Using ImageJ to measure cell number and cross-sectional area of confocal images

ImageJ is a very powerful image analysis program. In this tutorial we look at using ImageJ to count cells and measure cell cross sectional area in a confocal micrograph of cardiac tissue
©2016 James Clark, KCL

[@adminweb4430]

Thanks a lot. Help me to do my research. Well done for basic intro. From Penang Malaysia

[@DoryVideo]

You're welcome

[@mihoutaozz]

thanks a lot. This video helped me just in time.

[@zeli5182]

Very helpful. Thank you!

[@DoryVideo]

My pleasure

[@johnchen5405]

hi just wondering if there was a shortcut to adding noise?

[@yousefdehghani2050]

so helpful, ty.

[@DoryVideo]

My pleasure

[@mankindkn]

Thank you🙏

[@DoryVideo]

My pleasure!!

[@cooperdc2847]

Thank you. It's very helpful.I wonder if there are some plugins or macros that automatically measure the area of muscle fibers.

[@DoryVideo]

You could probably write one.

[@sebastienszczepanski8053]

Hello ! Did you find some macro that automatically measure muscle fibre area since your comment ? I loose so many time with the freehand method .. Thank you for your help :)

[@DoryVideo]

Yes we now have a macro. I’ll find the publication and post it here

[@DoryVideo]

skeletalmusclejournal.biomedcentral.com/articles/10.1186/s13395-018-0186-6#Sec15

[@wajeedatabassum5136]

i want add a new scale bar on the image. how do i do that? thanks for the video it was quiet helpful.

[@aysekoylu3531]

Thanks a lot!

[@DoryVideo]

it's a pleasure

[@sandy-rx3om]

❤

[@fajarfirstyaadam8756]

its very helpful, thanks anyway!

[@DoryVideo]

My pleasure

[@milansethy9698]

we want to do it in two different sections of tissues and compare them.So area need to be statistically same in both sections which is difficult to do in two different tissues.please help.

[@stella21xx]

Thank you for this! It was very useful :)

[@danielteh1452]

what if you are measuring many cells?

[@MShaman74]

Better choice, instead of noise, is Set Measurement>Add to overlay.

[@DoryVideo]

Maksim Logash yes that works too

[@dimensionstars97]

Is it possible to "mark/label" a structure as I am taking measurements from specific structures? (note that I want to measure, not count)? So that I don't repeat measurements...

[@tijpete_and_the_magic]

Very interesting. I was wondering: applying a threshold I could clearly highlight cells perimeter... Is there any tool inside the program which allows to "smart" counting cells by recognizing the perimeter?

[@DoryVideo]

Yes you can! but you would need to programme that in and that would take some programming

[@darioconstantinescu7492]

I have the same problem with determining cells in tomato fruit tissues!

[@umarahmiazi5364]

Hello! How do I measure the area, circularity and perimeter for cell's actin filament? should I measure the same way that was shown in the video?

[@DoryVideo]

Yes that would work. I can recommend a Wacom pad to help

[@umarahmiazi5364]

@@DoryVideo Thanks for the reply.The actin filaments that I have got are joined together and are in cluster. I can't separate them by following your procedure. Can you please give me any suggestion regarding that?

[@ElianaBalt]

Hi! Thanku for this great videos. I´m studing the emphisema in mice, and am using the H&E tincion to evaluate the loose of the alveolar septum trough the mean linear intercept. I have to use transparent overlay consisting of 10 horizontal and 10 vertical lines superimposed over H&E stained slides... Do you know where I can find this option in the softwere? or something similar. Thank u so much!

[@donatred3979]

how to add micro symbol in set scale

[@DoryVideo]

in Windows user ALT+0181

[@hollier8744]

With the pointer, are you actually tagging the cell, or just temporarily marking it to get a count? I.e. Can you mark the cells for subsequent analysis, like if you want to track specific cells in other time-stamped images?

[@TheRichardkino]

Very interesting video. However I'm having an issue which you don't seem to be experiencing. I set the scale as you have. However when I try to measure the area of a freehand drawing I get an area value far too large to be accurate (e.g 360000!). Is there an extra step I should have performed to specify the height of a pixel as well as you only measured the length?

[@DoryVideo]

pixels are square so I am not sure what you are doing wrong

[@juantapia881]

Make sure image is saved as TIF, sometimes that could be the reason.

[@danielteh1452]

press t instead of add noise

[@sujith94510]

What statistical test would you use on the obtained data?

[@DoryVideo]

It’s parametric data so any one of the parametric tests

[@sujith94510]

thank you :)

[@abdelkaderazou3134]

Thank you for explain but I have question about thresholding with ImageJ how I can devise histogramm of grey scale image in different ranges from 0 to 255 for image SEM nanoparticles Thank you

[@angelrenie]

Hello! I just wanted to pick your brain. How did you download ImageJ on Mac. I have been having hard time doing it; hence, I use another computer for measurements.

[@DoryVideo]

Um.... I just downloaded it from their website

[@DoryVideo]

imagej.nih.gov/ij/download.html

[@crazylisi]

Why measure the cell area this way instead of counting all cells and dividing the total area by that number?

[@DoryVideo]

you don't want to measure ALL the cells as some are not at the right angle. Cardiac myocytes are long and thin and it's always best to only measure cells at the right angle in the histological sample. for spherical or more uniform cells your method might, indeed work.