Microscopy – starter equipment

All the equipment here is what I use or have heard other students comment favourably on.
Any student of the soil food web school will receive recommendations for equipment. Trouble is – these are focussed on the US, so here is what I and a couple of others found useful in a European context, particularly the UK, incl:

• Microscope
• Camera
• Lab equipment

Equipment that is fairly easily to come by using an internet search is not linked.
Have you tried the search engine that plants trees?

Microscope

Technical Requirements

The Soil Food Web school’s recommendations are below, with occasional commentry from me.

Total magnification: 40X-100X-400X – which is the combined magnification of each of the objectives multiplied with the magnification of the eye pieces (10X).

Objectives: achromatic DIN 4X, 10X, 40X
Eyepieces: wide field WF10X
Viewing head: 45 degree inclined, 360 degree swiveling trinocular
Sliding adjustable interpupillary distance: 55mm – 75mm
Ocular diopter: adjustable on one or both eye-tubes – this allows you to adjust for your weaker eye, to keep the viewing comfortable and prevent headaches
Nosepiece: revolving quadruple – accommodates up to 4 objectives
Stage: mechanical double layer size: 115mm x 125mm
Stage x-y stroke (travel range): 70mm x 30mm
Condenser and diaphragm: NA1.25 Abbe condenser with iris diaphragm Transmitted (lower) illuminator: at least 3 Watt LED light, intensity adjustable.
Focus adjustment: Coaxial coarse and fine knobs on both sides
All metal mechanical components
Power supply: AC/DC adapter, 100V-240V (UL approved)
5-year warranty against manufacturing defects
Dust cover for protection – an essential piece of kit!

Anticipate how you want to use the microscope now and into the future, and what your budget can stretch to. For me, having a third tube for using a camera simultaneously as the front eye pieces was very important, hence I chose a used microscope from a trusted retailer.
If you just want to look at your compost and soil, two eye pieces and a phone camera adapter will be sufficient. But if you intend to take lots of samples, share images with others, I’d strongly recommend investing in a trinocular microscope.

My microscope

I equipped myself with the older version of the SP60 model from Brunel Microscopes in the UK, used and guaranteed. So far it has served me well.

As a standard, I received 4x, 10x, 40x and 100x magnification objectives. For the 100x objective you need oil. If you are prone to losing concentration or get over-excited wanting to look at the next level of magnification, there is a risk of damaging the 100x objective if it comes into contact with the sample or moisture.
Whilst doing a biology assessment it’s too much fuss switching between the oil-immersion objective and dry objectives. You can remove it and replace it with a screw-in dust cover.
Alternatively, you might ask to swap the oil 100x for a dry 60x objective – handy if you want to have a closer look e.g. at the mouth parts of a nematode to classify them according to their functional group. I also got x20 eye pieces that I quickly switch in/out if needed.
I really appreciate having that extra bit of magnification, though for the course 40x is sufficient.
If it fits the budget, consider plan objectives – they give you a crisper view across the whole field of view, not just the centre, which makes for a more pleasant experience. But if you use mainly the camera view, you won’t notice much difference.

Brunel Microscopes are a UK based company, knowledgeable and offer good customer service incl. remote support if needed. As a beginner microscopist, I felt well supported and was fortunate enough to have a personal introduction to the microscope in their workshop.
Have a question? Give them a ring, don’t be boggled by their multiple, at times somewhat difficult to navigate websites.

They do offer previously used models (typically ex-demo stock or when labs upgrade), so there are some cost savings to be made.

Apex Microscopes is a subsidiary of Brunel Microscopes.

I also heard good things about Euromex, some folks using BioBlue or an I-Scope.
For students enrolled with the SFW school, Euromex may offer a special discount of 10-15%. Contact the SFW school to enquire.

Often, if you get really into this subject, you may wish to upgrade. If you know yourself to really like your photography, or wanting to explore different microscopy techniques such as darkfield technology, you might want to invest a bit more upfront. If you know you’ll want to assess if roots are in symbiosis with endomycorrhizal fungi, consider one that you can upgrade with a fluorescent unit.

I wish I had known this before…

Case: Get yourself a storage and travel case right from the start. I tried to economise, and by the time I wanted to purchase a case, the particular model was out of production.
I now travel in style with my microscope, having modified a 1960s suitcase (dark chocolate brown colour – beautiful coincidence), but it takes longer to put all the padding securely in place.
When it comes to actually taking the microscope out on frequent road trips, I will need to have a case made, or customise an antique.

Measuring aids: In the soil food web foundation course you learn to detect different groups of microorganisms in soil and compost, and learn to quantify them.
This involves making estimates of length and width within the field of view of the microscope.
Sounds easy enough, but there is a fair degree of diversity in how each of us perceive length visually. And for some, judging length is outright difficult.

If you are mainly curious to find out which groups are present in your soil, I don’t think it matters too much, you’ll get an overall feel.
If you decide to go on to doing the consultant training programme, however, or want to be more specific with your numbers over time, accuracy will matter more, as you are calculating the total biomass of fungi to bacteria per area.
My aspiration is to be reasonably accurate, otherwise my analysis would be off.

Enter the micrometers, the rulers of the microscopy world! And what a joy to actually measure the width of fungi and confirm your estimates with numbers, rather than having to think, hmm, which is the smallest bacterium here?
The eye piece micrometer shows you a scale in one of your eye pieces.
To work out what this scale means when viewed through the different objectives, you also need a stage micrometer. With this, you measure and calibrate what each of the units you see in your eye piece mean in absolute terms when viewed through a 4x/10x/40x objective respectively. You only need to do this once for each objective.
You can read more about how to use the 2 pieces here.
These tools are relevant for completing assessments via the eye pieces.

You can use software to measure particular objects in your field of view using your microscopy camera software. I use this for some objects. For calibrating your software to measure, you’ll need a stage micrometer, too.
You can usually find these in the accessories pages for your microscope or ask your supplier for help.
For low-tech assessments using the camera view, have a look here.

Dust cover: I needed a larger cover, so I can leave the microscope and camera set up, yet well-protected. If need be, a bin liner might do temporarily, but their static energy tends to attract dust, so would not recommend for long.

Cleaning: Someone suggested pressurised air to dust off the microscope. I managed to blow particles onto my lenses that way! Would NOT do that again, and instead prefer manual, more gentle air dusting, in combo with a lint-free microfibre cleaning cloth and if needed, a brush, and lens paper.

Depending on the environment, regular professional cleaning of the microscope will prolong its life and joy of using it. For the day-to-day, have a look here.

Camera

Different options are available, from smart phone cameras with adapters to microscope cameras and digital SLR cameras.
I’ve used a hand-held phone to take my first pictures, and I could stay reasonably still to take photos, as long as there were no fast moving critters! Camera phones can be great for zooming in, too, giving a little extra magnification.
It’s the most cost-effective way of recording and sharing images and videos to start with.
It’s worth buying an extra eye piece and permanently fix a smartphone adapter. That way you can quickly align the phone in the right position.

With all cameras, the higher the pixel count, the higher quality still images you get. But there are compromises – price, and longer image processing times. This can be tricky, particularly when recording videos or sharing live. And with the kind of photos needed for microscopy, the highest pixel count does not necessarily give an advantage. Microbehunter has some very useful, clear videos to help make a decision on what would meet your needs.

If you want to go down the soil consultant training programme route, you will need to live screen-share with your mentor, so they can guide you.
For this, you need a camera that facilitates this.
A high resolution will reduce the number of images that can be taken per second (frame rate), so there is a trade-off between high-resolution still images and smooth motion videos. To get a smooth image, you’d want min. 11 frames/second.
Some cameras have the ability to record high pixel photos, whilst dropping their resolution when making video recordings. Such as the digicam I use.

I opted for a 5M USB digicam from for ease of use, though do admit sometimes I wish there wasn’t a cable. It’s a 5M LCMOS digicam from Brunel, with a CCTV adapter. It works reasonably well for me.

A camera with USB3 is faster than USB2, and if you throw other variables in the mix (internet connection, age and responsiveness of your computer’s operating system, general demand), going for slightly higher specs can make a difference between joy and frustration. Cameras with wifi connections are also available (though think wifi may reduce the camera’s resolution).

The camera needs special microscopy software, ToupView and ImageView are useful, I have them both and can’t see a huge difference between them for this level of microscopy. I got both from ToupTek as part of the camera package.
Check the camera and software you choose are compatible with your operating system and camera set-up.

Fellow soil food web explorer and full-fledged soil food web consultant Casey Williams from Fullcirclesoilhealth.com & Vitalgrowinc.com has put together some other useful considerations for microscope/camera which he has kindly made available in the linked document. Thanks!

Reflections

When chasing intriguing creatures under the microscope, the image quality is better through the eye pieces compared to the camera. I switch to camera when I want to make a recording for future reference or sharing, and then view soley through the computer (rather than switching between the two modes), as the light needs adjusting for the camera.
If it’s just to have fun in the moment, the quality through the eye pieces wins hands down.

Multi-tasking with getting to know the software as well as the critters in the field of view is not easy. It can be useful to decide what you want to concentrate on first, giving your sessions focus. As your confidence with different aspects grows, you can add it all together.

Mastering doing assessments with the SMAPP (quantifying app for soil biology) whilst also recording interesting creatures can be a bit overwhelming. In the beginning, I decided to focus on one or the other.

I was exploring using my Canon EOS2000D as a microscope camera with a USB data cable, using an SLR microscope adapter, photo eye piece and T2 ring. Your microscope retailer can advise you what is needed.
The camera picks up the images well from the microscope and you can view it on-screen, from where you then take reasonably shutter-reduced images (as long as the bus doesn’t go past your home at the critical moment!)
Unfortunately the microscopy softwares ToupView and ImageView do not detect this kind of camera – so it’s not suitable for LiveView. However, there is a way of importing images through the Canon Utility software into ToupView/ImageView.

It’s best to decide if you want to view your sample largely through your eye pieces OR the camera. Their focus is different, so you probably wear out your fine focus knob if you keep switching and need to re-focus the image either for your eyes or the camera. I’d certainly wear out my patience. If you already have a DSLR, it may be worth it, just for the image quality. You can also get an additional piece to make the camera parafocal with the eye pieces.
In that case consider if you can leave the camera set-up on your microscope permanently.

For the DSLR, I tested the following softwares:

CanonUtility:
Pros: no additional costs, does the job.
Cons: Clumsy when trying to switch between video/still images – you need to change hardware settings, so not great for work flow and quick responses.

qDSLR Dashboard:
Pros: Free of charge, easy switching between video/stills
Cons: Can be harder to detect the camera, and needs an extra driver. Still, my favourite.

DSLR Remote Pro (Breeze):
Pro: Good functionality, easy switching between video/stills, reliable
Cons: More cost intensive, with upgrades only for 1 year. After that, you need to purchase upgrade licences

Overall, I found white balancing a lot easier with the LCMOS camera and ToupView, but the video quality was poorer compared to the DSLR. The video quality and general photo quality with the DSLR is good, as long as I can make do with a more coloured background. If you know how to whitebalance properly with the DSLR, please share in the comments!

Try using your smartphone first, and if you want to go down the consultancy training route, you’ll develop a feel for what you need, and can buy a suitable camera later.

Try different microscopes, once you have a better understanding of what you need would be my recommendation, particularly if you intend to make the microscope a professional tool.
What you need is unique to your current and future use and budget. Talking it through with a specialist retailer will likely be more cost-effective and joyful in the longer term.

If it was just for my own personal only, just to find out what’s going on in my soil, I’d settle for something like the Apex Scholar Microscope with a smart phone adapter.

Lab equipment

Minor headache: The 15 ml test tubes. The Soil Food Web school specifies they should have 1ml graduations, and the typical procedure is to use a 1ml/1g sample of compost or soil.
I could not find test tubes that start with the 1ml graduation. Whilst the markings are in 1ml steps, they typically start with 2ml.
No trouble though, you can adjust use a 2ml sample and adjust your dilutions, and/or use a precision pocket weighing scale to consistently enter 1g/ml of your sample.

I generally find this is helpful, as density and pore space varies in soil or compost, so the 1g standard increases my internal consistency (admittedly, there remains variation due to different moisture content of the samples).

The test tube screw-top is important alongside good hand hygiene to minimise accidental contamination and infection, should your sample material contain human pathogens.

A test tube holder might be handy, though I am using an empty slide container to hold my test tube vertically when using the precision scale (just set to tare before weighing).

Transfer pipettes: 3ml graduated transfer pipettes (7 ml total volume). These need to be calibrated, by counting how many drops make up 1ml. Even when you buy several of the same batch, they can be different. Each needs to be calibrated individually for consistency, mine varied between 19-23 drops/ml. I write the number of drops/ml on the pipette with waterproof pen.
If you don’t want to buy a pack of several dozens or hundreds, you can get smaller quantities.

I have recently switched to glass pipettes that were a similar length. One thing that appealed was less waste, the other that once calibrated, the volume of a drop should remain stable (unlike a plastic pipette which changes with temperature). And they can be cleaned. Whereas other glass pipettes I had tried before were too long for my work flow, these ones seem to be my “Goldilocks” pipettes.

Cover slips: Ideally 18x18mm, though if you can only get hold of others, that’s fine. You can adjust your calculations according to your size.

Slide carriers: 25.4 x 76.2 x 1mm, though size for this is not as critical. Larger is fine.

The lab scoop: A small tool to transfer soil samples to your test tube.
I happened to have a present in the drawer, that was just waiting to become a lab scoop: A stainless steel gardening tool, intended for pricking out seedlings. Does the job perfectly!

If you find these resources save you time and agony, and you’d like to invite me for a virtual cuppa or help contribute to the running of the site, many thanks!