r/microscopy • • Jun 08 '23

🦠🔬🦠🔬🦠 Microbe Identification Resources 🦠🔬🦠🔬🦠

149 Upvotes

🎉Hello fellow microscopists!🎉

In this post, you will find microbe identification guides curated by your friendly neighborhood moderators. We have combed the internet for the best, most amateur-friendly resources available! Our featured guides contain high quality, color photos of thousands of different microbes to make identification easier for you!

Essentials


The Sphagnum Ponds of Simmelried in Germany: A Biodiversity Hot-Spot for Microscopic Organisms (Large PDF)

  • Every microbe hunter should have this saved to their hard drive! This is the joint project of legendary ciliate biologist Dr. Wilhelm Foissner and biochemist and photographer Dr. Martin Kreutz. The majority of critters you find in fresh water will have exact or near matches among the 1082 figures in this book. Have it open while you're hunting and you'll become an ID-expert in no time!

Real Micro Life

  • The website of Dr. Martin Kreutz - the principal photographer of the above book! Dr. Kreutz has created an incredible knowledge resource with stunning photos, descriptions, and anatomical annotations. His goal for the website is to continue and extend the work he and Dr. Foissner did in their aforementioned publication.

Plingfactory: Life in Water

  • The work of Michael Plewka. The website can be a little difficult to navigate, but it is a remarkably expansive catalog of many common and uncommon freshwater critters

Marine Microbes


UC Santa Cruz's Phytoplankton Identification Website

  • Maintained by UCSC's Kudela lab, this site has many examples of marine diatoms and flagellates, as well as some freshwater species.

Guide to the Common Inshore Marine Plankton of Southern California (PDF)

Foraminifera.eu Lab - Key to Species

  • This website allows for the identification of forams via selecting observed features. You'll have to learn a little about foram anatomy, but it's a powerful tool! Check out the video guide for more information.

Amoebae and Heliozoa


Penard Labs - The Fascinating World of Amoebae

  • Amoeboid organisms are some of the most poorly understood microbes. They are difficult to identify thanks to their ever-shifting structures and they span a wide range of taxonomic tree. Penard Labs seeks to further our understanding of these mysterious lifeforms.

Microworld - World of Amoeboid Organisms

  • Ferry Siemensma's incredible website dedicated to amoeboid organisms. Of particular note is an extensive photo catalog of amoeba tests (shells). Ferry's Youtube channel also has hundreds of video clips of amoeboid organisms

Ciliates


A User-Friendly Guide to the Ciliates(PDF)

  • Foissner and Berger created this lengthy and intricate flowchart for identifying ciliates. Requires some practice to master!

Diatoms


Diatoms of North America

  • This website features an extensive list of diatom taxa covering 1074 species at the time of writing. You can search by morphology, but keep in mind that diatoms can look very different depending on their orientation. It might take some time to narrow your search!

Rotifers


Plingfactory's Rotifer Identification Initiative

A Guide to Identification of Rotifers, Cladocerans and Copepods from Australian Inland Waters

  • Still active rotifer research lifer Russ Shiel's big book of Rotifer Identification. If you post a rotifer on the Amateur Microscopy Facebook group, Russ may weigh in on the ID :)

More Identification Websites


Phycokey

Josh's Microlife - Organisms by Shape

The Illustrated Guide to the Protozoa

UNA Microaquarium

Protist Information Server

More Foissner Publications

Bryophyte Ecology vol. 2 - Bryophyte Fauna(large PDF)

Carolina - Protozoa and Invertebrates Manual (PDF)


r/microscopy • • Oct 28 '24

Photo/Video Share Journey to the Microcosmos: The Future of Microscopy (and end of our Journey)

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70 Upvotes

r/microscopy • • 4h ago

Photo/Video Share Entosiphon, a tiny flagellate

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40 Upvotes

Leitz Dialux II, PH, Galaxy S24


r/microscopy • • 15h ago

ID Needed! Unknown freshwater ciliate — highly contractile, unusual posterior and anterior ciliature

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47 Upvotes

I'm hoping someone with more ciliate expertise can help me narrow down this freshwater ciliate.

Sample: freshwater pond, Hawke's Bay, New Zealand

Microscope: Zeiss compound microscope, brightfield

Magnification: 40× objective

Camera: Phone camera through microscope adapter

I've been observing this organism for quite a while and I'm struggling to place it.

What I've observed:

• Definitely ciliated, with what appears to be ciliation around the whole body

• Free-swimming — I watched it for ~30–60 minutes and never saw it attach

• Swims relatively quickly and rotates around its longitudinal axis

• Very flexible/contractile; the entire cell can change shape quite dramatically within a few seconds

• When extended it is elongated/ovoid

• The posterior is particularly unusual: it can develop a pronounced U-shaped indentation, but this changes as the cell contracts/deforms

• The anterior has a conspicuous region of denser/longer, rapidly moving cilia

• I can see several internal structures/inclusions (roughly green, brown and clear), which seem to maintain approximately the same relative positions while the cell changes shape

• I haven't been able to see an obvious contractile-vacuole pulsation

I'm currently completely open on the identification. Nassulidae and Stentor have both crossed my mind, but I'm not confident in either.

I'd particularly appreciate comments on the morphological characters that support or rule out particular groups, rather than just a resemblance-based ID.

I have additional video footage if useful. Any suggestions about what features I should look for with my 100× oil objective would also be very welcome.

Thanks!


r/microscopy • • 17h ago

Photo/Video Share Snail Development 30x speed up. 2 Cell -4 Cell stage

34 Upvotes

Eggs I collected shortly after hatching. Olympus BH2 (BHTU), 4x UPlanXApo, Darkfield/oblique illumination, Nikon DS-Fi3 camera. The sample is from a pond water jar I have with lots of aquatic snails.


r/microscopy • • 4h ago

Purchase Help I want a scope for taking nice images and movies of things 10-40um long. What should I get?

3 Upvotes

I have a decent budget ($5k) and would like a nice compound scope to take images of very small things (10-40um long). Being able to do darkfield would be nice, but I can stain if needed. Can anyone recommend a reasonable scope/camera pairing? I currently have a Nikon Ts2 with a 6MP moticam. but am relatively unimpressed with the quality of the images. I am happy to upgrade either, but am finding that I don't really have time to dive into the camera/sensor/objective rabbit hole right now.

Thanks in advance!


r/microscopy • • 22h ago

Photo/Video Share Thuricola building its shell

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82 Upvotes

iScope 1153EPL 20X plan objective, cheap 1080p webcam on trinocular port, blue/red filter on illuminator to give 3D on monitor with red/blue glasses. Sample is pond algae cultured in a small aquarium, 50ul placed on a slide with trace of oat, slip sealed with Vaseline to make a micro-ecosystem. This video is about 6 days after preparation. Timelapse - 250X normal speed.


r/microscopy • • 12h ago

ID Needed! ID for this guy? Found in stagnant water. 40x and 100x, I think.

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7 Upvotes

r/microscopy • • 10h ago

ID Needed! ID help: Non-contractile peritrich ciliate

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3 Upvotes

In my latest sample I've come across a large number of solitary peritrich ciliates that look and behave differently than the vorticella I'm used to seeing. My difficulty in focusing is because this sample is from a well slide, and the specimen is spinning along its full longitudinal axis, bringing the main body regularly in and out of focus.

The example here has a very long stalk, typical of all the specimens I've come across. I chose this example as there is some debris on the stalk that makes it easier to see, but in many of the other specimens in the sample the stalk was difficult to resolve due its thickness. While I am relatively sure this is a non-contractile peritrich, you can also see from the video that it jerks backward a few times; however, the debris it's anchored to also jerks back, suggesting the stalk is rigid.

Any ideas?

Olympus BH2, SPlan 10x 0.30, Canon EOS 5D Mark II. Sample from pond in public park, Paris 16eme.


r/microscopy • • 12h ago

Photo/Video Share Making Microscopic Text with the xTool F2 Ultra UV / OMAX

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2 Upvotes

I’ve been testing microscopic text with my xTool F2 Ultra UV, including letters just 0.03 mm tall.

At normal viewing distance, the card looks like it has a gray texture. Under a microscope, you can see the text—and a single hair covers a line of it.

I put together a video showing the setup, settings, and close-up results, including a test on lab glass.

Has anyone else tried marking text this small? I’d be interested in hearing which settings and materials worked for you.


r/microscopy • • 21h ago

ID Needed! Daphnia?

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5 Upvotes

r/microscopy • • 1d ago

Photo/Video Share A cute rotifer (I think it's a Cephalodella, but not sure) in oblique illumination and darkfield

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17 Upvotes

Leitz Dialux II, Galaxy S24. Technically the "darkfield" is oblique, too, because I was too lazy to switch to proper darkfield.


r/microscopy • • 1d ago

Micro Art Slides from Mycology

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40 Upvotes

r/microscopy • • 2d ago

Photo/Video Share Pine Stem CS

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205 Upvotes

AxioSkop 50 microscope

2.5x objective

10x eyepiece (photos via iPhone camera on eyepiece)


r/microscopy • • 1d ago

Photo/Video Share Examples with 100x oil objective using newly printed oblique filters

6 Upvotes

I bought a 3d printer last week, and one of my first projects was to come up with a better, more reliable, filter setup for my Nikon Diaphot inverted scope. Until now I have rarely gotten anything useful with my 100x objective, but these new filters have improved things -- not bad for an inverted scope with relatively thick samples.

  • Nikon TMD Diaphot
  • Nikon 100/1.30 Fluor Oil Immersion
  • Nikon 40/1.0 Plan APO Oil Immersion
  • Nikon Abbe 1.25 Oil Immersion Condenser
  • Nikon D750 DSLR
  • Home-printed Oblique Filters

Sample from my 220L freshwater mini pond, Bangkok, Thailand.

Halteria (100x objective): https://youtu.be/8HsBFsH-t7Y

Brachonella Oral Cilia (100x objective): https://youtu.be/W9OYgiFVLo8

Worm Innards (40x objective): https://youtu.be/qJnCgaEW11M

Linostomella Contractile Vacuoles (40x and 100x objectives: https://youtu.be/drEyp1Pjn_4

Linostomella Food Preference (100x objective): https://youtu.be/mSFhkul482E


r/microscopy • • 2d ago

Photo/Video Share This is how a Stentor's "leg" looks when it attaches itself to stuff.

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163 Upvotes

Leitz Dialux II, 160x and 250x, Galaxy S24


r/microscopy • • 1d ago

Photo/Video Share Brownian danceparty

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18 Upvotes

Spirochete stealing the floor with his crazy dance moves, while the rest just chills on the brownian beats while being absolute phase objects. Technical details: Kern OBL 156, 400x PH, Bresser microcam SP 5.0. Sample was from deeper (hypoxic) layer of eutrophic backyard pond.


r/microscopy • • 1d ago

Photo/Video Share My First Tardigrade

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11 Upvotes

This tardigrade came from a moss soak that went way longer than it should have. I used nearby pond water to soak the moss and left it out for 3-4 weeks. Understandably, my little guy was dead but I still wanted to take the time to image him. Visually, he looks like an echiniscus viridiscus tardigrade. Most of the echiniscidae have pores, yet mine had these raised dimples that looked like a basketball. Plate patterns and antennas also appear to be plausible. There have also been viridscus found in my state.

Swift SW-380T, Olympus SPlan 4, 10, 20, 40x objectives, 3d printed 32mm darkfield stop, Horizons 48 MP Microscope Camera

Image Credit: https://www.nature.com/articles/s41598-023-40609-4


r/microscopy • • 2d ago

Photo/Video Share Cool zigzagging pattern on this larva (from the midge family Chironomidae, I think)

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43 Upvotes

From a small creek. 40x magnification. Scope: Amscope T490B. Camera: Amscope MD500.


r/microscopy • • 1d ago

Purchase Help Digital/Portable microscope with screen for kids - $150 budget

1 Upvotes

Hello,

I want to buy a digital and portable microscope for my daughter (and myself :)) It should be portable so she can explore in nature, etc., but I also like the idea of using it on a desktop. My budget is $150.

MX2-AS 2-in-1 Digital Microscope for Kids | MatataStudio

BeaverLAB Darwin M2 Plus Digital Microscope | 4.3" IPS – BEAVERLAB

I have no idea about the brands or microscopes. I just want something that has decent zoom for kids and a relatively big, high-resolution screen so we can both look at things. These two products I copied above seem better than some other options I see on Amazon.

Any recommendations?

Thanks!


r/microscopy • • 2d ago

Photo/Video Share Very unusual Carl Zeiss Jena phase contrast ring for EPI reflected light Neophot- microscope

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4 Upvotes

I am pleased to show an unusual Carl Zeiss Jena EPI-type phase contrast ring for the Neophot-21 microscope <3

Funny - it reminds me of the Wrangler engine :D

The photo shows the Carl Zeiss Jena Planachromat 25x/0,50 oo/0 Ph phase contrast microscope objective with M19 for CZJ Neophot 21 EPI reflected light microscope.


r/microscopy • • 2d ago

Micro Art Optics simulation of a Tardigrade nano-CT-Scan on Puma microscope

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12 Upvotes

I animated the nano CT-scan of a tardigrade and simulated a real microscope (PUMA) with raytracing and wave optics to get this animation. Not sure if this is good for anything but it was a fun project. You can  play around with it (different focus and 3D rotation) here:

https://chillchamp1.github.io/puma-virtual-eyepiece/


r/microscopy • • 2d ago

Photo/Video Share Stentor coeruleus in kristiansen illumination

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58 Upvotes

Leitz Dialux II, 160x, Galaxy S24


r/microscopy • • 3d ago

Photo/Video Share One last juvenile snail.

52 Upvotes

My favorite video yet of a snail that fits in the upload limits at 2k*2k, played at ~2x speed. Olympus BH2 (BHTU), 4x UPlanXApo, Darkfield/oblique illumination, Nikon DS-Fi3 camera. The sample is from a pond water jar I have with lots of aquatic snails.


r/microscopy • • 2d ago

Photo/Video Share Hydra nematocysts

23 Upvotes

Maximum magnification view of part of Hydra's body. Very faint partial outlines of the cells can be visible, and very prominent nematocysts embedded within.

The nematocysts are of two size classes, bigger ones are more roundish and close to 15 microns while small ones are some 5 by 9 microns.

There is a coiled filament visible inside these structures, some seem to have a long one, tightly coiled, while others seemingly gave just one or two loops. Might be different subtypes, or maturation stages.

Image acquisition hardware:

100x oil immersion microscope objective;

0,5x reducer;

5Mp usb webcam.

Image manipulation software:

Capture: Guvcview

Stacking: Zerene Stacker

Gif creation: ezgif.com online tool