Thursday, 20 November 2014

Stacking!

I have been promising myself that I would do some image stacking to see how I get on with it. Image stacking is a technique that is used to produce a macro image where everything is in focus. With macro photography, the depth of field of a single shot is tiny, often less than 1mm. This means that anything over 1mm. wide will have some parts out of focus. Here's an example:


That shot isn't bad, but although the front-to-middle part of the shot is sharp, the rear part of the image is out of focus and blurred.

With image stacking, we take a number of shots from the same position, but with the focus point moved slightly further back each time. In order to get the stability required, we need to use a tripod and use manual focussing. The depth of the subject above is around 5mm., so I took 5 shots, each focussing around 1mm further away. The images are then fed into software which fine-tunes the positioning of each image to make sure they overlap precisely, and then it corrects for slight differences in perspective due to the refocussing. Finally, the software selects the sharp parts from each image and creates a single image which is sharp from front to back:


The entire procedure from shot-taking to final image took perhaps 30 minutes, but I'll be faster next time. I suspect it could all be done in perhaps 15 minutes.

"So what's the image?" I hear you ask.

It's a moth which has been killed by the parasitic fungus Cordyceps tuberculata, which is an extremely rare species, on the RDB list as Vulnerable D2. This specimen was found in Co. Cork and is the first Irish record. There are only 23 other records in the Fungal Records database and they are mostly from the east of England. I rather suspect this is a continental species, since most records are coastal, and it's possible that the victims were migrants. This is, however, pure speculation on my part.

The specimen has been sent to Kew for analysis, since they would like to eliminate the possibility that it's something even rarer.

Acknowledgements to Clare Heardman for finding the specimen and sending it to me for analysis.

5 comments:

Gill said...

Fascinating - never come across that software before but it looks fantastic, if a bit fiddly.
As for the specimen - is it the moth or the fungus that is very rare? By "moth" I assume you mean caterpillar in this instance?

stuart dunlop said...

You can buy specialist software, e.g. zerene stacker, but some photo editing programs do it too, e.g. Photoshop. It's the fungus that's rare (in BI, anyway). We don't know what the (adult) moth is, unfortunately.

Peter Archdale said...

I'm not surprised species like this fungus are rare, but are they uncommon species or just rarely recorded? In this case, probably both; I'm not sure I would have noticed it anyway. In what habitat/circumstances was the specimen found?

stuart dunlop said...

Good question, Peter, and I think we could classify both 'real' rarities and 'perceived' rarities. I'd say real rarities are those which are recorded infrequently, but are actively sought. A good example is Cerodontha silvatica, the leaf miner on Woodrush. I know of people who have been unsuccessfully searching for it for decades, and the plant isn't rare, as you know. True rarity can have a number of causes: perhaps we are on the extreme limits of the range, and only get bold explorers or specimens displaced by weather. An example of this could be the Phytoliriomyza miner on Balsam, which has few records, since it is just arriving here, but might become common in future. Other rarities occur because the precise circumstances required for their existence don't occur very often. For example, I know of gall-causing wasps that only create galls on hybrid trees, so both parents of the hybrid must be sufficiently close to each other for the hybrid to occur. But if you're a parasitoid wasp that needs that particular gall-causer, then you won't be found too frequently. Some fungi are successional, and can only exist if other species of fungi have already been present and paved the way for the followers to take hold. This, I think, is one reason that some rare fungi are found only in ancient forests: the correct conditions take a long time to arise. One reason for perceived rarity is where species are difficult to identify. I know from experience that parasitic wasps are very common, but there are very few records. I have investigated these quite closely, and I know that identification can require access to specimens, microscopes, reference collections and documentation which is sparse, out of date, and dispersed in difficult-to-find papers and journals. But I still intend to work at it...:) The specimen of the fungus in this post might well be both really rare and perceived rare. I think it's probably on the limit of its (current) range, and it appears to be more common in other, warmer, countries. That's why I suspected the host moths might be migrants. Early (1940's) English records were all east coast and this specimen was found in Cork. These locations are well-known for migrant arrivals from east and south. Having said that, these fungi are only studied by very few people, and the documentation is sparse, so getting the correct id is difficult even when it is found. This could result in a truly rare species being perceived as even rarer. For the record, this specimen was found in a greenhouse that contains organically-raised exotic fruits, so back-tracking the origin would be fraught with all kinds of possibilities.....;) Since I posted images, I have had a few "Oh, I've seen something like that, but didn't know what it was. Would you like specimens?" type of comments. We'll see what comes out of that.

Em Parkinson said...

Hello Stuart, I was sent over here by Pat...the Weaver of Grass....as she thought you might be able to help me identify something I've never seen here (Dartmoor) before. I'm not even sure if it's fungi or eggs so I wonder if you would mind having a look for me? This is a link to the post in question and the photos are about halfway through.

http://dartmoorramblings.blogspot.co.uk/2014/11/jack-be-nimble.html

Both could have done with your stacking advice! That's something I'd love to try and what a fascinating phenomenon the mothy fungus is. I must go back and have another look.

Thanks so much....in anticipation of your visit.....Em