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:

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

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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

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Wettest winter ever

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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!

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