How to count objects in image using ImagJ| counting cells in imageJ| imageJ cell counter
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- Опубликовано: 26 апр 2021
- This tutorial will guide you on how to count objects in imageJ. The same process applies to cell counting, particle counting.
#imageJcellcounter 
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Thank you so much for your explanation Alicerita, this video is very helpful! Doing experiments is always great, but analyzing data could be tricky sometimes!
You're welcome 😊
You are right, executing an experiment can sometimes be straightforward. However, analysing and interpreting the result is another level of serious brain work.
Dear Alicerita, thank you so much for those explanations!
You're welcome, Celine!
Many thanks, your tutorial video is very useful and clear!
Thanks Paulina, I'm glad you found the tutorial helpful. Cheers!
Thank you Alicerita, it was a very helpful video!
You're welcome, Code
Your channel is sooo GREAT 😍😍😍please keep up!
Thank you Andry, this comment made my day, thank you.
excellent video! thank you!!
Thank you for your kind comment 🙂
thank you alicerita. it is really helpful.
You're welcome!
Thank you ma'am it's really helpful. I have a question regarding the unit of area of individual cells. How can I set it to micrometers squared?
This was great thanks!
You're welcome
Informative video
#AVMCreations
Thanks AVMcreations
very good video, Thanks.
You're welcome 😊
Thank you very much for the Tutorial. Do you have any advice for automated quantification for IHC-stained muscle fibers? I have to count the positive fibers(not cells) and have been doing it manually. Thank you in advance!
Hi Anna,
Thank you for your kind feedback. I have not attempted the counting of the filaments before. But you can record the macro for the manual processing you have been doing and then use the script to automate the analysis. Here is a link for how to automate your analysis ruclips.net/video/V2mO4MC0dho/видео.html
@@AliceritaE , Thank you!
You're welcome
very good video, thanks
I am glad you found it useful 😊
Thank you. Do you think two images taken at different dates can be compared to show which spots are new and where. I don't think image j can do this but have you ever spoken to developers to expand function such as this?
Hi Yo, I am not sure of how to do this. A time-lapse would have been best to detect which is new or old. There are plugins you can try, Napari plugins and others maybe able to do this.
Hi Alicerita, your tutorial video is so helpful. Thanks for sharing. May I ask one question? If my object's signal is faint, when I was using "Phansalkar Threshold", there was so much background noise. So it is very hard to do counting particles. By the way, I could not change the confocal setting as I need to treat every group with the same parameters. Do you know how to deal with this problem?
Hi @lang Jiaqing
Thank you for your kind comment. You can improve the intensity by going to
PROCESS | ENHANCE CONTRAST
This will open a window to apply a % of pixel, just click okay and that should brighten your sample.
It's best to apply the same % to all your samples to keep the result consistent
Pls let me know if that works
Ma'am, thank you so much for this video. This is very helpful. I have a few questions since I'm a newbie in using Image J/ Fiji.
1. Do you recommend the same procedure for a confocal z-stack? Will making an MIP of the stack be a better option than counting it in 3-D?
2. What are the units of the values in the results? Are they in micrometres?
Hi Uzma Din,
The MIP or 3D quantification depends on the type of samples you are working with. If you feel that you see more in 3D than in MIP, then choosing 3D would Abe the recommendation l. However, if the MIP gives a good representation of the 3D, then that's better.
Before performing the analysis, image calibration is a good way of defining the output parameters. If ita a confocal .lif file, imageJ will automatically detect the image calibration and produce the result in micrometers
@@AliceritaE thank you for responding. My images are z stacks of 30 microns thick sections and I'm focusing on neurogenic ventricular zone. The brdu positive cells come in clusters. If i take an MIP, the clusters become a large blob in the 2-D.
I believe 3-d cell counting is a better option for me. Do you have any video explanation of 3-d counting? That will be of great help.
Good day to you!
Thank you Alicerita.
How do I just count the objects joined together (clusters/clumps) and how do I distinguish the total numbers of single objects from the clumps?
Also how do I graphically interpret this?
You're welcome Nelson.
Apply watershed, it will split the clumped objects into fragments
You can plot the total number of count in a sample to compare with a control. If you have different treatments.
Hi Alicerita! A big thank you for your video! Is it possible to create a batch analysis similarly to you video "Batch processing in Image J (…)"? I tried, but when I go into Process > Batch > measure, I can’t do an analysis. Do you have any idea how to do that? Thank you in advance!
Hi Alicia, thank you for your kind comment.
I will look into this and get back to younlater in the day.
Cheers!
Hi Alicia,
I trust your day is going on well.
Can I please see the code you are using
This will help me to know which part generates the error message
Dear Alicerita, nice tutorial thanks. Do you know how to determine the x y z coordinate for a z stack
Hello, I will check for it and make a new video if found.
hi alicerita, this was very helpful!! wanted to know how to make a graph from the above results obtained??
Thank you for your kind feedback.
you can export the data to Excel and plot size distribution.
Thank you for a very simple presentation I would like to get to know how to get porosity out of a ct scan image
It might be a similar process with extra tweaks because of the image type. Please send me an email aliceeseola@gmail.com
With sample image
Hello, thank you for this wonderful tutorial am giving a task to count number a number of floor tiles from an image, i would like to show you the image. the counts result am having is not convincing and I tried few threshold and its just getting worse. so can you please advice me on how to carry on? thank you
Hi,
Can you please a copy of the image to my email. I will take a look at it and get back to you.
@@AliceritaE thank you for the feedback. can you drop your email address please?
You're welcome
Hi
How can I export the results to shp format to work on them in QGIS? I'd appreciate the help
Hello, i do not know how to do that. I don't even know what QGIS is 😊
Thank you so much for your video Alicerita,. How do you go about counting cells in a specific area pleaase
Hi Jaden, by using the ROI to crop that particular area before processing.
The ROI are the shape tool on the ImageJ window
Thank you 😊
You are welcome
This is one of the things I have to learn.
Thank you for the educating video
Can we differentiate the particle for classification like metal, nonmetal, and fiber?
is it possible?
That is beyond my knowledge. A machine learning might be able to do that. But such requires more than 100 images to train the machine that A is metal, B is non metal AND c is fibre.
That way, the trained machine can analyse the rest of the data.
Alternatively, if you can differentiate them by side, if the three particles have a specific size range.
Hi! Could you help me counting bees on a frame. I do some things, but the result is not accurate.
Hi Craiu,
I can try if you send me a copy of the image
My email address is alice4all42@gmail.com
Hi Alicerita, do you know how to calculate collagen fragmentation index?
Hi Shazli, I don't know how but I can read about it
@@AliceritaE Thank you. If you find any source of information, please let me know
Ma'am I wanted to know if this method is applicable for bright field unlabeled particles image?
Hello Bhawna, it may work if the bright field image displays some contrast.
@@AliceritaE I am counting bubbles captured in bright field, but I am unable to get a correct count. Please help.
Can you please send me a sample image to see what the bubbles look likes? alice4all42@gmail.com
@@AliceritaE sure ma'am
Hello just watched your video thanks for the lecture. Am trying to count IHC puncta staining on a slide and I am getting off results. Will really appreciate your assistance.thanks
Hi Azeez, thanks for watching.
Can you please send a copy of the image to my email address to view. The email is on my channel page.
@@AliceritaE couldn't find your mail address
@@AliceritaE thanks
Mail sent
Thanks
Just got notification from Gmail that address not found
Hi Alicerita, I am currently having a big challenge counting senescence cells stained during galactosidase essay. This approach does not seem to solve my problem. please help out, Thanks.
Hi, can you send me a sample image to experiment with?
@@AliceritaE ok great. How do I send it please. Maybe I could do that through your LinkedIn account. I have sent you friendship invitation. Thanks.
I have been able to send about 3 images to you via your researchgate account. Thanks.
I've seen the files
Received
Hello I have a question
I want to count hair graft with imageJ
( i have numbers of grafts but when I use this app the results is not correct )
Would you please help me ?
Hi Zahra,
I will take a look at the image you sent me. I am busy until Wednesday. Then I will attempt to analyze it and get back to you.
@@AliceritaE Thank you so much
@@AliceritaE Hello can you please help me? I can’t find solution
@zahraahmadi2234 I looked at the image yesterday and felt discouraged from trying. There is almost no contrast between the red background and the grafts. So it might be inaccurate to count how many there are.
@@AliceritaE thanks so much for your help .Do you have a solution for this issue?
Hi ma'am, I wanted to know, if you received my email or not.
Hello Bhawna, I just finished testing one of the images you sent to me in email. It's difficult to accurately work out the measurements because 1. The bubbles are of different sizes. 2. Some of the bubbles are not in the perfect focus (therefore, masking the bubbles causes ring formation.).
Therefore, I gave up on the measurements.
I can try again layer at the weekend to see if there is a way to improve the image analysis better.
Thank you so much ma'am for looking into my images. I am truly grateful. If I may ask what do u mean by 'tmaome of the bubbles '?
Also, if I used labelled material which forms such droplets, can this issue be resolved?
Hi Bhawna, I'm sorry, that was a typo error. I wanted to write that some of the bubbles are out of focus'