Myxomycetes

Pitufo · Post by **Pitufo** » Wed May 11, 2016 11:47 am

Thanks to everyone on the forum for your help and advice which has allowed me to get started in my chosen field of myxos.

Some Myxomycetes from a recent trip to Scotland. MPE-65 with manually adjusted stage. 3 x Jansjo lights and plastic cup diffuser. Stacks of around 10-20 images.

Firstly, Hemitrichia calyculata

Metatrichia floriformis

As you can see in the final photo, I am getting trails in the background of the image after stacking (I have removed the worse offenders in GIMP). Is this likely to be dust on the sensor?

As always, any advice and tips greatly appreciated.

Greenfields · Post by **Greenfields** » Wed May 11, 2016 1:52 pm

Good pictures of the fruitbodies of these fascinating organisms.

I am getting trails in the background of the image after stacking (I have removed the worse offenders in GIMP). Is this likely to be dust on the sensor?

Yes. The nominal aperture values marked on the MP-E 65 lens are still the ratios of the entrance pupil diameter to the lens focal length despite the fact that this lens can never be used at those apertures because it cannot focus to infinity. The effective aperture is what matters, and that will be half of the nominal aperture (i.e. double the f/ number) at 1:1, and much less at higher magnifications. The calculations are complicated by the fact that the focal length of the lens changes - and not in a straightforward way.

This means that the effective aperture of the lens will be very small when compared to a conventional photograph, and that will produce shadows from much smaller dust spots than would normally be visible.

The effect is even worse with microscope objectives, but many microscope objectives are designed to be telecentric, which means that you can turn off the re-scaling and alignment options of the stacking software and get a much less obtrusive single spot rather than a trail.

I have never found this to be possible with the MP-E 65.

At long exposures you may also find trails of tiny bright crosses. These are only visible if you shoot raw images and the raw developer software does not eliminate these "hot pixels". Canon's DPP software, for example, does not deleted them. Although only isolated single photosites are affected (at increasing numbers at longer exposures) the demosaicing algorithm of the raw developer typically interpolates into adjacent pixels to produce more or less faint crosses.

Henry

Pitufo · Post by **Pitufo** » Wed May 11, 2016 3:21 pm

Thank you Henry. I haven't seen the "bright cross" effect yet - but I will know what it is when I do.

What, if any, is the solution to the background streaks?

boomblurt · Post by **boomblurt** » Thu May 12, 2016 4:39 am

I can't recall ever hearing of slime mold before but they seem amazing (and rather pretty) - off to find out more.

Thank you.

Pitufo · Post by **Pitufo** » Thu May 12, 2016 4:58 am

Thank you - they certainly are amazing.

Here's another one.. Trichia decipiens var. olivaceous in immature and mature state. The second image was taken 48 hours after the first.

Greenfields · Post by **Greenfields** » Thu May 12, 2016 6:17 am

What, if any, is the solution to the background streaks?

1] If you have a Canon DSLR collecting "dust delete data" by shooting an out-of-focus plain background with the same lens, magnification and aperture setting before shooting a stack may work.

The procedure is described in the camera manual and works very well with conventonal images. It maps all the reduced density areas caused by dust particles in the image then automatically brightens the corresponding spots in the captured image.

The underlying technology is disclosed in Canon patents but I do not know how many features an individual map can capture.

Other brands may have similar functions but I have only used Canons.

2] Once you have captured an image I'd suggest using the retouching tool of the stacking software. In Zerene, for example, you could select an image in which the boundary between the background and foreground is sharp and use the retouching tool to "clone" the background. The background of a single frame should be much cleaner than a stack making subsequent retouching of individual blemishes easier.

If the stack has a large number of frames, using a tool like SlabberJockey (which is free and works very well) with Zerene to produce "slabs" or sub-stacks makes finding a source with a sharp boundary easier.

I haven't seen the "bright cross" effect yet - but I will know what it is when I do.

You may never see this if your raw development software automatically detects and clones out the hot pixels.

Canon DPP (not even version 4) does not. I think that Photoshop and probably many others do.

In the case of Canon DSLRs "hot pixels" seem to appear at exposure times of the order of a second and become more numerous and obvious at longer exposures. Before they "burn out" to white crosses at the longest exposures their colour depends on the colour channel of the photosite affected. Canon have software which can load a hot pixel map into the camera's firmware when the camera is serviced. An instruction manual for the software has escaped, but I have never seen a working example of the software. Additional hot pixels will still appear as the camera ages. Their incidence is reported to be correlated with cosmic ray exposure (e.g. to be higher in cameras which have been on lots of flights).

Henry

Pitufo · Post by **Pitufo** » Thu May 12, 2016 6:47 am

Thank you Henry - that is an excellent answer and explanation.

I am using a Canon 70D but did not know about that function, so will investigate further.

The tip about cloning part of the background from a single image is really handy too. I hadn't thought of doing that.

Your help is much appreciated.

Kind regards,

John

David Sykes · Post by **David Sykes** » Fri May 13, 2016 1:05 pm

John,

do you know Professor Bruce Ing, the UK slimemould expert ?

He was a neighbour of mine in Mold (!), North Wales.
He has now moved to Scotland.

When I took macro stereo shots of slime moulds some years ago, I found that tungsten or flash illumination created a continuous streaming of spores from the fruit body.

David

Pitufo · Post by **Pitufo** » Mon May 16, 2016 6:29 am

Hi David

Yes, indeed - these photos were taken in collaboration with Bruce. He is on good form.

And yes - any change in air pressure seems to trigger spore release, often sooner than you would like!

Kind regards,

John

boomblurt · Post by **boomblurt** » Sat May 21, 2016 2:28 am

May be of interest ... not just pretty but clever.

http://www.abc.net.au/news/2016-04-27/s ... in/7363176

zzffnn · Post by **zzffnn** » Sat May 28, 2016 5:15 pm

Great images and very interesting!

Pitufo · Post by **Pitufo** » Fri Jun 10, 2016 12:05 pm

Thank you zzffnn and boomblurt

Here are a couple of more images of another myxomycete, Stemonitopsis typhina, taken today.

Pitufo · Post by **Pitufo** » Tue Jun 14, 2016 3:06 pm

I found another one today. I think this is an Arcyria and I'm looking forward to seeing what it turns into..

Pitufo · Post by **Pitufo** » Wed Jun 15, 2016 5:55 am

Approx 12 hours later... I think it could be Acyria incarnata or something similar. Microscopy of spores and capillitium will be needed to confirm. Spot the mite trying to get into the action.

Pitufo · Post by **Pitufo** » Thu Jun 23, 2016 11:05 am

Not quite the spectacular finale I was hoping for..

I am reasonably sure this is Arcyria incarnata. Spores and capillitium are shown below (in Lactic acid cotton blue)..