Archive for the ‘SEM techniques’ Category

Mites in the News

February 4, 2015

Zerconid_Idaho_3As the Good Book says: “To every thing there is a season, and a time to every purpose under the heaven” (Ecclesiastes 3:1). The last year hasn’t been the season for much new at Macromite’s Blog. Mites, alas, have been getting short shrift and I’ve been chasing platypus and butterflies and littering Facebook with the result. However, while I’ve been trudging around my new neighbourhood under the skeptical gazes of the kookaburras and wallabies, others have taken up the mite-art palette and brush with outstanding success.

Sam Bolton (or ‘Bolten’ as The Guardian misspelled his name) struck first in classic greyscale with his ‘Buckeye Dragon Mite’. Such is the power of a good monster picture that I’m told his paper was the most downloaded from The Journal of Natural History last year. Let’s hope someone also cites the paper in a scientific journal or two.

And now, Martin Oeggerli’s long quest to bring the wonders of the acarine world to the public’s attention has been fulfilled. Quite a spectacular feat, both in colour use and in attracting the attention of National Geographic, something that several acarologists that I know of were not able to do. But if you compare Martin’s header image – a zerconid mite – with my more pedestrian zerconid image above, it is easy to understand his success. The text is by Rob Dunn (and The Inquisitive Anystid and I checked it for accuracy).

For those who are not squeamish (and if you are please don’t go there), y0u can see Rob among others bringing you up-to-date on follicle mite research in this video:

Even I am feeling itchy after watching that, but at least the rumour they explode on your face has been put to rest.



Sellnickia: Details & Enhancements

January 17, 2010

Sellnickia anterior with details: sp. A, sp. B

Here’s some more on the predatory labidostome mite from the previous post – a closer and greener view of the anterior end. It’s greener, because I distinctly remember a live collection of a species of Sellnickia with unusually greenish mites running around, many with startlingly white Folsomia-like springtails crushed in their chelicerae. A reliable memory or a dream? I do dream of outlandish mites every now and then, some of my favourite dreams I might add, although my absolute favourite was when I discovered a giant trigonotarbid in a deep, misty, tree fern and liverwort covered canyon. Since trigonotarbids (allegedly) haven’t been around for a couple of hundred million years, I suppose this indicates one should be skeptical of their dreams.

In any case, this reminds me that Adrian has asked for more details on the time it takes to make these mite portraits.  Warning – what follows is lengthy.

To give even a general answer to ‘how long’, one needs to first decide how the image is going to be put to use. If the purpose is to illustrate morphology for a scientific publication, then the less time spent manipulating the image, the better. For example, the detail of the cuticle from sp. B in the image above was simply selected, copied and pasted. To illustrate why: I was once told a story about an early photographic plate of fossil aquatic scorpions. Although aquatic chelicerates typically have compound eyes (think horseshoe crab), modern terrestrial scorpions are typical ‘arachnids’ with at most lateral clusters of simple ocelli. No eyes were obvious on the aquatic rock scorpions in the photo plate, but I am told that the actual impressions in the rock have lateral compound eyes. Apparently, since scorpions weren’t supposed to have compound eyes, the ‘artefacts’ had been airbrushed out by the author so as not to confuse the reader. Once you start ‘improving’ an image, you run the risk of producing misinformation.

The time required to prepare a SEM for a scientific publication is primarily a function of specimen preparation time. For example, to produce a grayscale SEM suitable for publication of the Sellnickia sp. A above took less than 3 hours including selecting the mite, drying it through a series of solvents to eliminate its water content, placing it on a stub, sputter coating in gold, putting it into the electron microscope and achieving the proper vacuum, focusing and fiddling with astigmatism etc., and taking the images. Three hours is a lot of time to take one picture, so I always do lots of specimens on the same stub. Mites are excellent in this way – lots more fit on a stub (~10 mm diameter) than could dance on the head of a pin. So, 2-4 hours of preparation can result in 30-60 images in a 4 hour SEM run, depending on time needed to focus, resolution (the more resolution the longer the raster time for each image grab), software or hardware problems (all too frequent), and the quality of the specimens (finding specimens on the stub without dust, goo, dents, or broken bits).

The reasons this mite was easy are: (a) it is hard shelled (little or no deformation on drying) and relatively large (much easier to transport onto a stub) and (b) relatively flat (not much depth of field in a dorsal view).

The image in this post is from a single grab – if you look closely, some of the ornamentation and many of the setae are not in sharp focus and the blow-up of the detail (A) is a bit blurry.

The image of the full mite in the previous post is a composite of 4 – I divided the mite into quadrants and took four separate SEMs and then pasted them together in Photoshop – mostly to get a large image size (the camera was only capable of relatively low resolution grabs).

Masking – separating the image from the background – takes the most time. In the case of the full body image in the previous post, it took 7-8 hours to put together and mask – that is not bad and is a function of the outline of the animal – few setae and other protuberances to mask around.

In contrast, the anterior view in the image in this post took about an hour to mask this morning (including erasing the legs that were bunched up and out of focus on either side). Masking out artefacts (e.g. cracks and bubbles in the glue) or unwanted detail (e.g. the out of focus legs in this picture) can dramatically improve the quality of a greyscale image in a paper – but it takes a lot of time. It would probably be a good idea to mention in the legend of the figure that the legs have been removed.

Once the animal is masked, then you can decide it you want to colour it. I don’t think that a morphologial study needs colour, but a field guide or poster could benefit from colouring.  The problem with a grayscale SEM is that we have colour vision and when we see these mites they look bright yellow to green. Colouring can be simple – the full dorsal habitus view in the previous post took only about 20 minutes to do after masking, because I relied on the shade differences in the original SEM to be reflected in the final picture and used a single colourizing level in Photoshop. If I wanted to show more detail, then I would have to laboriously select the areas needing the different colours one by one.

I actually did this on this morning’s image – the anterior view in this post. I decided to give the mite a more greenish cast in parts of the cuticular design by selecting pixels within the reticula. I also decided to lighten the setae – the setae usually lack the colour of the body in life and appear white. This took way too long – especially trying to select the feathery bothridial sensilla that are overlain on the body. Finally, I decided make the tips of the chelicerae a slightly different shade. All of these changes should be making the mite look more realistic, or at least make it easier to see the different parts, but even these fairly simple selections took about an hour and a half.

So, the total time to prepare the image in this post was about two and a half hours on a Sunday morning. Getting the original image was a similar investment in time. I would consider this a low value for the average SEM that I colourize – the average is about one full day of manipulation of the original grayscale image(s). The maximum is about a full week – the extremely complex  image posted near thebeginning of this blog.

Box Mites

April 26, 2009

Phthiracarid mite - lateral

Phthiracarid mite - lateral

The evolutionary history of oribatid mites (aka beetle, moss, and armoured mites) must have been too full of adventure, because these are now the most unadventurous of mites.  Adults are slow-moving, deliberate, and heavily encumbered in armour.  Although their subordinal name, Oribatida (aka Oribatei, Cryptostigmata), may be derived from the Greek for ‘mountain’ (ori) and ‘one who roams’ (bat), it is hard to imagine oribatids lumbering uphill for any great distance (which begs the question as to how they came to be found in soil almost everywhere, including mountain tops and rainforest canopies).  Without a doubt, though, defence against predation is one of the dominant themes in the history of the Oribatida.


Ptychoidy in Mesoplophora

Ptychoidy in Mesoplophora

 One remarkable type of defence that has evolved at least three times in the Oribatida is called ptychoidy (more Greek, ‘ptych’, a fold).  Ptychoid mites are able to fold their legs into their bodies and close the anterior shell-like aspis over the legs, giving rise to a less English-tongue-twisting name, ‘box mites’.



A phthiracarid box mite - ventral view

A phthiracarid box mite - ventral view

Box mite seems an especially appropriate name for the members of the family Phthiracaridae that have large rectangular plates covering the genital and anal openings that rather resemble the leaves of a box.  For those of you wondering, yes that is the same ‘phthir’ as the Greek for louse – why ‘louse mites’ I have no idea, and why a somewhat related family are called ‘good lice mites’, Euphthiracaridae, is equally mysterious to me.

Sometimes ptychoidy doesn’t seem to be enough protection.  Here are couple of versions of an SEM (derived from single digital grab) of an Australian phthiracarid box mite that also encases itself with a layer of soil.  Presumably this serves as a visual or, more likely, tactile camouflage that increases the chance a predator will move on (‘get along now, nothing but a bit of dirt, your dinner is elsewhere’).


A dirty grayscale box mite

A dirty grayscale box mite

Above is a grayscale image that has been mostly masked from the low contrast or messy background of the original SEM.  The arrows point to a few areas in between the setae, claws, and legs where I had yet to clean out the background.  Masking around the setae is the most tedious part of creating these images.  The image below has been false coloured to show the sclerotized body as a reddish brown seen through the dirty tan of the soil layer, the legs a lighter colour, and the soft cuticle at the base of the legs (soft cuticle there is necessary for the mite to be able to withdraw its legs into the body) a sort of fleshy colour.  In life, this soft cuticle was a semitranslucent white, but I find white the most difficult colour to recreate without losing all detail.

A spruced-up version of a dirty box mite

A spruced-up version of a dirty box mite


Xanthodasythyreus toohey Walter & Gerson

April 26, 2009
Xanthodasythyreus toohey Walter & Gerson

Xanthodasythyreus toohey Walter & Gerson

Xanthodasythyreus toohey Walter & Gerson is a slow-moving mite hiding in a pincushion of 39 long, barbed setae.  It lives in dry surface soil such as the litter at the base of grass trees (Xanthorrhoea spp.) in the open forests of eastern Australia.


In order to capture as much of the mite in focus as possible, 18 separate digital scanning electron micrographs (SEMs) of about 1 mb each were needed.  Each image was made semi-transparent, then overlaid as a separate layer, then restored to full opacity in an image processing program.  The new composite image was then ‘masked’, that is isolated from the background and a new background was created.  Since SEMs are Grayscale, and mites are not, I then tried to recreate the colours of the mite as it was when it was alive.  In all, this image took about 40 hours of intense and concentrated work to produce.  That’s a lot of time in the evening and on weekends to spend on a single mite image, but this one has proven highly popular featuring, e.g. as a full page spread in Popular Science (A mite in a million.  Popular Science, October 2001, p. 44), on the cover of the just released A Manual of Acarology 3rd Edition (Texas Tech University Press), and so I am told, in Maxim under the title ‘A really bad hair day’.


Xanthodasythyreus is not found in North America, but another member of the family (Dasythyreidae), Dasythyreus sp. has been found on logs in boreal forest at George Lake in Alberta, Canada.  This may be the same species as Dasythyreus hirsutus Atyeo which bears 179 whiplike setae on its back and was described from tree bark in Arkansas, USA.  Fortunately, I do not have any SEMs of Dasythyreus, because I am sure that trying to layer and mask 179 pairs of dorsal setae (let alone those on the legs) would be a really bad hair month.  Dasythyreus species are known to be phoretic (i.e. hitch rides) on click beetles (aka elater beetles, Coleoptera: Elateridae).