Nancy's adventures with a microscope

I recently bought myself a microscope so that I could see my soil organisms, and hopefully monitor and maybe quantify how my soil improves in my natural gardening area over the next few years. This thread is to share some of the excitement and difficulties that I come across and hopefully make it easier for other people to follow, if they think it might be useful.
My microscope is an Olympus with a magnification up to 1000x. (how to chose a microscope thread) I don't have a camera for it, although I hope I can come up with some sort of arrangement soon, so I can share some of what I find here.
As well as the microscope, I bought some glass slides and coverslips, some sample tubes with lids and a small bottle of objective oil. I also bought a video from Tim Wilson on how to use the microscope, which I haven’t viewed yet.
The first thing I did when the microscope arrived was to check that it worked. It seems to. I put a drop of milk on a slide just so I had something to look at, but to be honest this wasn’t the best idea, since there is not much texture in milk, so it was difficult to focus on anything. I ended up looking at bubbles mostly!
So I had a go a day or so later with a couple of real samples. The first was taken from a bag of potting compost I have. I reasoned that this was likely to have a bit of microbial life. Oh my, was I right! The book title Teaming with Microbes suddenly becomes so much more apt. I could see a lot going on, lots of (presumably) bacteria scooting about. I had a little look at a soil sample from my growing area too, which was much less lively, although it was pretty cool to see the shards of silt, and I definitely had some testate amoeba in it, as well as much fewer bacteria. I haven’t tried to do any quantification yet, just a few slides to play with and get a feel for things.
I am struggling slightly to focus on the bacteria. I’m seeing what appear to me to be diffraction rings, rather than the edges of the organisms. Hopefully Tim’s video will help me get better images. I’m not really sure what the light focus and intensity knobs do.
The second slide I played with for so long that the slide started drying up, which is actually pretty annoying, all the bacteria start getting swept away!

That looks totally fascinating Nancy. I'm worried if I got one I'd be glued to it for hours a day watching all the movement. There are worst ways to spend time though Thanks for sharing - be interested to see how useful you find it.

Ha ha! Yes Jules, definitely a way of wasting time just exploring the wonder of tiny things - maybe a 'things to do a on a wet afternoon" perhaps. At the moment I am just trying to get familiar with how to take samples and get a feel for what I'm seeing. I'll try and do some more quantitative work nearer the growing season.
I've just watched Alan Booker's Garden Master miscoscopy introduction course and that is giving me some confidence. I 'won' that from the last kickstarter.

It looks like taking photos may be a bit more difficult that I'd hoped though. The camera adaptor for the microscope I have is rather expensive, and it doesn't look like it can be jury rigged to bypass it very easily. I'll probably come back to it again, since taking photos is a much better record for me than notes on a page. These were the resources I found that went into a bit of detail: Charles Krebs Basic Methods for Photomicrography and Alan wood on Olympus microscopes. My husband's pretty hot on optics, so I still hold out some hope that we may be able to come up with an affordable solution. But is definitely something else to consider when buying a microscope I think.

Nancy, that looks like great fun! One of my aims this year is to improve the microfauna in our soil and I hadn't even considered looking at what was already there - which seems ridiculous now!

I hope you manage to find a way to connect a camera before too long as I'd love to see some photos. I'm sure I'm not alone in that!

Have you looked into 3D printed adaptors? You could try searching thingiverse (a repository for printable models) for your microscope model to see if someone has made one. It might be a cheap and easy solution.

Luke Mitchell wrote: I hadn't even considered looking at what was already there - which seems ridiculous now!

If you don't know where you start, you don't know if you've improved. Actually I'm sure I would be perfectly fine getting better soil without the microscope, but it is nice to be able to quantify that in a different way, and hopefully show people here a real example.

Have you looked into 3D printed adaptors? You could try searching thingiverse (a repository for printable models) for your microscope model to see if someone has made one. It might be a cheap and easy solution.

Brilliant idea - I'll check it out. I don't think it will be simple - as I said there are optics as well as the physical camera adaptor - but you never know. I'm dusting off my physics A level here, but the problem is that the final image in the trinocular tube is a virtual one down inside the tube, so it need to be converted to one focused at infinity, so our eye or a camera can see it. There is also some colour correction (different wavelengths bend at different angles). I don't mind buying another standard eyepiece, or equivalent (maybe £50 as an early christmas present to myself) but another £200 gets a bit extravagant really since this is a toy for me and I have plenty that I should be spending my pocket money on.

Nancy Reading wrote: I'm dusting off my physics A level here, but the problem is that the final image in the trinocular tube is a virtual one down inside the tube, so it need to be converted to one focused at infinity, so our eye or a camera can see it. There is also some colour correction (different wavelengths bend at different angles). I don't mind buying another standard eyepiece, or equivalent (maybe £50 as an early christmas present to myself) but another £200 gets a bit extravagant really since this is a toy for me and I have plenty that I should be spending my pocket money on.

I believe you are correct - but the beauty of camera phones and adapters is that you don’t need to use the trinocular portion. The 3d printed adapters I have seen just fit over one of the eye pieces and line it up with the phone camera. I don’t have one, but I managed a passable picture just by holding my camera over the eyepiece. Harder to keep steady, but it works.

Actually, here is one that I took - just holding the phone.

Lina Joana wrote:Actually, here is one that I took - just holding the phone.

Wow, that's pretty good. I think that maybe my best bet. Shall I confess here I don't have a mobile phone, but I think my husband may have an obsolete one I can steal borrow.

A little update - still no pictures for you, but hopefully coming soon.
Through reading the Olympus instructions (not really a last resort - but definitely a help!), I have managed to achieve a better clarity of image. There are two stages to the bottom light - the field iris is the bottom one, which needs to match the field of view, and the aperture iris is the upper one just below the slide holder. This needs to match the objective (lower viewing lens) in use. The light intensity should be as low as possible to give a good image and not make the sample too hot. I guess LED microscopes have the advantage there.
I also managed to take a photo with my husband's old mobile phone. I put one of the eyepieces in the trinocular position and held the camera over the eyepiece as Lina Jones suggested. It was a bit tricky holding the camera in exactly the right position, but I'm surprised how good the photo turned out. Good enough to act as a reminder record anyhow. I'd really like to see if I can take video (it's easier to tell what's alive by the movement), but haven't tried doing that yet. I may buy myself another eyepiece so I don't have to keep swapping them out. I wonder if a 20x one would be worthwhile?
So I still need to devise a holder for the phone; we've worked out that it has a timer function on the 'shutter' to avoid any camera shake in future. I also need to be able to upload the photos, which ought to be a matter of finding the right lead, so hopefully not insurmountable.
The highest magnification objective lens, is an oil immersion lens, and I didn't have a chance to play use this again today. The objectives I have don't seem to be very close in focus when swapping from one to another (I wonder if it's to do with D plan and plan objectives?) so going to the highest magnification is a bit trickier.

This topic is of great interest to me. I have the microscope, but would welcome any suggestions on taking soil samples, isolating the microorganisms, or observing them.

Thank you for starting this topic!

Cathy James wrote:This topic is of great interest to me. I have the microscope, but would welcome any suggestions on taking soil samples, isolating the microorganisms, or observing them.

Thank you for starting this topic!

Well you're welcome to learn along with me if that suits your style!

A good place to start is probably Dr Redhawk's soil threads : here. This video of Elaine Ingham (https://www.youtube.com/watch?v=H8CClDH7jW) is good on preparing samples and taking notes, but she doesn't actually show you what you can see. This course (https://permies.com/wiki/180640/videos/Alan-Booker-teaches-Soil-Microscopy) with Alan Booker is pretty good, I got that by backing Paul's last kickstarter :)
I need to do more research on the actual organisms and what goodies and baddies look like. Tim Wilson has some useful resources on his site : http://www.microbeorganics.com/ and I've got another link to a pdf I found with images pf microorganisms I'll see if I can find and link here too. It's useful to find all the stuff together.

Nancy Reading wrote: ....
So I still need to devise a holder for the phone; we've worked out that it has a timer function on the 'shutter' to avoid any camera shake in future. I also need to be able to upload the photos, which ought to be a matter of finding the right lead, so hopefully not insurmountable.
The highest magnification objective lens, is an oil immersion lens, and I didn't have a chance to play use this again today. The objectives I have don't seem to be very close in focus when swapping from one to another (I wonder if it's to do with D plan and plan objectives?) so going to the highest magnification is a bit trickier.

I'm not sure I've ever used a microscope that did not need refocusing after changing objectives by rotating the turret, so this may be normal.  Just going on memory, the only one that could do this was an automatic and highly computer-integrated Zeiss microscope that could be programmed to auto-focus and then take "Z-stack" photos, starting at the bottom of the focal plane and automatically snapping photos as it re-focused farther and farther up through the sample.  The idea was to ultimately be able to compile all of the different sequential focal planes into a 3-D image of the specimen.  Cool.....but still laborious to get operating optimally.

I'll try to remember to snap some photos with my phone also when the chance next arises.....seem to hear many using this approach for, as you noted, quick record keeping.  If the phone you are using has any internet capability, you could attached the photos to an Email and send that Email from the phone to your computer.  Alternatively, you could send the photo via a "message" to another party who has in internet-connected phone.....and THEY could EMail it back to your Email address where you could download it to your computer.  Good luck!

John Weiland wrote:  If the phone you are using has any internet capability, you could attached the photos to an Email and send that Email from the phone to your computer.  Alternatively, you could send the photo via a "message" to another party who has in internet-connected phone.....and THEY could EMail it back to your Email address where you could download it to your computer.  Good luck!

The trouble is I don't think it functions as a phone anymore - my husband like to mend things and I think he has another that he swapped the SIM to (or something) and he cancelled his surplus phone account to save money. I'm sure it's just a matter of finding the right lead, or possibly bluetooth interpreter. My tablet has bluetooth and can 'see' the phone, but not what's on it......

The way to take excellent photos with a microscope is to use an SLR (Single Lens Reflex) camera. Today you would use a Digital SLR camera so you don't have to develop film to see your results. You can buy adapters so that instead of holding a camera to the microscopes eyepiece holder the camera's mounted to the microscope.

I bought a used Nikon D80 digital camera on eBay for $50 to replace one that I paid over a $1000 for back in the day. You can buy used digital cameras from most of the manufacturers. I looked as I write this and there are microscope adapters on eBay also for $15 to $150. eBay's a good place to look, learn and shop. for one thing the photos many times are better than the manufacturers photos. Big enough to get a good look at things. When you buy; if your purchase doesn't meet your expectations you can ask eBay for a return and you won't be out anything including shipping either way. If you buy a camera you wouldn't need a lens and they're sold that way but then you won't be able to test it as easily, and you lose the normal everyday camera usage. You should check that new batteries are still available before you pick the camera model.

Another advantage using an SLR camera is that since the camera is mounted to the microscope you can see the results in the viewfinder before you even take the picture. And you can combine a self timer on the camera with the mounted camera so that you can trip the shutter button but the picture won't be taken for a number of seconds by which time there's no vibrations.

Very kool.

I went down this trail when I was doing worm tea,  bought a microscope and an camera to take video of the critters.

Here are my videos I made of worm tea.

https://odysee.com/@Marthale7:f/aug-6-worm-tea-one-fourth-cup-molasses:d

https://odysee.com/@Marthale7:f/a-look-at-the-bacteria-in-worm-tea-with:7

The main problem I had was I could not find anyone local to talk to about what I was seeing with the microscope.    But I did learn how to make the bacteria explode in numbers.

Mart Hale wrote:

Here are my videos I made of worm tea.

https://odysee.com/@Marthale7:f/aug-6-worm-tea-one-fourth-cup-molasses:d

https://odysee.com/@Marthale7:f/a-look-at-the-bacteria-in-worm-tea-with:7

Brilliant! thanks for sharing. I particularly like the second video. I'm sure you can see testate amoeba there, presumably grazing on the bacteria, and all the little bacteria zooming about.

The main problem I had was I could not find anyone local to talk to about what I was seeing with the microscope.    But I did learn how to make the bacteria explode in numbers.

I'm hoping that I'll be able to use this thread to get some advice on what I'm seeing (when I can get the camera stuff all to work!) but as you say just getting more life at all would be a start.

Really cool thread! Looking forward to pictures. And about that: does that old phone have a USB/other port for data transfer? If yes, you could probably plug it into a computer's USB port with the right kind of cable, access the phone memory directly and copy any pictures you want to the computer. Some phone brands require that you have a specific app on the computer, and with some you have to mess around with the settings every time you want to transfer something, but I've transfered pictures from a couple different phones that way.

I'm a Pathologist and I took countless pictures through the eyepiece of my microscope with a Nikon Coolpix that had a small lens, about the same size as the eyepiece. You could hold the lens against the eyepiece and it was steady.

I've taken a few pretty decent shots using the cell phone but it's a lot trickier to get it all lined up. But the Cell camera seems to focus just fine through the eyepiece.

As pictures got more common, our hospital got us an adapter that fits in the top tube and we wired in an inexpensive camera so I could take pictures from the computer screen.

One thing you could do that is fairly cool is to stain the organisms on the slide. Methylene blue is easy, Iodine sort of works. If you can find a Gram Stain kit some of the bacteria will stain blue-black (gram positive) and some will stain red (gram negative.) Fungi stain dark with Gram.

But it's also cool as heck to just do a "wet prep" with a coverslip and take a look at all the little protozoa and arthropods jerking around!

Not sure why I did not think of doing this YEARS ago...

My first soil picture!
I think it was a x400 overall magnification, and you can clearly see the bacteria and little bits of soil particles and organic matter.
This was just taken by hand held phone camera down an eyepiece in the trinocular position. You can see it's a bit off set and it was awkward to get it steady and focused. I've now obtained a little camera module for my Raspad, which needs setting up yet, but should work in a similar way. I'll need to make an eyepiece adaptor to hold the camera bit steady in the right place without too much faffing around. Maybe I can even take videos - it's really cool to see the organisms buzzing about!

Well the camera and Raspad didn't really work out, but I have made more progress with the mobile phone camera. I hoped to get some real samples looked at earlier in the summer, but there is always lots to do outside when the weather in nice (and we've had a good summer for a change!). I managed to bodge up a phone holder using a feed funnel for my stand mixer mincer attachment held onto the trinocular eyepiece with a cardboard tube, it's a little flimsy, but OK as long as I'm careful not to knock it. I took a sample from my old compost bin as a trial. Not quite as much life as I'd hoped to see, but proving the principle:

Hopefully youcan see some bacteria vibrating and I'm fiddling with the focus when something large whizzes across at about 20 seconds. I didn't see this creature when I looked at lower magnifications...so these are obviously easy to miss if there aren't many.
So next I'm planning to take samples from each of my growing beds, and a sample from under the turf adjacent (to act as a control). The question is should I take three soil samples from different areas of the beds, and look at one solution of each, or take one sample and make three solutions, or three samples and three solutions.....It is taking me quite a long time to fiddle with the microscope as I'm a bit slow still, so I really don't want to take more samples than is necessary to get a reasonable comparison.

I just watched a fascinating video by the Weedy Gardener where he shows his composting process - bear with me - he also tests it at different intervals and looks at it through his microscope and the first of these is around the 13-minute mark.  He quickly shows his camera set up on the microscope around then too.  Just thought it might be of interest to those in this thread :)

PS. i think he used to be/is a professional cameraman/filmmaker so he does make rather lovely visuals!

I just got a microscope as a gift and I was wondering if anyone on Permies used one!

I'm planning on trying to interpret soil results as well as do fecal exams for my fowl.

I was wondering if you had any further recommendations of resources that teach you how to use a microscope to its full capacity? I've scoured the previous replies and am going to start looking deeper into each of them.

Where can we send our soil samples so you can tell us if they're good to go?

Oh my, this is a hoot. I hope you get a lot out of it because honestly, this is so far into the "yeah, I take this stuff seriously" category that you should be given an honorary degree in soil biology or something.

If you get a camera hooked up, I'll be the first to sign up for a subscription to the dirt bug channel.

j

Timothy Norton wrote:I just got a microscope as a gift and I was wondering if anyone on Permies used one!

I'm planning on trying to interpret soil results as well as do fecal exams for my fowl.

I was wondering if you had any further recommendations of resources that teach you how to use a microscope to its full capacity? I've scoured the previous replies and am going to start looking deeper into each of them.

Nice present! Not to be of much help, but I think there was a book recommended. It was a little expensive, so I haven't bothered with it. I did promise a link to the nice photo reference: here it is. It gives a simple intro to collecting samples and setting up your microscope.
My recommendation would be to pick a quiet afternoon and just have a play! What magnification does yours go to? Even x400 gives you an idea of the soil life, and is easier to set up. It is a bit of time consumer. I won't say waster, because I do get value from it, but it is surprising how quickly the time goes. I'm still not sure how much of the variation I'm seeing is from variations in my sample, or from my sampling method.
I have taken videos and pictures of three samples of each of my four beds. But there is currently little to say they are different from my untouched field area. I do hope to see more differences this year. It is nice to be able to record the samples this way. As I learn more, I will be able to get more information from them in future years too.

Jim Garlits wrote:Where can we send our soil samples so you can tell us if they're good to go?

Well don't send them to me! I'm strictly a pottering amateur!

Oh my, this is a hoot. I hope you get a lot out of it because honestly, this is so far into the "yeah, I take this stuff seriously" category that you should be given an honorary degree in soil biology or something.

If you get a camera hooked up, I'll be the first to sign up for a subscription to the dirt bug channel.

I'm one who always likes to learn something new. At least this is something I can do on a wet afternoon, which comes in handy (usually) in my climate! I didn't even do high school biology (far too much learning, you can't just make it up, or work it out like Physics!) I'm afraid my videos are mostly probably pretty boring for others to watch, although exciting enough for me!