Finessing focus stacking

I've been experimenting to see if I can improve the quality of microscope images I generate. The answer is - yes I can, but is it worth it?

DxO recently released their DxO PureRAW 6 image processing software. There are lots of reviews on YouTube if you'd like to know more. I downloaded a free trial copy and compared three different focus stacking variations. I'm not the first person to do this, just documenting it here in case it's useful to you:

1. Capture jpeg images in camera, focus stack with Helicon Focus, post-process with Affinity Photo. This is the standard method I have used until now. 
2. Capture raw (.ARW) images in camera, focus stack with Helicon Focus, post-process with Affinity Photo. Helicon will stack raw image files, so I tested this.
3. Capture raw (.ARW) images in camera, process with DxO PureRAW 6, focus stack with Helicon Focus, post-process with Affinity Photo. 

The results:

click for larger image

At this level, no real difference, and I need to pixel peep at 100% magnification to see the differences:

click for larger image

There is an improvement in quality from method 1 -> 2 -> 3. But what is the cost? 

• To make a focus stack using ~40 jpeg images typically takes me something like 15 minutes (sample processing, image capture, focus stacking, post processing). 
• Using raw images, Helicon stacking increases from 10 seconds to 240 seconds, the whole process taking ~20 minutes. 
• Processing with the sparkly new DxO DeepPRIME XD3 algorithm before stacking takes about 10 minutes, the whole process then taking ~30min. Although Helicon can output a raw (.DNG) image, DxO will only accept original images so it is necessary to batch process captured images before stacking rather than process a single stacked image. The more images, the longer it takes - I estimate making a stack with 100 images would take over an hour from start to finish. This isn't necessarily hands-on time, DxO will happily batch process in the background while I do something else, e.g. prepare the next specimen and capture the images. Sadly it's not possible to process the DNG file Helicon can put out - DxO processing really has to be the first stage of the workflow after image capture. 

There is an improvement in resolution dropping DxO into the workflow at the cost of much longer processing time. Leaving aside the cost of the DxO software, is it worth it? Not for routine images where I'm just documenting an ID. But on occasion, yes, maybe the extra quality is useful. 

Teeny-tiny wasp willies

I recently encountered Torymus rubi for the first time. It was on the host plant (Rubus) and with some help, I was able to get a definitive ID. Not all species in the Torymidae are so straightforward however. This brought up again the question of why hymenopterists seem so reluctant to use gen det to confirm difficult species. One paper describes Torymus male genitalia (Klymenko, S. (2012) Morphological Characteristics of Male Genitalia in Some Species in the Genus Torymus. Zoodiversity, 46(2), e-41). I have to admit, some are rather similar, and this paper only covers a few species. Fortunately, the T. rubi aedeagus is quite distinctive:

It's not a particularly difficult dissection, given the size of the insect. So what's the deal hymenopterists - why the reluctance to dissect?

 

He's only gone and bought *another* camera

In the year since I've had my Olympus OM5 camera I've become increasingly impressed with it. It's smaller and lighter than my previous Sony setup and the results are great. I was so impressed that I invested in the OM 90mm macro lens, selling the 60mm lens I originally bought with the OM5. I've developed a workflow for focus stacking which produces results I'm delighted with. However, there is one problem. As my system (and the quality of the results) has grown, so has the weight. The (absolutely brilliant) Cygnustech flying nun diffuser does the business, but it is cumbersome and a bit fragile, and I'm not keen on bashing the expensive 90mm lens around in the field. So I took the plunge and have invested in two complementary systems. 

Studio macro setup:

• OM System OM-1
• OM System M.Zuiko Digital ED 90mm f3.5 Macro IS PRO lens
• +/- Olympus M.Zuiko 1.4x Teleconverter MC-14
• +/- Raynox DCR-250/DCR150
• Godox V860IIIO flash
• Cygnustech flying nun diffuser

Fantastic, but here's the problem - this setup is a bit fragile, and weighs 1,830g. I don't want to drag that around with me outdoors, so...

Outdoor macro setup:

• OM System OM-5
• Olympus M. Zuiko 60 mm f/2.8 MSC ED Macro lens
• Olympus FL-LM3 Flash
• bit of packaging foam for a diffuser

This setup weighs 730g - 60% lighter and much more compact that the OM1 setup. In addition I have the option of adding a Raynox DCR-250/DCR150 if needed (I can't see me using this much outdoors), plus the lightweight Olympus M.Zuiko Digital ED 75-300mm f/4.8-6.7 (if I need reach). I suspect the convenience of this means it will also get used for quite a lot of quick snaps indoors! The teeny tiny FL-LM3 flash is great - no batteries as it works off the camera battery - although the recycle time is slow (2-3 seconds), which catches me out occasionally. 

And if even the OM5 is too much, I'll still be using my Olympus TG-6  for record shots and my iPhone (for landscapes). As ever, all this kit was bought used from trusted resellers (and guaranteed). Was the step up to the OM1 worth it? I'm still dialling in optimum settings and getting used to the camera, but first indications are favourable - focus stacks seem to be a step up from the OM5. 

 

 

Platycheirus ambiguus

 I may have bought a new camera (more on that soon), but I am by no means a Dipterist. Convenient then that when I took a turn round the garden to test the new kit that the very first thing I photographed happened to be Platycheirus ambiguus. Although not rare, this small hoverfly could not be described as common either, although the reason for that is almost certainly the small size (6mm). A happy accident. 

 

New Arachnid Recording Schemes Atlas

The British Arachnological Society recording schemes atlas has had a long awaited revamp and is now available, with 1.6 million UK Spider, Harvestmen and Pseudoscorpion records to play with. The new atlas is fantastic, with many ways to slice and dice the data. It's taken a huge amount of work to get to this and the team behind it are to be congratulated. It would be fantastic if all recording schemes could make their data available like this.

 

 

A troublesome wasp

 

For the last month I have been finding specimens of a chalcid wasp by beating Lawson Cypress and other ornamental conifers. It is one of the Pteromalidae, a real ragbag of a family in desperate need of taxonomic revision - "a polyphyletic dumping ground of taxa that do not obviously fit within previously established families of Chalcidoidea" (Burks, R., et al (2022) From hell’s heart I stab at thee! A determined approach towards a monophyletic Pteromalidae and reclassification of Chalcidoidea (Hymenoptera). Journal of Hymenoptera Research, 94, 13-88) (glad it's not just me!).  I've had several goes at keying out these wasps, getting a different, moderately unsatisfactory answer each time. Along the way I have eliminated a few possibilities, and my most recent attempt strongly suggests that it is Macromesus amphiretus. It has all the characteristics of this species:

• Prepectus extremely small, hardly or not detectable. 
• Lower face with additional vertical groove parallel to genal groove. 
• Antennal formula of female 11173 (male 11172).
• Tarsi of female heteromerous, fore and hind tarsi five, mid tarsi four-segmented; first segment of mid tarsi in female very long.
• Both mandibles with three teeth.

All good - except for the fact that the hind margin of the propodeum does not match any of the three illustrations for this species I have been able to find. This would be a huge problem, were it not for the fact that each of the three illustrations is different! I am therefore inclined to call it Macromesus amphiretus, unless I can find an expert to tell me otherwise. 

Graham, MWR de V. (1969) The pteromalidae of north-western Europe (Hymenoptera, Chalcidoidea). Bull. Br. Mus. nat. Hist. (Ent.) Suppl. 16.

 

Boucek, Z. & Rasplus, J.Y. (1991) Illustrated key to west-paleartic genera. INRA Editions, série Techniques et Pratiques. ISBN 2-7380-0343-5.

 

Entomology Update - March 2026

Some warm spring days but plenty of frosts - a varied month with the season moving on.

Leicestershire entomology reaches the end of (another) era

Field observations of cyclic metamorphosis in entomology.  

Swamped with Spangles

We're drowning in tiny wasps. With some help I've figured out what's going to happen next. 

Apolygus - simplified

Apolygus is a tricky genus, but the impact of a new paper (if widely accepted) simplifies things.

Notable Finds

Asaphes vulgaris - first record for VC55

Euplectrus bicolor - first record for VC55

Psilocera obscura - first record for VC55

News from Elsewhere

Wettest winter ever

We all know it's been wet, but how wet exactly?

Urban Spiders
A new paper shows that Steatoda nobilis and Zygiella x-notata typically made up more than 80% of the urban spiders in an Irish survey.

We don’t see two foot long dragonflies anymore

It's not the reason we thought!

Read previous updates

Latest photos

Apolygus - simplified

 

Apolygus is a tricky genus, but the impact of a new paper (if widely accepted) on that British list is that Apolygus lucorum and Apolygus spinolae are genetically indistinguishable with A. spinolae as the valid name for the 'two' species. 

As a confirmed taxonomic lumper, I approve! 

Namyatova, A. A., Dzhelali, P. A., & Bolshakova, D. S. (2026) Integrative delimitation of Apolygus (Insecta: Heteroptera: Miridae: Mirinae) species known from Russia with the emphasis on Apolygus lucorum and Apolygus spinolae having trans-Palearctic distribution. Arthropod Systematics & Phylogeny, 84, 47-93. https://doi.org/10.3897/asp.84.e161376

 

 

 

Swamped with Spangles

 

Over the last week we have been swamped with these tiny wasps. They're all over the inside of the windows and the car, and the moth trap was full of them. It wasn't hard to figure out they were gall wasps, but I generally draw the line at Cynipoidea - they are extremely difficult to identify unless reared directly from the gall. Fortunately my good friends the VC55 gall experts were able to help and to point me at some excellent resources, particularly Oak-galls in Britain by Robin Williams. This allowed me to confirm that these are the Common Spangle Gall Wasp, Neuroterus quercusbaccarum. 

Cynipoidea have complex life-cycles, and that of N. quercusbaccarum is a two-act play known as heterogony - an alternation between a sexual generation and an asexual (agamic) generation.

The Sexual Generation (Spring)

The sexual phase begins in the spring, from January to March or April, asexual females emerge from the leaf litter where they spent the winter. These females lay their eggs in developing Oak buds. This triggers the tree to grow a Currant Gall. Inside these galls, larvae develop rapidly. In June, both males and females emerge. They mate, and the fertilized females then seek out the undersides of maturing oak leaves to lay their eggs.

The Asexual Generation (Summer to Winter)

The eggs laid on the underside of Oak leaves cause the tree to form  Common Spangle Galls. In autumn, before the leaves drop, the spangle galls detach from the leaf and fall to the ground. Inside the gall in the leaf litter, the larva develops into a pupa. Crucially, these larvae develop into females only. No mating is required for the next stage - parthenogenesis. These asexual females emerge the following spring.

This alternating strategy is an evolutionary masterstroke. The sexual generation provides genetic diversity, while the asexual generation allows for a rapid population boom without the "resource cost" of finding a mate during the harsh transition from winter to spring.

Looks like we'll be getting a bumper crop of Spangle Galls this year.

 

Urban Spiders

A new paper shows that Steatoda nobilis and Zygiella x-notata typically made up more than 80% of the urban spiders in an Irish survey. 

Collier, B. L., Leonard, D., Lyons, K., Dunbar, J. P., Lawton, C., & Dugon, M. M. (2026). Survey of Synanthropic Spiders in Ireland Reveals Expansion and Dominance of the Invasive Noble False Widow Steatoda nobilis in Urban Habitats (Araneae: Theridiidae). Ecology and Evolution, 16(3), e73193.

https://doi.org/10.1002/ece3.73193

 

Leicestershire entomology reaches the end of (another) era

Yesterday was a sad day for me personally, but from a wider perspective...

After 38 years, Leicestershire and Rutland Entomological Society (LRES) has scaled back operations due to falling participation and an elderly demographic. It's not completely gone, and the intention is that arrangements will be made for publications to continue (the plan is that the Natural History Section of the Leicester Lit & Phil Society will pick up the remaining activity of LRES, notably publications), but there won't be any more dedicated entomology meetings. We're not, of course, the first or the only society this has happened to. 

A VC55 entomology society has blinked into and out of existence and number of times, first as an offshoot of the Zoology Section of Leicester Literary and Philosophical Society. In the second half of the 19th century Leicester was an entomological powerhouse. Before a dedicated society existed, entomology in the region was driven by the "Lit & Phil", founded in 1835. Perhaps the most famous name associated with this is Henry Walter Bates, the Leicester lad and explorer who discovered "Batesian mimicry." In the momentous year 1844–1845, a young Alfred Russel Wallace moved to Leicester to take up a position as a master at the Collegiate School, teaching drafting, surveying, and English. While he was already interested in nature, he hadn't yet found his specific calling. Everything changed in Leicester. Here, Wallace met Bates, a local man who worked in his family’s hosiery business but spent every spare second obsessed with entomology, spending his limited free time collecting beetles in Bradgate Park and Charnwood Forest. Their friendship quickly turned into a professional partnership. By 1847, Wallace was bored with teaching and proposed a radical plan: they should travel to the Amazon rainforest to collect specimens and sell them to museums and collectors back in London. They left for Pará (now Belém), Brazil, in 1848. While they eventually split up to cover more ground, their time in Leicester remained the foundation of their careers. Frederick Bates, younger brother of Henry Walter Bates, began publishing in the Transactions of the Leicester Literary and Philosophical Society from the 1850s. In the late 19th century, figures like William Armston Vice and Frank Bouskell pushed for a specialized entomological section. For a time, a "Leicester Entomological Club" operated within the Lit & Phil, eventually evolving into Section F (Entomology) by the 1880s, producing the first comprehensive local checklists for the Victoria County History (1907). The Entomology Section ceased to operate during the 1939-45 World War and was not restarted after the War. 

 The Great Hiatus and the 1988 Rebirth

Following the 1939-45 World War, there was no formal entomology society. Naturalists of all shades typically met at the Leicester Museum, which acted as a de facto hub. Notable Leicestershire entomologists tended to interact directly with national entomology organizations. The modern society was born from a desire for a more focused, member-driven group when on June 8th 1988, a meeting was held at the University of Leicester to discuss forming a society. On September 5, 1988, the Leicestershire Entomological Society (LES) held its first official meeting at the New Walk Museum. A small number of founder members still remain. The society has always covered Watsonian Vice-County 55 (VC55), which encompasses both Leicestershire and Rutland. To formally recognize this, the society officially rebranded as the Leicestershire & Rutland Entomological Society (LRES) in 2022.

And now, it's over again - for now. Perhaps the "Leicestershire Entomological Club" will naturally re-emerge. Whether we blame Covid, social media, or Margaret "there is no such thing as society" Thatcher, I'm not happy this has happened on my watch, but the cyclic nature of Leicestershire entomology allows me to take comfort in the philosophy of Heraclitus - 

No man ever steps in the same river twice, for it's not the same river and he's not the same man.

Entomology Update - February 2026

February was a varied month, spring-like at times but mostly wet. I didn't get out much but made some interesting finds when I did. 

Culture Wars - Scientists versus Citizens

I try and stay well away from culture wars, but it recently came to my attention that there is some new terminology I should be aware of.  

TG Camera News

OM System has launched a new version of the TG-7 camera for microscope use.

Card Protector Sleeves

Transparent card protector sleeves (widely available online) are useful for harmlessly restraining insects for photography, including under the microscope.

Notable Finds

The observant may notice a theme to this month's Notable Finds. I haven't had chance to write about this yet but will do so next month. 

Cyrtogaster vulgaris, first record for VC55

Callitula bicolor, first record for VC55

Delphacodes venosus, second record for VC55

Epiclerus panyas, first records for VC55

Ooctonus vulgatus, first record for VC55

Microterys tricoloricornis, first record for VC55

 

News from Elsewhere

Jam today

You're not a real naturalist unless you have a strong affinity for jam jars. We all made our first specimen collections in jam jars - turns out they were a good choice! 

Read previous updates

Latest photos

Card Protector Sleeves

Transparent card protector sleeves (widely available online) are useful for harmlessly restraining insects for photography, including under the microscope. They're a little too shiny to be perfect so you need to arrange the lighting to avoid surface reflection. They are earier toi use in the field than the alternative - floating frames. 

 

TG Camera News

The PetaPixel website reports that OM System has launched a new version of the TG-7 Kit made for microscopes. The TG-7 Industry is a slightly modified TG-7 but the NY-TGV Super Adapter Kit is of most interest. I can't see any reason why this couldn't be used with any TG5, 6 or 7 camera. 

I don't think this is the best or most cost-effective solution for a microscope camera, but if you already have the TG5, 6 or 7 the adapter kit might be worth checking. 

The kit will be available in a few months time, UK pricing not available yet, but it is aimed at industrial users (who clearly have deep pockets). 

 

Culture Wars - Scientists versus Citizens

I try and stay well away from culture wars, but it recently came to my attention that there is some new terminology I should be aware of:

Citizen Science - typically top-down. Usually initiated and managed by professional scientists or by institutions. To collect large amounts of data labour is "crowdsourced" to the public.

Community Science - typically bottom-up. Usually initiated by a group of people who have a specific concern about their environment. The community are co-creators and owners of the research and frame the question(s), design the study(ies), and interpret the results.

Rule of thumb: If a project asks you to "help us help science," it’s likely citizen science. If it asks "how can science help us?" it’s likely community science.

 

Entomology Update - January 2026

After a freezing start, January was mostly ... wet, limiting entomology opportunities. 

Phone-based retirement

The weather hasn't helped but are we all spending too much time on our phones? 

An odd spot

The ladybirds appear to be plotting something, I'm not sure what they are up to. 

The Mysteries of the Metapleuron

It would be quite handy to have a metapleuron. 

Oligometry

The twisted tale of a wonky antenna. 

Two videos: 

Macrophotography Methods

and: 

Getting the most from your Olympus TG camera

 

Events 

• Leafhoppers & Allies: identification, ecology and recording - Alan Stewart
• VC55 County Recorder Conference

News from Elsewhere

Tiny forests ... are an (expensive) con

But don't take my word for it: Tiny forests, huge claims: The evidence gap behind the Miyawaki method for forest restoration. Journal of Applied Ecology, e70242. https://doi.org/10.1111/1365-2664.70242

It's the pits

A new paper shows that the sensory pits on the cuticle of planthopper nymphs (Fulgoromorpha) sense electric fields.

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Latest photos

Oligometry

In Peritrechus, the structure of the antennae is an important diagnostic character. In Peritrechus geniculatus, ant3 is as thick or thicker than ant1, whereas in the other very similar species it is thinner. This recent specimen was missing the left ant4 but still identifiable as P. geniculatus. Then Jim Flanagan pointed out something odd to me. Maybe the left ant4 never got lost - it just didn't grow? The key is that the left ant2 is longer than the right - this is called oligometry and is frequent in Lygaeidae. Oligometry usually results in one of the antennae having three segments (it can also affect both antennae and then it is known as bilateral oligometry). It is thought to be caused during late development phase but precise reasons behind this deformation are not well known.

 

 

The Mysteries of the Metapleuron

I've always found Nysius to be a difficult genus to identify, apart from the obviously hairy N. huttoni. I turned up a few at the weekend but this time I used the key published by by Dolling, Het News, Issue 2, Autumn 2003. This turned out to be much easier than the other keys, and in the blink of an eye I had this one down to a species pair - N. graminicola vs. N. senecionis. The hind tarsi indicated which of these two it was, but to confirm I had to check the metapleuron, which confirmed that this was Nysius senecionis. 

Which raises the question - what the heck is a metapleuron? In Nysius the metapleuron is the lateral sclerite of the third thoracic segment and is the primary platform for the metathoracic scent gland (MTG) system. It consists of:

• The ostiole: an opening on the metapleuron through which the MTG reservoir empties its contents.
• The peritreme: a specialized cuticular structure (often shaped like an auricle or spout) that surrounds the ostiole. This directs the liquid secretion away from the body and onto the evaporatorium.
• The evaporatorium (or matt area): a distinct, non-glossy region of the metapleuron characterized by a highly micro-sculptured, "mushroom-like" or reticulated cuticle which increases the surface area significantly, allowing the defensive fluid to spread rapidly and evaporate (volatilize) almost instantly. This creates a "scent cloud" that deters predators before they can make physical contact.

The most important physiological role of the metapleuron is the dispersal of repellent defence chemicals. An additional role is in pheromone communication, acting as a broadcast structure for alarm, aggregation and sex pheromones. The specialized cuticle of the metapleuron evaporative area also prevents defensive secretions from being absorbed back into the insect's own underlying tissues.

I don't know about you, but it seems like a metapleuron might come in quite useful.

 

An odd spot

I made my first ladybird records of the year yesterday. Since December, through all the rain, frost and snow of January, through Storm Gorblimey, these two 7 Spot Ladybirds, Coccinella septempunctata, (which had a good year), had been huddled up on a Yew planted a few years ago precisely to give overwintering shelter for invertebrates. But rather than seeking shelter they were clamped to the tip of a branch in the most exposed spot possible. I was starting to wonder if they were alive, or semi-alive (parasitised), but when I took their photo (without touching or disturbing them as far as possible), they wandered off in a huff and settled down again a few inches away. 

In the afternoon, clearing out the garden nestboxes, I found a 2 Spot Ladybird safe and warm in a cozy woodcrete winter home. Sadly, I did have to evict this one in order to clean out the box, but yesterday was warmer so it will be fine. 

Phone-based retirement

The Atlantic

I don't write about sociology but I am interested in the collapse of social capital, especially as it relates to engagement with natural history. In the US there has been a lot of discussion recently about "phone-based retirement" - retired people are spending more time on (mobile) screens, with less engagement in traditional activities (such as stitting in chilly church halls listening to natural history talks). In his book Bowling Alone, sociologist Robert Putnam used the collapse of US 10 pin bowling leagues to illustrate the decline of social capital. While Putnam was describing a pre-Internet society, the same trends have continued and probably accelerated (Covid or no Covid). Putnam says he doesn't know the "answer" to this. Which is good, because neither do I. Currently it's hard to see how this trend could be reversed. For a mere £9 a year I can "participate" in all of Cambridge Natural History Society's talks online via Zoom. That, together with the super output of the Biological Recording Company, is in some ways an amazing prospect; and in others, thoroughly depressing. 

It's the pits

A new paper shows that the sensory pits on the cuticle of planthopper nymphs (Fulgoromorpha) do not respond to sound, ultrasound, mechanical stimulation, temperature changes, or magnetic fields. They do, however, respond to stimulation with very low intensity electric fields. This, together with the arrangement of these special sensory structures on the body surface of planthoppers, imply that these sensory organs perceive electric fields in the environment. The authors suggest that this sense may help the bugs to avoid predators or parasitoids. This finding also corresponds with recently published observations for treehoppers (Membracidae), where the horn-like extensions of the pronotum contain similar sensory pits. 

Electrosensitivity in planthoppers (Insecta: Hemiptera: Auchenorrhyncha: Fulgoromorpha). (2026) Journal of Comparative Physiology A, 1-13. https://doi.org/10.1007/s00359-025-01790-1