How To Automatically Count Bacterial Colonies Using ImageJ

File, open
Circle Tool
Edit, clear outside
Image, type, 16-bit
Image, adjust, threshold
Process, binary, watershed
Analyze, analyze particles
EDIT: YOU CAN CONVERT PIXEL NUMBERS TO METRIC MEASUREMENTS BY USING THE LINE TOOL TO MARK A KNOWN MEASUREMENT. THEN USE THE ANALYZE, SET SCALE COMMAND AND TYPE IN THE KNOWN MEASUREMENT W/ UNITS.

[@karmellahaynes3763]

Excellent tutorial! I really appreciate how you used a very challenging image, completed an analysis that was less than optimal, and then walked through how to make it more accurate. I am sharing this with the college and grad students, and technicians in my lab at Emory.

[@davidshanker6711]

Thanks for your comment. I was Kai's teacher when he made this for his high school research program senior project. I have since retired but I will try to contact Kai and let him know that this is still useful.

[@carlosmaffessoni4638]

Nice lecture! Congratulations, a simple but complete colony counting explanation with ImageJ.

[@raccoongf]

this helped me so much with my 12th grade research paper thank u!!!

[@jundisedwardanthony147]

Thank you for showing us how to this!! Saved our research!! Salute to you, Sir!

[@WhatAMagician]

Great guide, this has helped me with a class project. top work

[@krnleclx]

Thank you very much bro, I Speak Spanish but i understand you very well, great, new subscriber

[@Kartik-xw7yt]

Thank you ! It helped me a lot, would love to see few more imagej application videos like this 😊👍

[@bambangsupriyanta3806]

Thanks very good tutirial

[@taylorsmithbr]

Pretty cool - counting colonies are frustrating enough!! This made things so much easier - I hopes this works!!

[@julianbarron1680]

Holy crap! this is awesome, thank you so much for the tutorial!

[@yiwang1480]

Great job, thanks!

[@francescadayesee8324]

Life saver! OMG
Thank you :)

[@t3sla752]

Good Video - Thanks

[@taylorsmithbr]

Can you speak to how safe opening this application is? Scary to think about corrupting my laptop

[@jerryfreilich6551]

I cannot thank you enough for this video!! I've been tearing my hair out for several days trying to figure out these precise tasks in ImageJ .... using their manual.... using trial and error .... etc. You solved all my problems in 15 short minutes. Nicely done job... I hope you are on your way to a great scientific career. I need to tell you that I am PhD scientist who's worked with video image analysis for 30 years. I am also a graduate of Hewlett High .... I assume you are in Lynbrook, LI ? I'm in central Oregon now... and wish you and the Lynbrook Science Program all the best!!

[@davidshanker6711]

Yes this video was made by an Lynbrook High School student (Long Island, NY) student. Thank you for your comments.

[@mitalidas5020]

Thank you for your video. I am following your video step by step but when I get to the thresholding point my background becomes red as well as the colonies. My colonies have been stained with crystal violet. So when I try to use the watershed function to separate out colonies the lines go through the background creating a grid rather than splitting up the colonies if that makes sense. Can you suggest why this may be?

[@m3lisa15]

Thank you very much for the tutorial. Can you make a tutorial on how to measure the length and diameter (for example: tree root) of many images at once?

[@katiebamman6103]

congrats great video kai :)

[@Zombie2685]

Thank you!!!

[@martanavarro9646]

thank you

[@jamesburford6531]

Great video. Thank you. Quick question. Could this be applied to counting algal cells expelled during thermal stress experiments? Il have multiple pictures over periods of time and id like to analyse the differences in symbionts expulsions between them over time. Thanks again.

[@kaibeattie2093]

Hi James, you can shoot me an email ([e-mail]) if you're still interested in discussing this. Depends on the morphology of the algal cells and the resolution of the images- I presume this is related to coral bleaching research efforts?

[@chhavipandey5621]

Thanks 🙏

[@gustavoespinozamd2500]

Excellent video! I have a doubt. I want to supress a part of the image in the middle so I can analyze particle then. I have the feeling that everything ive tried doesnt work. Do you think you can help me. Maybe by email or from here?

[@blitzwolf1012]

photoshop

[@xen_crimsonyt7401]

try doing the circle tool but instead of edit then clear outside, do edit the just clear

[@roman.s.ovchinnikov]

Thanks a lot bro!)

[@lynbrookhsresearchprogram3227]

It's our pleasure.

[@xen_crimsonyt7401]

@@lynbrookhsresearchprogram3227 part 2?????
where is it tho

[@kaibeattie2093]

Xen_Crimson YT th-cam.com/video/-5p-qms1KCs/w-d-xo.html

[@francescadayesee8324]

where's part 2 btw? :)

[@PraveenKumar-xq7xb]

th-cam.com/video/-5p-qms1KCs/w-d-xo.html