Using ImageJ to measure areas in histological samples

Deminstration using ImageJ software to measure areas of colour on histological samples. In thgis examle I am using a 750µm slice of an infarcted heart stained with TTZ metabolic stain which stains healthy myocardium brick red and dead myocardium white or pink.
©2013 James Clark, KCL

[@Nanilo25]

Very useful tutorial. Was looking for days how to do it until I found your tutorial. THANK YOU!

[@sanportes]

After watching so many tutorials, this one did it for me, thanks!

[@MokoChocoRoco]

I just want to say this video saved me SO much time when measuring the lesions of my aorta samples so THANK YOU

[@DoryVideo]

my pleasure!

[@JBoardOnly]

Very helpful, thank you. we need this technique for our research.

[@bandaragajanayake]

Excellent explanation. Thank you so much.

[@yordyrmz94]

Great video. It was super helpful!

[@Linda-hd5ew]

Thank you very much, it saves a lot of time and make sense.

[@DoryVideo]

Glad it helped your work

[@wyan5158]

Thank you so much for it is clear and helpful.

[@xihuantiyu]

Thank you. It s very helpful

[@phuocnguyen6863]

Thank you! This is exactly what I need.

[@DoryVideo]

My pleasure. Please subscribe as I’m adding more videos all the time

[@henrygomez59]

Hi, thanks for the video - it has been most helpful. I am attempting to do something similar with lung tissues. However, I am more interested in the total perimeter of a shaded section. At 9:51 you click 'select' which puts a line around your shaded area. I am able to do this, and measure the area of the selection and the perimeter. HOWEVER, when I zoom into the selection line, the line appears extremely pixelated and segmented - not linear. Do you have any idea how I can create a line of best fit with my selection line to make my measurements more realistic?

[@obohoeminue5442]

Hi Dory videos, please how can i use image J to analyse JPEG images of a soil surface crack; to measure crack area as against total area of the bacjground, and also to measure the crack widths, length and angle of intersection.

[@davidszone2788]

This was a very helpful tutorial. Very clearly explained. Well done. I am sure that this method could be adapted to measure colour intensity or even fluorescence intensity in a particular area. Using your method, is there an obvious way of doing this? For example in your image, how would one calculate the intensity of red staining at any given region?

[@DoryVideo]

This also works with three colours but you need to play with the settings

[@woodyxiao263]

Great demo! it is really helpful.

[@DoryVideo]

My pleasure. Please subscribe as I’m adding more videos all the time

[@stemcelltalkslondon5944]

Is there a way to save your HSB settings so that you can streamline tissue quantification?

[@sumitkolkata1]

Hi, I am interested to determine xylem vessel area from stem cross sections. Could you let me know how to do that using imageJ?

[@sarahkroeker2136]

THANK YOU!

[@Terunz]

Hi, just wondering if you have this method published so that people can cite you for reference?

[@GEORGIAKIOUM90]

Hello thanks for the video. I am doing similar experiments and for the presentation of my results I have calculated the int. density and divided the selected area. I took a result per pixel. But does ti happen to know which is the units for the int. density/ pixels? Thank you very much

[@afsanehkhoshkerdar9328]

Thank you so much. so useful!!!

[@sergiorodriguezmalaga6019]

Hi, Dory Vídeo. How I can calculate the area of a single cell (in microns(2)) using the scale of the microscope image? can I use the set scale indicating that 1micron correspond to 100 pixels (eg)?

[@opetundeadepoju]

Hi, could you please do a video on how to calculate ulcer score with Image J?

[@sarahkroeker2136]

Do you have any advice for if I am trying to measure individual sections without going in and measuring theme each time? Like look at grains of rice in a picture, wanting image J to find roughly all the different grains sizes/approximate shapes and measure how big each of them is, instead of just the area of all of them? Like in your example, if you were to measure and approximation of each separate white or red section.

[@Redsg1995]

Do you have links to any papers that use this method of quantification? I want to use it but will need a reference

[@priscarogi2183]

Thank you! If I could I would hug you!

[@DoryVideo]

I have no idea whether this will work with 3D images, sorry.

[@tiffanyrodriguez4843]

Hello, I wanted to know if the same application can be utilized to measure cerebral infarction on mice

[@muhammadaqil2869]

please post tutorial on how to treshold or segment 2 similar color, like plant and weed...

[@tizianarosa9782]

As I use Evans Blue for staining the heart, how can I measure the infarct size having three different coloured parts (blue, red, white) instead of two?

[@simonix182]

Is there a way to measure te error associated with the threshold?

[@felipejoia1693]

Man thanks you very much, you help me a lot. Can I make it with 3D imagens?

[@matthewreynolds4382]

Awesome voice.

[@hebaallahahussein2280]

You said at 5:40 that you can't calibrate this image so why? because it is TIFF?

[@Californyadr3]

what is the are of the black region then is it the red area - 282x272 pixels

[@helenarc5790]

very helpful, thank you!

[@DoryVideo]

Glad it was helpful!

[@Shumayal]

Can you make a Gwyddyon tutorial please.

[@bosonglin7462]

Thanks! very helpful!

[@DoryVideo]

thanks for watching!

[@athpage2232]

I'm trying to do this now but my slides have a white background and, given that I'm using bone marrow, I can't seem to get a clean outline of my tissue of interest. How did you get a black background on your scanned slides? Thank you :)

[@DoryVideo]

I put the sections between glass and scanned them with the LID OPEN on the scanner in a dark room

[@megacoolerbaum]

Thank you!👌🏻

[@DoryVideo]

No worries!

[@flawlessegyptian1]

How did you highlight the areas you wanted to measure in the first place??

[@DoryVideo]

they were stained with a metabolic tissue stain

[@calixtepelo9146]

Hey guys! Wish this message finds you well. Is there anyone here have the text tutorial of this software so he could share it with me via my e-mail please? I need it a lot to estimate the severity of bean anthracnose for my thesis. Thank you in advance!

[@nurhabibah1417]

Thankyou so much sir

[@DoryVideo]

Most welcome

[@rodrigoprado9158]

congratulations

[@DoryVideo]

thanks!

[@kilanihassan]

HOW CAN I DOWNLOAD IMAGE J

[@DoryVideo]

its free... just google it

[@bozkurtkubilayisk1520]

I wish you spoke slowlier so that non-native English speakers could benefit from it more.