Newbie learns to take images, dtsh edition

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dtsh
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Newbie learns to take images, dtsh edition

#1 Post by dtsh » Fri Apr 09, 2021 8:51 pm

I am very much the newie when it comes to imaging, so please don't expect too much. My intent is to have a place to put what I've learned and to have a spot where I can look back on what I have accomplished (or not!).

I have a few different microscopes, but I will try to mention exactly which one is in use for the imagaing as I often find myself looking at the images others take and wonder about the setup. Please feel free to ask questions, offer advice, etc.

The microscope this was taken with is an American Optical Series 10. I have a few of these as I took the "buy several used scopes and cobble together the best" path of acquiring what I wanted. There are features I really like about the AO 10 series and features that aren't so great, but the good far outweight the bad IMO and one can get a really nice system for not a lot of money. This isn't the nicest one I have, but it's the one I most recently cleaned and lubbed, so it makes sense to test it out.

Kindly allow me a slight diversion before I get started for those not familiar with the AO10. It's an infinity based system, so one is somewhat limited to the objectives produced by AO, but on the plus side they produced a number of good objectives. One of the features I really like about the AO10 is that the stage is fixed and doesn't move, instead it's the nose/objective turret that moves up and down for focus. What that means is if you focus down too far the objective just rests on the slide instead of crushing the two together. The focus mechanism, when cleaned and lubricated, is silky smooth. I really like the focus mechanism and maybe I'll take pictures of the next one I tear down to clean. The issues I've seen on some other platforms where the focus drifts due to gravity isn't a problem with this design.

All of the obbjectives on this one are plan achromats, 4x (1017), 10x (1019), 40x (1309), and 100x (1311). The 40x and 100x are "Advanced Plan Achromats" and perform a little better than the previous models they replaced. The objectives for this series are compatible with the 110 series, though usually the 110's have the newer objectives and many of the stock 10's the older ones. For the most part, even the older series objectives perform very well.

The condenser is the aspheric (1084) with the auxiliary lens to give the 4x a fully illuminated field. I have the basic Abbe condenser for the AO10 as well, but it's on another stand. Two points about the standard condensers on the AO10 platform; one, they aren't centerable, the fork aligns them and that's that. I don't find it a big deal myself, but there is a less common centerable condenser which I have on one of the other stands as well. The second is that the filter holder isn't very nice, but a simple 3D printed adapter allows using most of the common filters fine. Do note that on non-centerable condensers some filters, such as darkfield patch stops, might not work quite as well. This doesn't matter so much to me as I have a darkfield condenser on yet anouther stand (have I mentioned how inexpensive the AO10 are if you're patient and how many accessories they have?)

The illuminator is the 17w 1036A with the 1051 transformer. The 1036A has adjustments to allow the light to be centered under the condenser, but is otherwise the same as the 1036, both having a neutral density filter that can be swung into place.

The head is a trinocular, the switch flips it between 100% eyepieces and 100% photo tube. Most of the heads I have needed cleaning and lube badly as the interpupilary adjustment was siezed with old grease. If you try fixing these, you'll need a set of bristol spline wrenches for a couple of the screws.

I think that's a good enough overview of the microscope itself, now onto the rest...

The camera is an older Canon T2i (18MP) that I coupled to a 10x (171) eyepiece inserted into the phototube with a simple 3D printed adapter. The camera is using an 18-55m lens set on roughly 28mm or so. I'm still experimenting with this a bit. I'm using a wired remote to trigger the shutter. I'm just now reading camera docs, so kindly excuse my nearly total ignorance in this area.

For stacking software I'm using ufraw to convert from Canon's CR2 format to png, mogrify (from ImageMagik) to convert from png to tif (I get errors if I go directly from CR2 to tif with ufraw), then I use align_image_stack from the Hugins tools, and lastly enfuse to assemble it all together. I'm using these because they're what I have and didn't cost me anything, not because I think they're superior. Any other image processing is largely done in gimp.


So all that text and now for some images.
First, the AO10...
AO10_1.jpg
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And now with the camera set in place.
AO10_canon.jpg
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And lastly, the first attempt I'm happy enough with to share (it's not my first attempt, but not far from it). It's a small copepod collected here on my property. Imaged with the 10x objective from 21 images.
copepod_s.jpg
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DonSchaeffer
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Re: Newbie learns to take images, dtsh edition

#2 Post by DonSchaeffer » Fri Apr 09, 2021 9:54 pm

A proud achievement!

ScienceMatters
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Re: Newbie learns to take images, dtsh edition

#3 Post by ScienceMatters » Fri Apr 09, 2021 11:26 pm

A great start! With the older scopes, it takes a lot just to get to that point! Nice work.

dtsh
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Re: Newbie learns to take images, dtsh edition

#4 Post by dtsh » Sun Apr 11, 2021 2:35 am

Today's attempt is a single image of pollen from a Stellaria spp using the 40x objective, mounted in G-PVA.
Stellaria_pollen2.jpg
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dtsh
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Re: Newbie learns to take images, dtsh edition

#5 Post by dtsh » Tue Apr 13, 2021 3:51 am

Today's image is another single image, this time it's the first ick of the season. For this one I was focusing on he hypostome (the central part with the hooks)

A quick look makes me think it might be an Amblyomma species, but there are a few things that don't seem quite right. I'll look into it more later.

Edit: On review I'm pretty sure this is a Dermacentor variabilis, a tick I am not quite as familiar with. It's an interestig subject, so will attempt to gather more images of it.

Amblyomma.jpg
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dtsh
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Re: Newbie learns to take images, dtsh edition

#6 Post by dtsh » Tue Apr 13, 2021 11:42 pm

A slightly better result from stacking.
Dermacentor_hypostome.jpg
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dtsh
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Re: Newbie learns to take images, dtsh edition

#7 Post by dtsh » Wed Apr 21, 2021 11:58 pm

I changed things up a little as I have been playing with the Raspberry Pi V2 camera a bit lately. Here's a stack of images of a section of wing from what I believe to be an unidentificed Chironomidae. The scope is the same AO 10 as before with the 10x objective, the only change is the V2 camera module with it's default lens. 50 images in the stack.
Chironomidae_wing.jpg
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DrPhoxinus
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Re: Newbie learns to take images, dtsh edition

#8 Post by DrPhoxinus » Thu Apr 22, 2021 4:26 am

I enjoyed your description of the AO10. I have two, one for BF and one for phase, although the wrenches are in rounded out my sockets

I am interested in your filter adapter, as I could use one of those. Besides the AO10s I have a 410 with a series 10 trinoc head and an AO150. I have 3 Leitz and 2 Zeiss but there is something cool about the AOs, and they are a bargain.

I enjoyed your photos.

Gerard

dtsh
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Re: Newbie learns to take images, dtsh edition

#9 Post by dtsh » Thu Apr 22, 2021 1:03 pm

DrPhoxinus wrote:
Thu Apr 22, 2021 4:26 am
I enjoyed your description of the AO10. I have two, one for BF and one for phase, although the wrenches are in rounded out my sockets

I am interested in your filter adapter, as I could use one of those. Besides the AO10s I have a 410 with a series 10 trinoc head and an AO150. I have 3 Leitz and 2 Zeiss but there is something cool about the AOs, and they are a bargain.

I enjoyed your photos.

Gerard
If you have access to a 3D printer, the filter adapter model is here: https://www.thingiverse.com/thing:4836163
If not, shoot me a PM with your address and I'll print one and drop it in the mail, it's small enough I don't think it even requires an NMO stamp.

My first microscope in the AO line was my 410, but I got curious about the AO10 series and ended up buying a small lot so I have...too many. Most of them were gummed up with dried grease and the usual issues one sees with instruments of this age, but I enjoy tinkering as much as using them so it's been a pleasure dismantling and cleaning. My 410 is setup for phase and I have a 10 set aside for darkfield and brightfield, but the one I'm using here is one of the spares destined for a new home someday. I figured the best way to ensure everything is working properly is to use it.

Some of the features of the AO infinity series scopes are quite impressive. I'm more used to 160mm scopes, but I am really liking the infinity design, it has some limitations in what objectives you can use, but it adds some new capabilities as well; always trade offs. The price is proably the best part and there's an amazing array of addons to expand the system that are also, comparatively at least, inexpensive.

dtsh
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Re: Newbie learns to take images, dtsh edition

#10 Post by dtsh » Fri Apr 23, 2021 2:08 am

Today's subject I believe is the algae Spirogyra. A stack of 26 images taken with the pi camera v2. I didn't make note of the magnification, but I believe this was at 400x.
Spirogyra.jpg
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dtsh
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Re: Newbie learns to take images, dtsh edition

#11 Post by dtsh » Sat Apr 24, 2021 5:48 am

Today was an unexpected opportunity to record my first video through the microscope. I believe this to be the algae Synura. Rpi camerav2 again with the same AO 10 though this is the last video from this scope, it's packed up and headed out next week.

https://imgur.com/FSg85yK

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Re: Newbie learns to take images, dtsh edition

#12 Post by dtsh » Fri Apr 30, 2021 11:28 pm

Taken using the v2 and the HQ camera on an AO10

Mosquito wing, 100x and 400x.
1.jpg
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3.jpg
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chrisimbee
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Re: Newbie learns to take images, dtsh edition

#13 Post by chrisimbee » Sat May 01, 2021 3:14 pm

very nice photos!!!! woaw !
microscope Olympus BH2-BHTU+epifluo RFC @ 470 nm
Zeiss neofluar x16Ph, x40Ph, x100 oilPh
LOMO Ph x10 X20 X40 X90oil
Olympus SPFl x2
Olympus SPx20, SPx40 SPx100
camera astro ZWO ASI 120MM (n&b) et ZWO ASI 120 MC (colour)
Nikon D3100

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Re: Newbie learns to take images, dtsh edition

#14 Post by BramHuntingNematodes » Sat May 01, 2021 3:31 pm

The HQ camera is very decent for this application.
1942 Bausch and Lomb Series T Dynoptic, Custom Illumination

dtsh
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Re: Newbie learns to take images, dtsh edition

#15 Post by dtsh » Sat May 01, 2021 5:16 pm

Thanks for the comments.

While the HQ camera is certainly nicer, the much smaller V2 is better than I expected and I was relatively satisfied with it, but I had an HQ just sitting around and in the process of sorting through an older box of optical stuff I found some nice c mount lenses which I believe came off some video cameras (Bosch or Pelco I believe) to pair with it. They work nicer than the old Bosch zoom lens I had experimented with.

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Re: Newbie learns to take images, dtsh edition

#16 Post by dtsh » Mon May 24, 2021 3:43 am

I made a diversion with an AO One-Fifty I acquired, images in it's own thread.
https://www.microbehunter.com/microscop ... 24&t=12867

It seems good so it is on the shelf to await packing.
Off to the next AO 10...

The serial number on this one is unreadable due to what looks like poor stamping at the factory, but a guess would be "9888??". The objectives are 4x(1017), 10x(1019), 40x(1023), and 100x(1079). The condenser is the 1.25 NA without catalog number.

Another pass at some mosquito scales.

First with the 4x objective.
210522_Aedes_scale_ao10_4x.jpg
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10x objective
210522_Aedes_scale_ao10_10x.jpg
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40x objective
210522_Aedes_scale_ao10_40x.jpg
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a crop of the 40x
210522_Aedes_scale_ao10_40x_crop.jpg
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And with the 100x oil (a different scale, taken the following day.
210523_Aedes_scale_ao10_100x.jpg
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dtsh
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Re: Newbie learns to take images, dtsh edition

#17 Post by dtsh » Sat Jun 12, 2021 6:16 am

Another attempt at Dermacentor variabilis hypostome. Stacked, taken with the 10x objective and cropped.
The mount turned out pretty bad, I didn't go through enough changes and there was still a little water left in the tick. It's somewhat salvageable though. Two ticks, male and female, both boiled in 10% KOH until significantly lightened. I think the heat may have been too much and next time will test with 10% KOH over time at room temp to see how it compares.

Imaged with an AO10 with 10x (Cat 1019) objective through a 10x (Cat 180) eyepiece onto the RPi HQ cam.
D.variabilis_hypostome_100x.jpg
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Re: Newbie learns to take images, dtsh edition

#18 Post by BramHuntingNematodes » Sat Jun 12, 2021 7:16 pm

Water, such a nuisance! Gray recommends palpating the bugs every few hours while soaking in Koh(or NaOH for more delicate treatment) to expel the goo inside
1942 Bausch and Lomb Series T Dynoptic, Custom Illumination

dtsh
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Re: Newbie learns to take images, dtsh edition

#19 Post by dtsh » Sat Jun 12, 2021 9:58 pm

BramHuntingNematodes wrote:
Sat Jun 12, 2021 7:16 pm
Water, such a nuisance! Gray recommends palpating the bugs every few hours while soaking in Koh(or NaOH for more delicate treatment) to expel the goo inside
I had read somewhere about using a small spatula and I didn't quite understand, but I think I am starting to. Is one supposed to nick the body too or is that not necessary? For what is effectively my second attempt at mounting something like this, I'm relatively happy with the result. There's certainly room for improvement at every step, but it's better than the first attempt by a long shot.

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Re: Newbie learns to take images, dtsh edition

#20 Post by dtsh » Sun Jun 13, 2021 1:52 am

Imaged with an AO10 with 10x (Cat 1019) objective through a 10x (Cat 180) eyepiece onto the RPi HQ cam. (same setup as previous image)

Queue up some cheesy music and don't ket the kids see this....

Dermacentor variabilis again, this time we're getting freaky with an image of a genital pore.
Dermacentor_genital_pore_20210612_s.jpg
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dtsh
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Re: Newbie learns to take images, dtsh edition

#21 Post by dtsh » Fri Jun 18, 2021 5:48 am

Same setup as before, AO10 with Pi HQ camera through a 10x Cat.180 eyepiece. Minimal processing outside of cropping and color correction.

This sample is a wing of a Chrsops spp (deerfly). The mounting medium is PVA-G and it's still very fresh so I didn't dare attempt oil immersion. Stacked images.

First is at 4x. Even at this relatively low magnification it's probably hard to picture the whole wing. In the 40x image there's a spot where one of the hairs at the leading edge of the wing is missing, leaving an empty socket; the same socket is visible in the 10x image, but it is of course, much smaller.
Chrysops_wing_4x.jpg
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The 10x objective
Chrysops_wing_10x.jpg
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And the 40x objective.
Chrysops_wing_40x.jpg
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Re: Newbie learns to take images, dtsh edition

#22 Post by hans » Fri Jun 18, 2021 5:38 pm

Nice steady progress. What lens are you using on the Pi HQ?

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Re: Newbie learns to take images, dtsh edition

#23 Post by dtsh » Fri Jun 18, 2021 7:30 pm

hans wrote:
Fri Jun 18, 2021 5:38 pm
Nice steady progress. What lens are you using on the Pi HQ?
It is a mystery item, a product of a madness which makes me dismantle "trash" and keep parts with the prospect of "I might use that someday"; that day came for one of them (I have 3 more).
I am pretty sure it's from a Bosch or Pelco analog security camera (I think) and if I were to guess, I'd say the Bosch. At one point in time I spied a box of cameras at work on their way to the dumpster and was informed that they were mine if I wanted them, so I took a few. I also have a Bosch zoom lens I used for a while, but it is significantly bulkier.

It has a bit of mass for it's size, which suggests to me someone designed it where performance was a greater factor over cost. I'm incapable of evaluating it at thiis point in time, but it seems to do what I need and it seems to me to be a bit better than the zoom lens, so it's what I am using until I learn enough to know what would be a better replacement.

These are the only apparent markings on it.
mystery_c_lens.jpg
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dtsh
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Re: Newbie learns to take images, dtsh edition

#24 Post by dtsh » Fri Jun 18, 2021 9:53 pm

Here are a couple of images of my setup; perhaps it will help.


I can pretty easily swap it from the AO10 over to the Cycloptic and when I get around to the trino head on the 410, I intend to do the same. Since both of my scopes have a different eyepiece requirement I decided to leave the coupler with a close, but easy fit around the C mount lens so that I can move the camera to whichever scope and it settles in at the correct distance on top of the correct eyepiece with little fuss. The lens has a nice even boss on it's focuser that rests against the coupler which is handy as an index.

I'm a long time native unix user, so the Pi is pretty natural to me. I ssh in from my laptop and run a comand line python script I wrote to display the camera on the connected monitor and to record images when I hit [Enter]. One could do it from the console as well. For processing, I rsync files from the Pi over to my laptop or other machine and process or stack them there. I suppose one could do some of that on the Pi itself, but it would probably take longer.

I am certain the setup has a lot of room for improvement as I sometimes see red on one side in the band at the fieldstop, so I think there's some misalignment sometimes that needs trued up.

Here's the whole setup, zip-tied to the far side of the photo tube is a mount that the Pi's case slot into. It comes off easy for when I need to move it. There's an 18"/457mm camera cable between the Pi and the camera, so it has a little reach.
RPiHQ_stack.jpg
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Here's the parts separated. Not much to it, eyepiece, coupler, camera lens.
RPiHQ_stack2.jpg
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dtsh
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Re: Newbie learns to take images, dtsh edition

#25 Post by dtsh » Sat Jul 03, 2021 4:37 am

I changed things up a bit, these were taken with the AO Cycloptic stereo microscope through a 147 eyepiece using the Pi HQ camera setup as I have with the AO 10's.

Mostly idle curiosity looking at some grass flowers and the flowers of a sedge, I did not take note of what magnification I was using for either. Both are created from many images stacked.

First up, the grass. I haven't identified this so it's just a random unnamed grass.
grass_s.jpg
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Next up is the sedge, also unidentified.
sedge_s.jpg
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Re: Newbie learns to take images, dtsh edition

#26 Post by Aenima » Wed Jul 14, 2021 7:43 pm

Great images dtsh.
I can totally sympathise with being a newbie, it's actually much harder than it sounds to simply take a photograph through a microscope. Most of the learning curve is, or was for me, comprised of many mistakes and the occasional ah-ha moment. This forum is very helpful and just reading through old posts and threads can be a big step forward. I really like your approach, keep at it. 🙂

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Re: Newbie learns to take images, dtsh edition

#27 Post by dtsh » Thu Jul 15, 2021 2:17 am

Aenima wrote:
Wed Jul 14, 2021 7:43 pm
Great images dtsh.
I can totally sympathise with being a newbie, it's actually much harder than it sounds to simply take a photograph through a microscope. Most of the learning curve is, or was for me, comprised of many mistakes and the occasional ah-ha moment. This forum is very helpful and just reading through old posts and threads can be a big step forward. I really like your approach, keep at it. 🙂
Thanks for the kind words and I agree wholeheartedly about old threads being useful. Without the many very useful posts by newbs like me trying to figure something out, the assistance offered by those who have figured it out, and the help and suggestions of everyone in between, I would still be struggling to figure out the very basics. Thank you to all who help prisoners like me, chained deep in the bowels of Plato's cave; there's still more to go, but I can see the shadows are shadows now. :)

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Re: Newbie learns to take images, dtsh edition

#28 Post by dtsh » Thu Sep 02, 2021 1:09 am

AO10, 45x achromat (1116), Pi HQ cam
First attempt.

Diatom (Gyrosigma attenutatum) (Edit: misidentified originally as G reimeri (seems I can't read labels))
Gyrosigma reimeri.jpg
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Last edited by dtsh on Fri Sep 03, 2021 10:50 pm, edited 1 time in total.

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Re: Newbie learns to take images, dtsh edition

#29 Post by dtsh » Fri Sep 03, 2021 10:33 pm

Another attempt with a diatom, this time Gyrosigma reimeri (the above was originally mislabelled (by me) as G reimeri)
None of these have come out especially well, but it will be nice to refer back to them as early attempts.

This one was nearly impossible for me to see in brightfield so I switched over to darkfield. AO10, darkfield condenser, 100x Cat#1079 with darkfield funnel stop.
Gyrosigma reimeri.jpg
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Re: Newbie learns to take images, dtsh edition

#30 Post by dtsh » Wed Sep 29, 2021 12:19 am

Same AO10 setup, no changes to the instrument.
Objective 45x Cat 1116

According to the label, the diatoms are:
Stauroneis phoenicenteron
Gyrosigma attenuatum
Gyrosigma reimeri
Navicula oblonga
Pinnulara nobilis
diatoms.jpg
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