to shoot at wide aperture? shutterspeed should be higher. Need everything in focus (high F-number/narrow aperture)? shutterspeed should be lower. Here's the best part: the camera (in this case) does all the thinking for you and automatically calculates the ratio for which settings will produce perfect exposure. A little tick mark on the exposure "bar" in the viewfinder will tell you when you've got each setting at an appropriate place - this is called the exposure meter. If you have your F-stop setting where you want it, just move the shutterspeed dial until the tick mark goes right in the middle; it might jump around a little to +/- 0.25 or so, and that's fine. Shutterspeed will be brought up again below on the issue of camera shake.

ISO is a different issue - this is the sensitivity of the digital sensor to light. Let's say you need to take a photo at narrow aperture, but with appropriate shutterspeed, your photos are blurry because you 1) are shooting in some dimly lit mildewy museum basement, 2) either have drank too much or not enough coffee, or 3) need to eat or 4) do not have a tripod. In this case, not enough light is getting in even with a longer shutterspeed, and the long shutter time is letting motion blur from shaking the camera to make the photo blurry. You can increase the light sensitivity of the sensor by increasing ISO. ISO should normally be set low at 100 or 200. For sub-optimal lighting conditions setting it to 400, 600, or 800 can fix most problems, whereas 1600 ISO essentially permits you to take pictures at night. The flipside is that the higher the ISO the more artifacts make it into the picture - all sorts of graininess which looks shit, anomalous blips of color (usually red), and that doesn't really work well for a published picture. For the most part, unless your shooting fossils at night, ISO won't need to go so high as to introduce noticeable artifacts - and even then, raw photos I've taken of the aurora borealis at midnight in Montana can be edited using so that 90% of the artifacts go away. Again, adjusting ISO will be factored into the camera's exposure meter. ISO can generally be left on a fairly low setting if you are shooting with a tripod or camera stand, and is thus mostly relevant towards handheld shooting.

Here's some examples of different photos of a xenorophid dolphin vertebra taken with varying exposure achieved through different means:

Handheld, on auto, with flash, f/5.6, 1/40 second shutterspeed, and ISO at 400. There's no lighting from upper left, there's a bit of shine, and some weird shadows which make editing challenging.

Taken in manual and handheld with exposure set to zero, f/32, 1/4 second shutterspeed, and ISO 1600. Camera shake! Even with ISO set so high the image is still blurry. I initially set the aperture to be tiny to get this effect for educational purposes. Setting a wider aperture (down to f/5.6 on mine) would have permitted a faster shutterspeed.

Underexposure! Taken using tripod, underxposed by approximately 1-2 full "stops" - f/16, 1/8 second shutterspeed, ISO at 100.

Overexposure - f/10, 1 second exposure, ISO 100. This actually doesn't look too horrible.

This image is ideal, and made use of a tripod, f/16, 1/5 second shutterspeed, and ISO at 400. ISO isn't needed to be that high for this shot, but from an earlier session I discovered our second floor vibrates when large vehicles drive by outside, meaning camera shake even when on a tripod!

A very basic lighting setup, here photographing a small xenorophid dolphin skull on a white sheet. LED lamp at upper left, camera in foreground.

Basic tips 4: lighting

From the prior section it should be obvious that the most important aspect of photography is getting the correct amount of light into the camera. There are ways around shitty lighting, but you don't have to accept dim lighting and deal with it - you can always bring your own light. Spotlights can be useful, but the bulbs burn very hot and can explode. A cheaper alternative is LED lamps - little banks of 100s of LEDs which can be battery powered or plug into an outlet. These use far less electricity, do not get hot, and are very very portable. Most come with a little miniature tripod, but can also be mounted on their own full size tripod. I have one of these, but at U. Otago we had three or four to use. Light intensity can also be adjusted.

Convention dictates that lighting should come from the upper left in published photographs, so that shading and shadows are consistently in the same direction. DO NOT think this translates to "let's use a single light source in a dark room - we still need to see the lower right side! Ideally, you could use four light sources, and have all but the upper left turned to lower light intensity, with the upper left set higher - this will give maximum lighting of all features and conform to the standard "upper left" rule. Only have two lamps? Put the second one at the lower right, but at lower intensity. Only have one? Ambient lighting can be used for most of it (think low F-stop, slow shutter speed, higher ISO) with your lamp positioned again at upper right.

If you have access to a camera stand with four lamps, "great" - many camera stands do not allow adjustment of the light intensity, and I find most to just be cumbersome and awkward and thus to most museums I bring two tripods and an LED lamp which is ultimately more flexible. Alternatively, diffusers can be used to dim non-upper right light sources, or to soften light that is too "hard" (see below).

If working with larger specimens, lighting can be very tricky - at U. Otago we used several large size sheets of white styrofoam to reflect light. It's not quite as effective as a mirror, but still has a noticeable effect and you can really get light into all the tough to see spots on a large specimen with minimal lighting and lots of white sheets. Tyvek cloth works as well - anything you can reasonably use that is white and reflects lots of light in the direction you need it.

Most LED lamps can be placed directly onto the flash mount of a DSLR camera.

Another trick, if you need to get a lot of reference shots but they do not 1) need to have a nice background or 2) need to have consistent lighting from upper left: if you have one, take your LED lamp and stick it on the flash mount - voila! You now have a consistent light source that doesn't flood your fossil with shiny highlights. Set F-stop down at its lowest possible number, and there will be a "Program" setting where you can set ISO to the desired level, set F-stop where you want it, and the camera will automatically set shutterspeed. If ISO is high enough and F-stop low enough, the shutterspeed will be fast enough to take hand-held shots with your lamp mounted. I've done this a lot and it works great. I first experimented with this on my colleague Rachel Racicot's face at the La Brea Tar Pits. This method also saves your camera battery - and most LED lamps run on batteries (double A). Mine has its own special rechargeable battery AND works on double As, and I use a set of rechargeable double A batteries so that one the regular battery wears down, I put in the double As and put the other back onto the charger, and then recharge the double As when necessary - allowing nearly continuous photography.

Osedax craters in the holotype skull of Waharoa ruwhenua, photographed with ammonium chloride coating and low angle diffused LED lighting. From Boessenecker and Fordyce 2014: Lethaia.

Need to photograph subtle surface texture such as patches of bryozoans, bite marks, or other traces? Use low angle lighting - i.e. place the light source low on the "horizon" of the surface being photographed.

Lastly, any increase in the amount of light you can achieve will 1) permit you to shoot at higher f-stop (and therefore with a broader depth of field so more will be in focus), shorter shutter speed (reducing camera shake and therefore reducing blurriness), and lower the necessary ISO (reducing the number of ISO-derived artifacts in the image). More light = better conditions for photography.

OK one more point: unless you know how to manually tinker with flash, DO NOT USE FLASH. Flash often makes fossils appear shiny and often negates all the careful tinkering you've done to master the f-stop, shutter speed, and ISO above in basic tips 3.

Basic tips 5: tripods, camera stands, and shutter release
Camera shake is a terrible thing, and unless you know how to set exposure, play around with f-stop and ISO to get a working shutter speed, you will end up with shitty, blurry photos that will drive your colleagues insane. Fortunately, tripods are cheap! Mine cost 35$ at WalMart. Stick your camera on a tripod (remember to never over-tighten the screw) and you can take long exposure shots with ease. If crappy lighting is all that's possible, just dial down the f-number and shutterspeed and you'll be able to achieve a decent exposure - just don't cough, bump the camera, or let a train or 18 wheeler drive by. Do not press the shutter button yourself - even if done carefully with a super heavy duty expensive tripod, the pressure being released by your finger on the button will cause the camera to shake. Use the timer - on my camera it can be set to 2, 5, or 10 seconds. I'm an impatient bastard, and my camera makes a horrid beeping sound during it and I use an old school manual shutter release - a cord with a button on the end. The button can even be depressed halfway for autofocus - how about that! Remote shutter releases also exist, but I find them equally irritating as some of them need to be recalibrated with the camera every 10 minutes and have a battery of their own. Also, the remote can be lost or misplaced. Corded ones are cheaper, run off of the camera's battery, and are stuck right onto the damned camera so it's pretty difficult to lose them. Most of this applies to camera stands as well: stands reduce camera shake, but often (especially during museum visits) you might be stuck with inflexible lighting.

A lightmaster lightbox my lovely wife got me for my birthday - rather than use conventional halogen or tungsten bulbs, this one is LED powered and is less than 1 cm thick. Though I'll be using it for drafting and artwork rather than photography.

Our giant light box at U. Otago - an old drafting lightbox the size of a refrigerator. The glass was not frosted, so we just laid down a bunch of large sheets of tracing paper to give it a more diffuse effect; LED lamps can just be placed directly on top like this.

One of the lumbar vertebrae of OU 22163, a juvenile specimen of the eomysticetid Waharoa ruwhenua, photographed on a lightbox with diffused soft lighting from upper left - original photo (left) and edited image on right as used in Boessenecker and Fordyce 2015: PeerJ. With the even background and consistent contrast on the crisp edge and lack of shadows, editing this with the magnetic lasso tool took all of ten seconds.

Want to make editing the photographs much, much easier? If you can, find a large light box - many geology departments will have old large ones used for drafting cross sections and geologic maps, likely to be in mothballs thanks to the use of software like GIS. I'm a bit old fashioned and love to do lots of stuff by hand, and gleefully admit that I still use light boxes for drafting (my lovely wife - Hi Sarah! - got me a spectacular light box for my 30th birthday last fall). Back-lit fossils are super easy to edit in photoshop. What a light box achieves is a continuous light tone around your fossil, which makes editing the image and getting rid of the background (either through the magic wand tool or the magnetic lasso tool) 3-10 times faster. The flipside is that light boxes are expensive. Light boxes do another thing: they seriously increase the amount of light available for your camera - again drastically improving lighting conditions.

Basic tips 6: what to put your fossil on

This may be intuitive: anything you care enough to learn all this crap for is likely important enough that you don't want to damage it during the process of taking photos. If a fossil, use foam! Or sandbags. Since you're not storing the fossil permanently like this it is OK to use non-archival materials for a couple of hours. Fossils should be propped up so they don't fall over. Sand bags and wedges of foam are great for this.

The holotype skull of Tohoraata raekohao perched on a series of sandbags and foam blocks covered by a sheet of white tyvek, with a giant sheet of white styrofoam behind to provide a degree of backlighting for ease of editing, and of course diffused lighting from upper left.

Another consideration is what the background around the fossil will look like. Most are going to crop out the background in photoshop so that the pile of ugly sand bags and other random objects stuck together like a house of cards underneath your fossil aren't cluttering up your published image. How can we make this easier? For smaller specimens on a flat surface that won't stand the way you need , you can use a lump of plasticene clay (which can leave grease on your fossil) or playdough (which does not). It's best to not have any of this material visible to keep editing time down. Another trick is to use sheets of Tyvek, which is super thin and lightweight. For gods sake do not use black cloth! Black cloth doesn't reflect much light and produces much crappier lighting conditions often leading to underexposure of your fossil around the edges or in cracks along the periphery. If you need to build a large pile of styrofoam blocks and sand bags to jug up several bones or a large awkward one into an appropriate orientation, cover the whole thing with tyvek which can settle into all the nooks and crannies and voila! The monstrous 3D support pile you've meticulously constructed is now hidden and easily edited away!

A temporary diffuser made out of an ethafoam sheet and a piece of scotch tape...

Advanced tips 1: diffusers

Hard lighting can cast small shadows that may obscure some detail and increase "local" contrast in spots so that small highlights are overexposed and shadows are underexposed. Using a diffuser can scatter light and produce softer lighting. Diffusers can be purchased, but we're paleontologists - we're ingenuitive and often broke! Make your own diffuser and spend the money on a better lens instead. Diffusers can be made with sheets of vellum, mylar, or even tracing paper - anything thin and semi transparent works. Too much light coming through? Use another sheet! At Otago we had a number of different homemade diffusers made from a card matte from a picture frame with mylar or vellum taped in place, stuck onto a wooden base to keep it upright. Different sizes are great. For a large light that's on a tripod, you don't need to waste time making a four-foot tall diffuser: just get some sheets of mylar or vellum and use artist tape (the blue masking tape) and stick it directly onto your lamp! Also: make sure not to knock your diffusers over onto your fossil during photography if your fossil is precariously balanced. If you're shooting in a museum and don't have any of those types of paper, thin sheets of ethafoam can be used in a pinch.

...and a much better diffuser, seen at left, made out of vellum and a wooden frame. This is a better example since it also showcases the soft lighting produced.

Professional photographers who photograph small (e.g. jewelry) to large objects (e.g. people) often use light tents - which essentially is a 270 degree diffuser that also acts to provide backlighting. I'd love to try using one of these. Here's an example below, and here's a how-to guide on making your own light tent.

A collapsible light tent - from

Advanced tips 2: focus stacking

Can't get a fossil to be completely in focus? Short of increasing the amount of light you have and closing the aperture severely, sometimes some specimens just won't fully go into focus. Luckily there's a technological fix for that called focus stacking. If you take photos under the same lighting conditions with the focus set at different overlapping levels of the subject, you can digitally merge those using Photoshop or another program which takes the parts of your photos that are in focus and merging those whilst ignoring the parts that are out of focus. To take appropriate photos, you can 1) keep the focus fixed on the camera and slide the camera back/forth on a rail (expensive) or 2) just manually adjust the focus, taking 3-10 photos depending on how much of the subject is in/out of focus. Note: this will be more important if shooting with prime lenses at low F-numbers.

Focus stacking: image on left is one of five original photos. In this photo (holotype periotic of Tohoraata raekohao) the parts of the bone closest and furthest away are out of focus, while the middle of the bone is in focus; five photos spanning all parts of the subject were taken and then merged using focus stacking to produce a photograph with continuous focus (right).

Digital merging can be done in Photoshop CS5, CS6, and above, and tutorials for it can be found online - but very briefly, you load individual photos into photoshop as layers (adobe Bridge is the easiest way to do this) within a single PSD file, then go edit->align layers, and once that's done, edit->merge layers. Photomerge doesn't really work too well at this. There are other dedicated freeware programs, but from what I've tried they're all awful. All of my earbone photographs from my Ph.D. thesis on New Zealand eomysticetid whales were shot at different intervals and focus-stacked... literally over 100 different images composited from 4-12 separate photographs.

A large (but by no means the largest!) specimen being photographed in the stairwell at U. Otago; the block is the rostrum of a referred Tokarahia lophocephalus skull, and is positioned right next to the giant penguin Kairuku display case for those familiar with the Otago geology department.

Advanced tips 3: photographing large specimens

Large fossils - some dinosaurs and whales come to mind - pose a whole host of problems. Occasionally fossils are embedded into a wall of plaster or are in some sort of a mount - or worse, in a dark corner in a basement and are too large to move. In these cases, some creativity is needed with lighting and camera angles. For very large specimens, you can either use a very, very tall ladder (if available, say at an oversize facility like UCMP's Regatta building in Richmond, CA, or USNM's Garber facility in Maryland) and photograph the fossil on the ground. This means handheld shooting or the use of a swing arm that can clamp onto a railing. At U. Otago, we had no room for something like that, but we did have a very tall stairwell - so we'd literally place a whale on the floor at the bottom, clamp a camera onto the railing on the second story (first story had ~12 foot ceilings, so the camera was nearly 20' up). All of my photos of eomysticetid skulls for my Ph.D. thesis were taken like this.

If a fossil can be tilted so that you can shoot horizontally, even better! Just go far away from the fossil until everything is in frame and shoot horizontally as if it were a deer out in nature or something. If the specimen is too fragile, this option is probably not a great idea.

Can't fit a tripod or a flood light in because the fossil is too damned huge? Stick a white sheet or a large plank of styrofoam at the desired lighting angle, and aim a spotlight or LED lamp at the foam - and bounce the light off the foam at the desired angle (e.g. upper left). This is a workaround for photographing enormous specimens in cramped areas.

Sometimes you're stuck with a specimen that is too big to shoot from above and too heavy or large to move. The holotype skull of the eomysticetid Tokarahia kauaeroa is such a case - the basement ceiling at U. Otago is about 7' above the floor, and the block needs about six people to lift - it's quite scary to do so, and logistically a nightmare. So, we took photographs from the highest point possible using a tripod, and stitched the photo together. This ended up looking not quite as great as a photogrammetric 3D model I put together, so we ended up just using an arguably undistorted image derived from photogrammetry. Point is - creativity means that there is always more than one way to skin a cat (or dead whale).

An OKish photo of a cow shark upper anterior tooth, shot horizontally at UCMP (Berkeley) with my zoom/macro lens from about three feet away.

Advanced tips 4: photographing tiny specimens

Macro lenses and good lighting mean that you do not need to screw around with cameras attached to binocular microscopes. With a proper macro lens (a type of prime lens ideally suited towards closeup photos) you can take photographs of objects 4-15 mm in size with excellent resolution, no microscope needed. It's a great way to photograph the middle ear ossicles of whales and tiny shark and dolphin teeth.

I have a bit of a "ghetto" macro lens - it's a telephoto zoom lens with a macro lens feature. It can take great closeup images, but only from about 30-40 cm away at the closest. What this means is that it's really awkward to use this on a camera stand, and I have to get up on a chair to look through the viewfinder and risk falling over. So, rather than bother with all that crap, I set up my tripod, light, scale bar, and shoot horizontally on a table top. Problem solved!

Advanced tips 5: light temperature

When I was four I saw a light bulb turned on up close for the first time, and it was within reach, so I reached out my hand and touched it with my right index finger. It took a second before I realized the pain, and within minutes I had a pretty gross blister; I was a stupid child. Light temperature does not refer to how hot a bulb gets. Rather, different bulbs will produce a different color. Tungsten bulbs produce yellow light - and though most cartoons depict the sun as somewhat yellow, it is far from it - a blinding white light. LED lights look a bit blue in comparison to tungsten - but are actually daylight temperature. The point of all this is that if you care enough, it's perhaps best not to mix different temperatures - the two most common being daylight (LED, camera flash, halogen) and yellow light (tungsten bulbs). Note that this does not matter one bit if your final image is going to be converted to black and white. It *might* look weird if going for a color image, but most are not going to notice so this is something I never really worry about.

 Yours truly coating the holotype specimen of the sea lion Neophoca palatina for a paper with Morgan Churchill - coming soon in Journal of Paleontology. Note the glass place and cake turntable below; the glass plate allows blacklighting with a lightbox.

Advanced tips 6: ammonium chloride coating

Fossils that are dark brown or black pose a problem in that little surface detail will be apparent no matter what the lighting conditions are. An old school method to solve this problem is to coat a fossil with sublimated ammonium chloride. Ammonium chloride is mostly harmless and can be placed into a glass vessel that somewhat resembles a crack pipe: ideally it will have a small nozzle followed by an expanded bulb, and then a tube to which you can attach a little air puffer or a slow stream of compressed air. Solid ammonium chloride is placed into the bulb (which is unfortunate since the chemical looks like white powder) and then, even worse - you heat the bulb up over a bunsen burner or other comparable flame. It sublimes - in other words, goes directly from a solid to a gas - and a gentle puff of air pushes the gas out the nozzle, and onto your fossil - where it sublimates back into a solid, giving a very thin coating of white. This coating is easily removed with water - make sure your fossil can take a brief and gentle soaking to remove the ammonium chloride. Be careful though, it will come off on your fingers - meaning another spraying is in order. Some practice is necessary to get a nice even coating. Another tip: you do not have to start over fresh for each view. I would spray as much as possible on the first try, take the photo, flip the specimen, spray the other side, and repeat until everything is photographed. Remember the focus stacking described above? Each of my eomysticetid whale earbones was ammonium chloride coated AND focus stacked. Goddamn that was a lot of work. This is sort of unnecessary if you can publish in color, unless a fossil is really, really black like the inside of a black hole (phosphatized bones/teeth for example).

Bunsen burner and ammonium chloride in the glass tube, chemical is present in the bulb - you can see a bit of whitish gas escaping: this is what is blown onto the fossil.

Quick note: if shooting with backlighting on a light box, you do NOT want to pick up the fossil and so at Otago we would place the fossil onto a sheet of glass, coat it, and place the glass onto the light box so the light can still shine through.

At other institutions that will kindly remain unnamed, some sort of aerosol can spray crap has been used as a shitty alternative to ammonium chloride - but unless removed immediately, this stuff becomes rock solid and will not be easily removed except with diligent scraping. I've seen many fossils unnecessarily and potentially irreversibly harmed this way, and the hardened paint-like substance is nearly more difficult to remove than the actual rock the fossil was initially entombed within. Please, for the love of god, do not abuse your fossils like this!

Advanced tips 7: shooting in raw

DSLR cameras can shoot in two modes: they will save a jpg "preview" file - the image most digital cameras will produce - as well as a "raw" file. Raw files are difficult to edit and only a few programs can actually open them, and even those do not permit the image to be permanently tinkered with. Raw files are great because they can be adjusted and a jpg or tiff file generated from them, but no information is lost. In other words: if you want to increase contrast in a jpg and save the file, you lose information from that image and it is altered forever unless you have an original backed up someplace. With a raw file, the "sliders" in the program can just be reset and the image is never permanently altered. Essentially, raw files are "archival" image files. The flipside is that raw files are large, and may be a bit cumbersome to edit, and require specific image editing software. Different camera companies use different file types: Canon (what I use) uses CR2 files whereas Nikon uses NEF. Adobe Bridge can open up some (NEF). I personally hate software that isn't free, so I use the very flexible freeware program "RawTherapee". A word of caution: shooting in raw takes a lot of harddrive space; my Ph.D. dissertation folder on my computer has nearly 20 gigabytes of photos thanks to raw files.

Advanced tips 8: efficiency

Lastly, a word on efficiency. A good lighting setup can take anywhere from 10 to 45 minutes to set up, depending on how much room you have to set up, if you have help, or alternatively, have somebody in your damn way or distracting you. Or if all of a sudden it's afternoon tea and it would be rude to continue shooting. It takes a while to set up all of this crap, and it's not fun. Many, many arguments with my lovely wife were started by me taking too damn long to take all my thesis related photos on campus during my Ph.D. Hours spent taking photos without food or water plus bright lights is a great cocktail for a massive headache.

So: get an assembly line started and photograph everything you can over a few hours. This also really helps if you need to maintain consistent lighting; you may very well not remember how to mimic a certain lighting setup you had before (take a cellphone picture). This is especially relevant if you are taking ammonium chloride coated photos.

Don't get too caught up in the details; it's simply not possible to produce a perfect photograph, though many will try under the delusion that it is reachable. If you begin to think that you're wasting a lot of time doing some of this, perhaps you're right! Think about how you could work around a particular problem or how to be more efficient. Photography is not art - I'm sorry to photographers, but after doing a fair amount of it, it takes a tiny fraction of the amount of skill required for fine art. What I mean is this: there's nothing really special about it, and a fair amount of judging of photograph quality is a bit of a black art and fades quickly into the realm of minute subjectivity. Photography is easy to learn, and anybody can read what I've written and use these tips to produce better quality images. Photography is mostly scientific, but bending the rules to get a better picture - or the same quality picture for less effort - requires a bit of creativity.

Further reading:

The Fossil Forum: Fossil Photography subforum

Photographing fossils PDF by Wayne Itano

Photographing Burgess Shale Fossils by Royal Ontario Museum

High Dynamic Range photography in Paleontology by Jessica Theodor and Robin Furr in Palaeo Electronica

Thursday, February 11, 2016

Paleontological research tips II: field notes, continued

Other posts in this series:

Paleontological Research Tips I: field notes for amateurs and professionals alike




Here's the second part in my series, and admittedly, it's a (short) continuation of the first post on field notes - a couple of additional tips, and what to do after the field with notes and specimens.

Q: What do you do with field notes after you're back from the field?

A: Keep them. Forever.

My dad is an attorney, and there is a similar problem in law: a full paper trail documenting all aspects of a given legal case is required to be kept by the attorney for 10 years. My dad does get a bit of business, so growing up I was a bit confused about why we had so many banker boxes filled with boring legal documents sitting in our garage. About once a year, he'd go out and dispose of whatever case files were over 10 years old. It's a pain, but it's got to be done in order to "cover your ass", so to speak. Fortunately in science we don't quite have that same level of paper to churn through - in a decade of research I've filled up about a dozen field notebooks and a half dozen moleskine lab notebooks - it won't even fill up a single banker's box. But here's the catch: in science, there is no statute of limitations. We've got to keep our notes forever; the best way to go about this is to literally deposit your notebooks - or a copy of it - with the institution housing the material the notes are associated with. Disclaimer: I still haven't actually done this for UCMP, but have transcribed all the notes for individual specimens that are now in their collections - so they have all the information, just not in notebook form. This way, in case your house burns down, or your cat pees on your stuff (it happens, trust me) there is another copy someplace. An even better idea - scan your notebooks to pdf; I did this with all of my notebooks before leaving NZ.

Here's all of my notebooks - see, you don't throw them away when you're done. Safeguard them!

Traveling? I always carry my notebooks on my person - I NEVER trust the airline (or shipping company) to do the right thing. So, my bookbag coming to/from New Zealand was a bit heavy, as I literally carried every single one of my notebooks on me rather than risk the fate of losing them if my bag was misplaced, stolen, or just got wet or damaged. I once had a partial fossil baleen whale skull from a tidepool in Santa Cruz - shipped as a checked bag (well, cardboard box) - sit on the tarmac overnight in the rain at SETAC on my way back to Bozeman for spring semester. Now, the skull was fine because 1) it sat in a tidepool for probably a century and is fairly immune to water (it was covered in algae and barnacles and smelled HORRENDOUS when it was delivered the next day, but that's another story) and 2) is in a concretion and practically indestructible. But say that had been a non-waterproof duffel bag with handwritten notes in it? Sayonara! My buddy Lee Hall has lost his checked luggage while flying to Canada twice (once at the 2006 Ottawa Society of Vertebrate Paleontology meeting, including all of his nice clothes) and luckily got all of his stuff back the first time (can't remember if he got his bags back the second time). Losing clothes (and field gear the second time) is frustrating enough - but it could happen if something really important is placed in checked luggage.

Moral of the story: don't trust yourself to be the only steward of data. Scan it to pdf, email it to the host institution (or print it out and snail mail it to them), upload the pdf to cloud storage if you're really paranoid.

Q: What do you do with fossils after you're back from the field?

A: A bit more nuanced than the answer above. I'll explain more.

Presumably you've followed my advice from the prior post and have started using field numbers for fossils - if so, great! If not, go read it again and reevaluate why you want to be a paleontologist - professional or otherwise. Now, after returning triumphantly from the field, your first interest (aside from taking a shower and sleeping) might be to start preparing the fossils. And that's fine - this is the stage of the process where you can paint numbers onto a smooth exposed surface. I recommend sticking with archival materials - use acrylic white paint and an archival micron pen to write with. Now, if you still need your field notebook - or if your notes are in shorthand, as mine are - you're going to need to transcribe them somehow in order to keep that data physically associated with the fossil. You can write out the field number, collection collector, date, identification, location, and stratigraphic level onto a small sheet of paper - these are the basics, and many museum databases do not give the opportunity to include intra-formational stratigraphic data, so including this information will help future researchers interested in higher precision data use your fossils.

Here's an example of one of my specimen cards: I print out 6 of these on a letter size sheet (single sided, of course). It's got all the basics: ID, museum specimen number, field number, locality number, collection date, plus a more specific description of the locality and stratum.

Or, if you're more organized and prefer something standardized, you can use pre-made collection sheet forms that are small enough to fit all relevant data that 1) links the field number and museum number and 2) also includes more detailed information that cannot easily be included into a database. I'll admit I got the idea for mine from seeing these sheets in UCMP collections filled out by marine mammal paleontologist Ed Mitchell (the guy who named Valenictus, Imagotaria, Allodesmus kelloggi, and Llanocetus denticrenatus) and used a similar approach.

A distal humerus of the walrus Dusignathus collected this summer by Dick Hilton during fieldwork in Marin County. It's a future UCMP specimen, but until it is formally accessioned there it can be tied to relevant data by my field number - RBPR-46 (meaning Robert Boessenecker Point Reyes), written on the swatch of acrylic paint at the upper left corner of the specimen in this photo. When the specimen is formally accessioned, the field number stays and can be checked across my field notes years from now.

Some other tips:

-Don't write field numbers in permanent ink, and don't write directly on the bone; according to work done by former Museum of the Rockies artist-in-residence Michael "Spiff" Holland, if it ever goes on display the only way to get around permanent ink written right on the bone is to paint over it, with a matching "bone" color. A swatch of white acrylic paint is fine, and can be removed if you so desire.

-If you prepare multiple fossils at the same time, make sure you keep something clearly indicating what field number belongs to a particular specimen until the time comes when you can paint a label onto it. Preparation is the easiest stage at which field numbers can disappear. I tend to keep incompletely prepped fossils sitting on their actual field ziplock bag until they're fully prepped and labeled.

-What if a fossil is too small to write on? Use a smaller plastic bag and write on that! There are archival tiny plastic bags (and yes, they do resemble the ones drug dealers use) that can be used. If a fossil is super super tiny, I use two-part ~250 mg pill capsules and cut out a tiny rectangle of index card and write the field number in archival ink. And because the capsule is still tiny, I then put that inside a smallish bag and write on that too.