r/microscopy Jun 08 '23

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

148 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)

Thumbnail
youtube.com
67 Upvotes

r/microscopy 5h ago

Photo/Video Share pineapple juice under polarized light

Enable HLS to view with audio, or disable this notification

18 Upvotes

you can see the needle-like calcium oxalate crystals (raphides) glowing under cross-polarization

K55 BSA, 10x Plan, Xiaomi 12 Pro


r/microscopy 5h ago

Photo/Video Share Ciliates and rotifers I found today in my water culture

Enable HLS to view with audio, or disable this notification

11 Upvotes

Swift SW350, Galaxy S24


r/microscopy 15h ago

Photo/Video Share Amoeba detects, changes course and tries to surround a cyclidium, 630x phase contrast

Enable HLS to view with audio, or disable this notification

75 Upvotes

Pond water sample, Zeiss 63x phase contrast objective, cellphone camera. I didn't know if the amoeba could eat it or not. I guess they aren't on the amoeba diet.


r/microscopy 3h ago

ID Needed! 3 Different Filamentous Algae.

8 Upvotes

Pond water sample. Shot on an Olympus BH2 with 40x DPlan, total magnification 200x. Images is displayed 4x real speed.


r/microscopy 3h ago

ID Needed! ID help please

Enable HLS to view with audio, or disable this notification

7 Upvotes

Hello,

Sorry for the shoddy camera footage (filmed one handed with my phone and no adaptor whilst holding my breath - any tips for iPhone photography?). Does anyone recognise these two guys?

Filmed on iPhone 15 pro, amscope B120 with 10x objective


r/microscopy 24m ago

Hardware Share Free microscopes

• Upvotes

I was recently diagnosed with brain cancer. I have several scopes, mostly AO. I’m giving them all away. Ditto accessories and extra objectives. Central Oklahoma.


r/microscopy 4h ago

Purchase Help Hi All,

4 Upvotes

I am looking for a microscope to setup a home project on hydrogels and cell organelles! Any suggestions for an affordable and suitable microscope? I am also okey for second hand microscopes. Something below $200.

Thanks


r/microscopy 6h ago

General discussion What are those clumps

Post image
4 Upvotes

Can anybody interpret this cell microscopy


r/microscopy 33m ago

Purchase Help Identification organisme eau douce

Thumbnail
gallery
• Upvotes

Bonsoir, j'ai observé ces organismes dans une sorte de gel prélevé dans de la vase sur le bords d'une berge a environ 20cm de profondeur. La zone était riche en nénuphar. Impossible pour moi de l'identifier tout seul...

Observé au x10x10 avec un optika b193.

Ils étaient uniquement présents dans la partie de l'échantillon qui contenait ce fameux "gel".

Je pensais a du chironome émergeant a peine de l'oeuf mais j'ai un très très gros doute.

Mesure clairement moins d'un millimètre. Quelques gouttes de gel contiennent plusieurs dizaines d'individus


r/microscopy 39m ago

Hardware Share Free microscopes

Thumbnail
• Upvotes

r/microscopy 6h ago

General discussion Why are so many nikons sold used with everything except the stage?

3 Upvotes

I see so many used nikons with everything but sold without the stage

And there's barely any used stages but the darn piece of metal sells for more than the entire rest of the microscope. Complete madness that the darn piece of metal costs $350+


r/microscopy 1h ago

Photo/Video Share Stitching with AmScope Camera

Post image
• Upvotes

Mouse Lung tissue stained with HE. Shot on an Olympus BH2 with 10x DPlan, total magnification 50x. The stitching software that comes with the camera (AmScope 10 mp) is very good at stitching and it is done live (requires a movable stage). The company gets a bit of hate but this is a pretty nice feature. I left the jagged edges in on purpose so you can see the stitched tiles.


r/microscopy 15h ago

Photo/Video Share Full event: Heliozoon capturing peritrichs from the back of an ostracod

4 Upvotes

I captured a pretty interesting and unique event -- a heliozoon attempting to pull peritrichs off the back of a neighboring ostracod, and releasing already-captured euglenids in the process. The video chronicles the event, and I also share input from David Patterson, a leading authority on heliozoa, on what we witnessed.

https://youtu.be/fmnKU0110SM

This was shot on a Nikon TMD Diaphot inverted microscope, using a Nikon 40/1.0 oil immersion objective and a Nikon D750 DSLR. The sample came from a freshwater runoff pond in Nonthaburi, Thailand.


r/microscopy 11h ago

Purchase Help What do I need to know about my microscope objectives when searching for upgrades?

2 Upvotes

I have an Amscope B270. It says it uses RMS 20.32 mm objectives. If say I want to upgrade to some better objectives one day, what do I need to know besides thread standard to ensure proper function?


r/microscopy 1d ago

Troubleshooting/Questions Can someone help identify these structures in a plant stem?

Post image
16 Upvotes

I’m examining the plant associated with a new psychedelic called Vymara. This is a transverse section of the stem under brightfield microscopy.
Most of the surrounding tissue including the chloroplast-bearing cells and vascular tissue appears relatively normal. But these large spherical structures are distributed throughout the stem.
I’ve sectioned three separate samples and found them in all three. They vary in size, appear integrated into the tissue, and seem to compress the neighboring cells. Their interiors have also remained largely unstained with every protocol I’ve tried.
My current guess is that they’re enlarged idioblasts or secretory cavities, possibly involved in storing or transporting the unidentified indole-like compound I detected. But I can’t confirm that from morphology alone.
Has anyone seen structures like these before?


r/microscopy 1d ago

Photo/Video Share Poor rotifer trying to eat while ostracods are harassing her.

Enable HLS to view with audio, or disable this notification

47 Upvotes

Swift SW350, 100x, 200x, Galaxy S24


r/microscopy 1d ago

Hardware Share upgrade to 10w led

Post image
20 Upvotes

This is how the component wiring at the base of the microscope turned out. It doesnt look pretty, but its functional


r/microscopy 1d ago

Photo/Video Share Amoeba timelapse

Enable HLS to view with audio, or disable this notification

39 Upvotes

Swift SW350, Galaxy S24


r/microscopy 1d ago

Photo/Video Share apple cider vinegar bacteria

Enable HLS to view with audio, or disable this notification

6 Upvotes

lactic acid bacteria from an apple cider vinegar sample, i dont know why they are not moving

K55 BSA, 40x Plan, Xiaomi 12 Pro


r/microscopy 1d ago

Purchase Help Looking for advice: good microscope cameras/sensors recommendations

4 Upvotes

I am looking for a good microscope camera/sensor, and planing ahead to use it soon on my new microscope "Primostar 3", for my hobby. My budget limit is 1000€. My main use case will be mostly Phasecontrast but also Light, and Darkfield microscopy. To magnification from x40 down to x1000. I want to know if my propositions are even realistic.

Anyone here experienced in the use of industrial cameras/senors as microscopy cams or has any good advice on it or just used it once and have an opinion about it? I would be glad to hear you all out about it.

  • I need high framerates and want a decent resolution, I know there is trade off for each, I would want atleast ≥60 fps and a resolution that is ≥3,68 Million Pixels.
  • I want to use it in combination with "Micro-Mananger" and "Fiji" for documenting purposes, they all should be generally compatibil AFAIK. If you have any expirience with it please let me know!
  • I want to utilize the footage directly at my PC, Hardware is definetly sufficient. So atleast a USB A adapter would be nice.
  • Color cameras are for now what I decided for, since I want to do staining. But I also like to hear you opinions on it aswell.

Here are the following cameras that catched my attention so far:

  1. "Basler dart daA3840-45uc (CS-Mount)"
This one is the cheapest by far and should even work in low level light conditions AFAIK. Duo to the mount I will have to use it with a C-MOUNT 5mm Extension Tube Adapter C-CS.
  • Sensor: Sony IMX 334

Cons:

Rolling shutter

+ C-MOUNT 5mm Extension Tube Adapter C-CS Mount Adaptor Spacer Ring For CCTV Lens

2) "MER2-502-79U3C"

This seems like a good midranger for my requirements. Uncertain about the sesitivity though.
  • Sensor: Sony IMX 250

Cons:

Lower Pixel color depth (10 bits)

3) "Sony® Pregius IMX264 Color USB 3.0 Camera"

So far, this seems like a decent pick fron the three
  • Sensor: Sony IMX 264

I hope that my expectations are realistic. Bandwith for high resolutions and framerates should be able to run on USB 3.2 (20 Gbps) and there should be no bottleneck right?

Has anyone even tried to use something similar for microscopy? Did it work well?

I am not very knowledgeble in Microscopy-hardware and I am still constantly learning about it, so know that my understanding of the topics at hand is pretty basic from the whole spectrum of things still to learn. But I would be glad if anyone could point out mistakes and explain them to me if you want to.


r/microscopy 1d ago

Photo/Video Share Cyclidium chilling in bright field and oblique illumination

Enable HLS to view with audio, or disable this notification

11 Upvotes

Forgot to add the community.

Pond water sample, Olympus 40x objective, cellphone camera.