1 long diatom

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75RR
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1 long diatom

#1 Post by 75RR » Sun Sep 02, 2018 3:39 am

Plan 40x/0.65, DIC, 275µm length x 15µm width, 3 stacks stitched in Photoshop.
This image (linked from imgur) is 1400 x 600. Tried it at 1024 pixels but the detail is lost.

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GaryB
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Re: 1 long diatom

#2 Post by GaryB » Sun Sep 02, 2018 11:57 am

Excellent details, nicely done!

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75RR
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Re: 1 long diatom

#3 Post by 75RR » Mon Sep 03, 2018 9:46 am

Thanks GaryB

Here is another long one, 540µm no less. Different species, though I could not say which.

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vasselle
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Re: 1 long diatom

#4 Post by vasselle » Mon Sep 03, 2018 11:22 am

Bonjour
Très belles images
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Crater Eddie
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Re: 1 long diatom

#5 Post by Crater Eddie » Tue Sep 04, 2018 12:14 pm

Superb! Good work there.
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Re: 1 long diatom

#6 Post by billbillt » Tue Sep 04, 2018 1:28 pm

Wow!... More wonderful photos.. Thanks for sharing...
BillT

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KurtM
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Re: 1 long diatom

#7 Post by KurtM » Tue Sep 04, 2018 3:00 pm

Are the undulations real, or artifacts of PP?

Cool images, we seldom see super long-n-skinny pennate forms in their entirety because they're so difficult to image effectively. And living ones to boot! 8-)
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75RR
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Re: 1 long diatom

#8 Post by 75RR » Tue Sep 04, 2018 3:36 pm

Many thanks vasselle, Crater Eddie, billbillt and KurtM
Are the undulations real, or artifacts of PP?
Had not noticed that until you mentioned it. I think it is partly Photoshop and partly a mysterious blotch which is hiding out somewhere, perhaps on the camera sensor, which I have not been able to find and cleanup as yet.
As the image consists of several stacks stitched together (9 in total), what appear as undulations is partly an effect of the 'blotch' making a sequential appearance. Should have tidied up the background more.
Can therefore confirm (if my memory is to be trusted) that the Diatom is indeed flat :)
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Re: 1 long diatom

#9 Post by charlie g » Tue Sep 04, 2018 5:20 pm

Nice work, thanks 75RR. Quite a while back I was stymied on how to keep the resolution of a 40X 0r higher mag objective...for the entire body of Spirostomum huge ciliates (mm's in length!).


I mused about the way to keep entire body, yet have good resolution on the wonderful body ciliature. So I ask, 75RR..where a long bodyform like your diatoms posted here...is it that at the 'stiches'...you loose some details..perhaps you omit a section ( yes a small section of the body)...perhaps you unwittingly repeat a small segment of the diatom? I am thinking of the huge ciliates where the bands of ciliature form crisp traceries which to small degree get artifact-disrupted in 'stiching' an entire organism from a collection of high mag images..is the finished composite image always with artifacts/disruptions at 'stich areas'? Other than sketches of huge ciliates...I'm not sure I've ever enjoyed entire body crisp resolution images of these organisms..it's their traceries of ciliature which in active motion give such charm to these huge protozoans! thanks for your postings, Charlie guevara

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Re: 1 long diatom

#10 Post by KurtM » Wed Sep 05, 2018 12:49 am

Hope it didn't come across like I'm picking at the imaging process. Rather, I have studied teratogenic forms (basically "deformed" diatoms) a bit, and am always on the lookout for them. It seems most common in Surirelloids, whereas super long pennates like you show are invariably arrow-straight as far as I have ever known. But then, you're sampling a location on the other side of the world that's pretty exotic to me. Plus, it just seems like those spindly pens should be especially prone to it...

At any rate, I am always particularly interested in the diatom images you post, please keep 'em coming! 8-)
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Re: 1 long diatom

#11 Post by Hobbyst46 » Wed Sep 05, 2018 8:02 am

Very enjoyable photos, 75RR!
Given my zero knowledge of diatom identification, and hoping this is not a stupid question, could it be that the two photos are different views of the same diatom? Like, girdle view against valve view?
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75RR
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Re: 1 long diatom

#12 Post by 75RR » Wed Sep 05, 2018 9:55 am

Thanks charlie g, KurtM and Hobbyst46
So I ask, 75RR..where a long bodyform like your diatoms posted here...is it that at the 'stiches'...you loose some details..perhaps you omit a section ( yes a small section of the body)...perhaps you unwittingly repeat a small segment of the diatom?
To stitch there must be a large overlap between the images or the software simply refuses to work. I think in general that there is some image adjustment by software in both stacking and stitching - though not nearly enough to compromise the images as a whole. The benefits of stacking far outweigh such minor tweaks.
At any rate, I am always particularly interested in the diatom images you post, please keep 'em coming!
Will do
... could it be that the two photos are different views of the same diatom? Like, girdle view against valve view?
Good question. Believe you could well be right. Found this (thanks to your tip) which would seem to indicate my two photos are different views of the same species.
Not marine but fresh water and in South America rather than the Mediterranean but there are similarities. So ... a saltwater cousin of Ulnaria? All guesses welcome!

https://www.researchgate.net/publicatio ... ca_Bolivia
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Re: 1 long diatom

#13 Post by coominya » Thu Sep 06, 2018 8:07 am

75RR wrote: ... As the image consists of several stacks stitched together (9 in total), what appear as undulations is partly an effect of the 'blotch'
Is it necessary to stack micrographs in every instance 75? Is it necessary with bright-field imagery? I understand with astro pix it's necessary because of the low light levels and the movement inherent in the mounts that the scopes sit atop but I fail to see why it's necessary with our microscope pix.

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75RR
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Re: 1 long diatom

#14 Post by 75RR » Thu Sep 06, 2018 9:32 am

Is it necessary to stack micrographs in every instance 75?
Indeed not. There are valid reasons for doing it (see attached image + link from Wiki), but at the end of the day it is just a personal preference.

https://en.wikipedia.org/wiki/Focus_stacking

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Re: 1 long diatom

#15 Post by mrsonchus » Thu Sep 06, 2018 9:47 am

75RR wrote:Many thanks vasselle, Crater Eddie, billbillt and KurtM
Are the undulations real, or artifacts of PP?
Had not noticed that until you mentioned it. I think it is partly Photoshop and partly a mysterious blotch which is hiding out somewhere, perhaps on the camera sensor, which I have not been able to find and cleanup as yet.
As the image consists of several stacks stitched together (9 in total), what appear as undulations is partly an effect of the 'blotch' making a sequential appearance. Should have tidied up the background more.
Can therefore confirm (if my memory is to be trusted) that the Diatom is indeed flat :)
Hi 75! As per the 'blotch'.... Worry-ye-not my friend, that is no blotch. This effect happens almost every time with stitches of my own images through the 'scope. It's quite maddening at first, as there's no visible variation across the illumination of the field through the 'scope, but when the camera takes the image there's very often a trace of unevenness in the background's brightness, as though illumination is uneven, which it isn't. I've come to the conclusion (out of puzzlement and desperation rather than the use of any knowledgeable logic) that it's 'something' the camera's exposure/processing causes. I suppose I'd call it an artifact from the camera.

One thing I can definitely echo is that it's not an indication that the subject isn't flat - this effect is seen when imaging my perfectly flat 3-4µ mounted sections also.

For a single image I sometimes use (but in all honesty rarely bother) the free Olympus background removal utility. The vast majority of the time I simply use the 'magic selector' tool in PSE (v9) to auto-select the background then use the 'average' tool to even-out the background. This may be applied to the individual images or the finished stitch.......

The stitching process doesn't add or subtract from the final image - simply overlap the series by about 30% for a nice stitch.

That's how I stitch my images, all of which are really pretty difficult to stitch and almost impossible to stitch without seeing this 'darkening of one side' or apparent unevenness of illumination.

It does look to the eye like undulation, just the repetition of the effect as you suggest.

Keep up the good work old chap, excellent images with bags of interest!

John B.
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coominya
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Re: 1 long diatom

#16 Post by coominya » Fri Sep 07, 2018 12:15 pm

75RR wrote: Indeed not. There are valid reasons for doing it (see attached image + link from Wiki), but at the end of the day it is just a personal preference.

https://en.wikipedia.org/wiki/Focus_stacking
Ahhhh, I see one value of it now. No doubt there are many more too :D
Very clever what computers can do, given a good program...

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Re: 1 long diatom

#17 Post by ImperatorRex » Tue Sep 11, 2018 3:56 pm

Recently tried also stacking, but I am not really experienced.

Not Stacked
Image

Stacked (5 pics)
Image

Side effect of the stacking may be that it looks a bit "flat"?

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75RR
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Re: 1 long diatom

#18 Post by 75RR » Tue Sep 11, 2018 5:51 pm

ImperatorRex wrote:
Side effect of the stacking may be that it looks a bit "flat"?
Shouldn't really. It helps if one visualizes the areas that will be combined in the final image.
I tend to do a dry run first to see what sections I need to get in sharp focus to create the final image I want.
Note that it is possible (depending on the subject matter) to focus too deep, this can ruin a stack.

You might want to do a test using just two or three of those images - see if it improves.
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