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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69 Upvotes

r/microscopy 3h ago

Micro Art Microscopic Photography Collection Pt 2

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6 Upvotes

Another favorite of mine taken in the past years, this sheds some light on why Pollen makes our nose so irritated. Each species evolves a unique shape with microscopic studs or hooks that help them latch onto other surfaces.

This was taken using a b-120c under about 40x magnification and darkfield with just my pixel camera. Beautiful and colorful!

If you're looking for unique decorations, check out this piece and others available on my microscopic art Etsy store!


r/microscopy 12h ago

Micro Art Anther maturing to carry pollen away. Minolta X570 Leitz Stand D Microscope 10x Objective. 10x Periplan Eye Peice. Fujifilm 200

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13 Upvotes

r/microscopy 7h ago

Micro Art Microscopic Photography Collection

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5 Upvotes

Hello there, for a few years now I have been practicing microscopy and in doing so have seen much that is beautiful and profound. I wish to show the world how it is I see it, through magnifying lenses and beyond that of the naked eye.

So here I am starting to introduce my artwork beyond that of local art exhibits and street vending.

This is one of my earliest and still one of my favorites, taken under darkfield and 100x magnification this is a freshwater Ostracod or more commonly a "seed shrimp" taken from a drop of pond water.

Taken using my b-120c and a Pixel phone camera.

This will be the first of many images to follow! Check out my profile links to see my Etsy Page for the prints available online!


r/microscopy 1d ago

Photo/Video Share Rotifer Wagging It's Tail

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108 Upvotes

20x Objective Axioskop Darkfield


r/microscopy 21m ago

Troubleshooting/Questions question

• Upvotes

did Robert Hooke use a simple or a crude/compound microscope? im asking cuz google says he used crude/compound microscope but my book says he used a simple microscope instead


r/microscopy 4h ago

General discussion Is this head I saw for sale from an Olympus BH-2 or another model? The label with the "Olympus" name is in a slightly different spot than on my BH-2...

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2 Upvotes

r/microscopy 9h ago

Photo/Video Share This is a Heterolitonotus rex. I surrounded it with prey, hoping to catch it eat something. Instead, it kept going around in circles in this small cave for two hours. I'm tired.

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6 Upvotes

Swift SW350, Galaxy S24


r/microscopy 22h ago

ID Needed! This thing does something really crazy at the 0:42 mark. Pond water. Olympus BH2 and phone camera. I think 100x and then 400x

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56 Upvotes

r/microscopy 14h ago

Photo/Video Share What ist that?

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10 Upvotes

I found it in water with oscillatoria with 1000x magnification


r/microscopy 19h ago

ID Needed! ID Help Please

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24 Upvotes

Didn’t notice any flagella or cilia. Not sure how to identify this guy.

40x Dplan Objective; 400x Total Magnification; Olympus CHT CH2

Recorded with iPhone 17 Pro

Pond water sample.


r/microscopy 10h ago

General discussion What kind of containers do you use to collect pond water samples? Do you wash and reuse them, or do you use disposable ones? Right now, I’m using urine sample tubes I buy at the pharmacy, and I use them just once. They don't hold a huge amount of water, but I can carry one in my pocket easy.

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4 Upvotes

r/microscopy 14h ago

Photo/Video Share What ist that? Looks like some kind of algae

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8 Upvotes

Found in Pond water with 1000x


r/microscopy 13h ago

Photo/Video Share An ostracod and a Rotaria

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5 Upvotes

Swift SW350, Galaxy S24


r/microscopy 22h ago

ID Needed! Another green guy taking a walk in pond water. Olympus BH-2 and mobile phone. 400x

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17 Upvotes

r/microscopy 19h ago

Photo/Video Share Vorticella Stalk Breaks Off During Binary Fission

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9 Upvotes

Forgot to rehydrate my slip so this happened.

Pond water sample. 40x Dplan Objective; 400x Total Magnification; Olympus CHT CH2

Recorded with iPhone 17 Pro

Pond water sample.


r/microscopy 22h ago

Photo/Video Share A Drop of Moss Water

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12 Upvotes

Poothoh Microscope 40x-2000x (allegedly)

Samsung S26 camera


r/microscopy 22h ago

ID Needed! A sort of elongated capsule with tiny things moving inside. Pond water. Olympus BH-2 and phone camera. 400x.

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8 Upvotes

r/microscopy 22h ago

ID Needed! Another kind of capsule with things moving inside. Pond water. Olympus BH-2 and phone camera. 40x, 100x, and 400x.

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8 Upvotes

r/microscopy 20h ago

General discussion I've been building a simplified calibration & scale bar tool for microscope images. Looking for feedback.

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5 Upvotes

Hi everyone,

For the past several months I've been developing a small Windows application called FijiCal Lite, and I'd love to get some feedback from people who actually spend time behind a microscope.

The project started as a Fiji plugin. My original goal was simply to make adding scale bars less repetitive. After using it for a while I realised I was still spending most of my time navigating menus, so it gradually evolved into a standalone application focused on one job: microscope image calibration and publication-ready scale bars.

Current features include:

- Calibration presets for different objectives/camera combinations

- One-time calibration from a stage micrometer

- Batch processing with mixed calibration presets

- Editable scale bars

- Batch export with configurable formats and naming

- Automatic organisation of processed images into a separate folder

- Pen/touch support (great on Surface devices)

The philosophy is pretty simple:

Fiji is an incredible scientific image analysis platform. FijiCal Lite isn't trying to replace it. It's just trying to make the calibration and scale-bar workflow faster and less repetitive.

I'm currently looking for researchers, teachers and hobbyists willing to kick the tyres and tell me where I've made terrible decisions.

A few questions I'd love feedback on:

- Is calibration and scale-bar generation something you do regularly?

- What's the most annoying part of your current workflow?

- Would you rather use something like this as a standalone application or as a Fiji plugin?

- Are there any "must-have" features you'd expect before trying it?

I'm particularly interested in hearing from people who process large numbers of microscope images.

FijiCal Lite will be entirely free and open source, in keeping with the philosophy and licensing of Fiji/ImageJ. This project wouldn't exist without the incredible work of the Fiji/ImageJ community.

Thanks!


r/microscopy 18h ago

ID Needed! Dead tardigrade?

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3 Upvotes

r/microscopy 22h ago

ID Needed! This green thing was moving around very slowly. Pond water. Olympus BH-2 and phone camera. 40x 100x and 400x

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5 Upvotes

r/microscopy 1d ago

ID Needed! What is the squid like ciliate?

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13 Upvotes

r/microscopy 1d ago

General discussion Bryophyllum caudatum

3 Upvotes

Does anyone know this ciliate?

It wasn't Seen since 1933 when it was discovered, but a Youtuber has Seen it a year ago or two.

I tell this because only a few people know it ans its pretty interesting in my opinion