r/microscopy • • Jun 08 '23

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

150 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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72 Upvotes

r/microscopy • • 12h ago

Photo/Video Share Ramazzottius tardigrade

86 Upvotes

Just a lil gal


r/microscopy • • 5h ago

Photo/Video Share Vorticella doing some filter-feeding

13 Upvotes

Leitz Dialux II, 250x, Galaxy S24


r/microscopy • • 9h ago

ID Needed! Paramecium?

13 Upvotes

r/microscopy • • 4h ago

Purchase Help MECHANIC ROBOT7060T-TG

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3 Upvotes

Has anyone used this specific microscope model for studying seeds or any type of macroremains? This microscope is supposedly oriented for technicians in those who work on repairing electronics, i know it's a stereo microscope like any other but I'm just skeptical and want to make sure it's suitable for that specific purpose, thank you.


r/microscopy • • 20h ago

Photo/Video Share Fennel (Foeniculum vulgare) Stomata on epidermis of the leaf

35 Upvotes

Using the red-blue computational extracted focus slice movies of the fennel cells and stomata to create the 3d point cloud and animate them, including some of the 2 second focus slice video to create the z-axis on the point cloud. Image contrast on living cell, computational blue red subtraction for the contrast Python OpenCV for the video, Python Open3D for the point cloud. Objective 60x amscope no oil, 40x olympus 10x olympus 0.5 reducer industrial camera (color) Video cut with OpenShot. Goal is to have super cheap imaging work-flow.


r/microscopy • • 18h ago

ID Needed! Nostoc sp. - Eterocyst visibile?

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13 Upvotes

Today at university, I had a microbiology lecture where we discussed cyanobacteria, specifically the structure of heterocysts and their role in nitrogen fixation.

While looking back at some photos I had taken with my microscope, I came across this spherical, filamentous thing. After a quick search, I discovered it's a cyanobacteria that belongs to the genus Nostoc.

Could anyone tell me if this larger cell (circled in the second pic) is a heterocyst?

Thanks in advance


r/microscopy • • 23h ago

Photo/Video Share Hairy Gastrotrich

37 Upvotes

Koristka Milano microscope (around 1920), magnified with phone camera


r/microscopy • • 21h ago

Photo/Video Share Fennel (Foeniculum vulgare) Stomata on epidermis of the leaf

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19 Upvotes

Using computational red-blue contrast 60x 40x 10x with 0.5 reducer and industrial camera real-time imaging of the living cells. Python OpenCV idle script direct capture USB port.


r/microscopy • • 18h ago

General discussion Update the sim - Going opensource soon

12 Upvotes

r/microscopy • • 1d ago

Photo/Video Share Tiny flagellate stuck inside a diatom shell

46 Upvotes

Leitz Dialux II, Galaxy S24


r/microscopy • • 23h ago

Photo/Video Share Colpoda ciliate

9 Upvotes

Koristka Milano microscope , magnified with phone camera


r/microscopy • • 1d ago

Techniques Some samples with and without filters

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62 Upvotes

Experimenting with some dark field and Rheinberg filters. On an off for comparison. Paramecium, stentor, and volvox.


r/microscopy • • 21h ago

Photo/Video Share Beckman Coulter Optima L-90K Ultracentrifuge

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1 Upvotes

r/microscopy • • 22h ago

Purchase Help Help adapting Sony A7s mirrorless camera to Bresser Researcher Trino Microscope

1 Upvotes

I am trying too figure out what to buy to attach my Sony A7s full frame mirrorless camera to my Bresser Researcher Trino Microscope. What i figured so far is that for best results i need the BRESSER SLR-camera-adapter 2x T2 23.2 mm and a T2 ring but it's way too expensive. Could i get away spending less with acceptable results? Like using a telescope 2x barlow , or not using any lens at all just some adapters.

Thank you, any insight is appreciated.


r/microscopy • • 1d ago

Photo/Video Share Apple skin transverse section

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91 Upvotes

​

Bought big red apples at grocery store, and got an idea to look at one a little bit closer.

Made several sections using cheap microtome from AliExpress, and examined them with my microscope.

Turned out, the apples are covered in continuous wax cuticle, of circa 20 microns thickness, which is smooth on the outside, but hides a rough surface, as epidermal cells protrude into it somewhat.

There are a couple of layers of pigmented cells, under which starts fleshy part of the apple.

There is no sharp transition between skin and flesh of apple, going from skin inward cells become bigger, and pores are opened between them.

Images captured via 20x objective lens, 0.5x reducer and 5Mp usb webcam.

Focus stacking using Zerene Stacker.

Gif animation using ezgif.com free online tool.


r/microscopy • • 1d ago

Micro Art Dark Knight

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10 Upvotes

Nikon D5300 + tube macro + 35 80mm f4.5


r/microscopy • • 2d ago

Photo/Video Share I couldn't use my microscope in the last 1-2 weeks because I was tinkering to make the LED upgrade work, but I finally managed to finish it. Here's a Lepadella.

99 Upvotes

Leitz Dialux II, Galaxy S24


r/microscopy • • 1d ago

Purchase Help Compound microscope recommendations for casual user?

2 Upvotes

Hi all,

I’ve recently taken a liking to looking at algae under the microscope through my labs. Diatoms have become my recent obsession. They are just so fantastic. Would it be practical to consider buying my own compound microscope to keep in my apartment?

If yes, what brand/model microscopes would you recommend as a decent cost-quality ratio?

Thanks in advance.


r/microscopy • • 19h ago

Photo/Video Share Chat GPT can summarize a reddit post, here is my thread on snail development.

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0 Upvotes

r/microscopy • • 1d ago

Troubleshooting/Questions High background in confocal images of synaptic staining

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12 Upvotes

Hi everyone,
I’m having trouble with high background when imaging immunofluorescence staining for synaptic markers by confocal microscopy. The background makes it difficult to distinguish individual synaptic puncta confidently, and I’m concerned about how this might affect quantification.
I’d appreciate any advice on how to troubleshoot this and work out whether the background is mainly related to the staining, tissue autofluorescence, or imaging settings.

I brought these slides back from Germany, where I was learning the staining protocol. The staining looked much cleaner when we imaged them there, but I’m now seeing a lot of background when imaging the same slides at my home institution.

Here is also one representative image after deconvolution in Imaris.


r/microscopy • • 1d ago

Troubleshooting/Questions Attaching condenser in a light microscope

0 Upvotes

So I just bought a microscope that is pretty cheap but I'm trying to make it custom made to at least be at the same standard ones that my university uses. So far I have already attach a mechanical stage into it so that its easy to move slides and observe specimen. Now, I'm trying to attach a condenser with a built-in iris diaphragm that I'm thinking of putting in it but I'm afraid that won't be possible because I haven't seen a proper tutorial on how to attached it to a light microscope that doesn't have one. Does anyone here have tried it before?


r/microscopy • • 1d ago

Purchase Help Compound microscope recommendations for casual user?

1 Upvotes

Hi all,

I’ve recently taken a liking to looking at algae under the microscope through my labs. Diatoms have become my recent obsession. They are just so fantastic. Would it be practical to consider buying my own compound microscope to keep in my apartment?

If yes, what brand/model microscopes would you recommend as a decent cost-quality ratio?

Thanks in advance.


r/microscopy • • 1d ago

ID Needed! Can any determine what kind of bacteria is growing in this culture bowl?

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5 Upvotes

This was originally a Paramecium Multi bowl cultured on 9.3.26 with spring water and wheat seeds. None of the other bowls from this date turned a blood red color. There is clearly a fungal mold growing on top. What could have made it turn into this red color?

There are no Paramecium in it anymore, but there are a bunch of dinoflagellates swimming around in the bowl.

The seeds turned red and seems to be a clumpy bacteria around them. Not stringy or any other texture.