Diatom id?

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LouiseScot
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Diatom id?

#1 Post by LouiseScot » Tue Apr 06, 2021 12:22 pm

I'd be interested if anyone can id this quite intricate marine diatom from the Eastern Mediterranean :) Prepared slide in Pleurax.
40x objective, slightly different views and lighting:


NoDo415nmNikon40x_Crop100pcScale00017.jpg
NoDo415nmNikon40x_Crop100pcScale00017.jpg (70.04 KiB) Viewed 2130 times

Med_Do_10W_Nikon40x_Crop100pc00002.jpg
Med_Do_10W_Nikon40x_Crop100pc00002.jpg (87.17 KiB) Viewed 2130 times

Med_Do_10W_Nikon40x_Crop100pc00001.jpg
Med_Do_10W_Nikon40x_Crop100pc00001.jpg (84.32 KiB) Viewed 2130 times

Do415nmNikon40xCrop100pcScale_00013.jpg
Do415nmNikon40xCrop100pcScale_00013.jpg (123.37 KiB) Viewed 2130 times


Thanks!


Louise
A Nikon CF plan 20x; A Swift 380T; A DIY infinity corrected focus rail system with a 40x/0.65 Olympus Plan, a 10x/0.30 Amscope Plan Fluor, and a 20x/0.75 Nikon Plan Apo

Hobbyst46
Posts: 4277
Joined: Mon Aug 21, 2017 9:02 pm

Re: Diatom id?

#2 Post by Hobbyst46 » Tue Apr 06, 2021 12:58 pm

A guess - an Amphora species.

LouiseScot
Posts: 1167
Joined: Tue Jul 07, 2020 1:51 pm
Location: Scotland

Re: Diatom id?

#3 Post by LouiseScot » Tue Apr 06, 2021 3:04 pm

Hobbyst46 wrote:
Tue Apr 06, 2021 12:58 pm
A guess - an Amphora species.
Oh ok - there seems to be an awful lot of them!

Here's a quick stack I did (8 frames). I'm not very skilled at stacking...


'High' preference

Med40xNikon415nm_sup1_Hi20_fil1_8F_Crop100pcscale.jpg
Med40xNikon415nm_sup1_Hi20_fil1_8F_Crop100pcscale.jpg (73.06 KiB) Viewed 2111 times

'Low' preference

Med40xNikon415nm_sup1_Lo-20_fil1_8F_Crop100pcscale.jpg
Med40xNikon415nm_sup1_Lo-20_fil1_8F_Crop100pcscale.jpg (72.8 KiB) Viewed 2111 times

Louise
A Nikon CF plan 20x; A Swift 380T; A DIY infinity corrected focus rail system with a 40x/0.65 Olympus Plan, a 10x/0.30 Amscope Plan Fluor, and a 20x/0.75 Nikon Plan Apo

Hobbyst46
Posts: 4277
Joined: Mon Aug 21, 2017 9:02 pm

Re: Diatom id?

#4 Post by Hobbyst46 » Tue Apr 06, 2021 3:34 pm

The excellent resolved stria pattern of image "Do415nmNikon40xCrop100pcScale_00013" is not visible in the stacks. My opinion is that for this diatom, to choose the few images that manifest well focused surfaces and stack them. So I did for a twin of this diatom, albeit I had phase contrast images.

LouiseScot
Posts: 1167
Joined: Tue Jul 07, 2020 1:51 pm
Location: Scotland

Re: Diatom id?

#5 Post by LouiseScot » Tue Apr 06, 2021 4:06 pm

Hobbyst46 wrote:
Tue Apr 06, 2021 3:34 pm
The excellent resolved stria pattern of image "Do415nmNikon40xCrop100pcScale_00013" is not visible in the stacks. My opinion is that for this diatom, to choose the few images that manifest well focused surfaces and stack them. So I did for a twin of this diatom, albeit I had phase contrast images.
I only used Picolay here - Since the end of last year I have Zerene Stacker (on another system) but haven't got around to trying it yet!
I never quite understand how stacking works when you want to see internal structures. I suppose it doesn't, very well! The focus at high NA is critical. I made a little lever to aid adjustment :)

FocusLever_Crop.jpg
FocusLever_Crop.jpg (19.53 KiB) Viewed 2103 times

I'll certainly try again, and as you suggest though my expectations aren't great... The striae patterns were only in more or less one layer, I think, so not many options. But I'll have another go and see what I can do - many thanks!

ps Have you posted pics of your phase contrast version? I'd love to see them :)

Louise
A Nikon CF plan 20x; A Swift 380T; A DIY infinity corrected focus rail system with a 40x/0.65 Olympus Plan, a 10x/0.30 Amscope Plan Fluor, and a 20x/0.75 Nikon Plan Apo

Hobbyst46
Posts: 4277
Joined: Mon Aug 21, 2017 9:02 pm

Re: Diatom id?

#6 Post by Hobbyst46 » Tue Apr 06, 2021 4:29 pm

I think that the main differences between stacking softwares is speed, efficiency, user friendliness etc rather than the quality of the final product.
My preferred stacking program is Toupview (free I think). Tab "Process"->"EDF" (extended depth of focus). Superb software in general.
Here is a stack. Although, re-thinking, phase contrast are not ideal for stacking.

P.S. I like the focusing lever !
Attachments
Stack of phase contrast images of a marine diatom.jpg
Stack of phase contrast images of a marine diatom.jpg (38.01 KiB) Viewed 2099 times

LouiseScot
Posts: 1167
Joined: Tue Jul 07, 2020 1:51 pm
Location: Scotland

Re: Diatom id?

#7 Post by LouiseScot » Tue Apr 06, 2021 4:36 pm

Hobbyst46 wrote:
Tue Apr 06, 2021 4:29 pm
I think that the main differences between stacking softwares is speed, efficiency, user friendliness etc rather than the quality of the final product.
My preferred stacking program is Toupview (free I think). Tab "Process"->"EDF" (extended depth of focus). Superb software in general.
Here is a stack. Although, re-thinking, phase contrast are not ideal for stacking.

P.S. I like the focusing lever !
Yours is overall much better than mine!
Picolay is free - written by a German, I think - www.picolay.de
The Zerene Stacker wasn't free!
My hands don't always do quite what I want them to these days :( The little lever helps. It just clamps on so easy to remove, if necessary.

Cheers

Louise
A Nikon CF plan 20x; A Swift 380T; A DIY infinity corrected focus rail system with a 40x/0.65 Olympus Plan, a 10x/0.30 Amscope Plan Fluor, and a 20x/0.75 Nikon Plan Apo

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