Measuring the area of crystals in TEM image using ImageJ

Hi everyone,

I am working on some TEM image data-sets containing lattice pattern of 2D protein crystals. I am interested to find out the area of the regions that contain lattice pattern of crystals. In order to measure area I’m using this approach in ImageJ :

Selection of crystal lattice pattern by freehand / polygon selection method >> Analyze >> Measure

At output I am getting result of areas, such as let say ‘‘Area=842842’’ along with values of Mean, Min, Max etc.

However, I am unable to understand few things and have following queries:

  1. Does this value of area depicts the number of pixels? (means in that particular section there are 842842 pixels?) or something else?
  2. Secondly, If it depicts simply the area, then what is the unit describing this value? µm, cm, m, m2?
  3. Lastly, as I had captured the TEM images at 100 nm resolution. So how may I convert above area value in terms of nm resolution?

My questions may be too basic as I am new in ImageJ forum, sorry for that. But, I would highly appreciate if someone help to make me to understand above questions.

P.S. Image is attached here for reference.

Hi @Ali -

Welcome to the Forum! And don’t worry at all about ‘simple’ questions… this forum is for everyone at every level. And I’m not expert either - but I will do my best to help. :slight_smile:

So… this depends on your image’s metadata. You can take a look at the top of your image window. See these examples (the first is in pixels, the second is calibrated in µm):

You can always see the unit of length in the Image Properties window. And you can set it with Set Scale (more on that one later…).

Whatever unit is indicated at the top of your image window (as above) - that is what is used for those calculations. So for the first example - everything would be calculated in pixels - and for the second image, in µm.

As long as you have the calibration of your images… you can make those adjustments in Set Scale. This way - you can represent your measurements in calibrated units.

I hope this at least helps a bit. Perhaps others have better / more-thorough answers … but at least this gives you a start.

eta :slight_smile:


Hi Eta,

Thank you very much for your kind reply. :slight_smile:
You replied all of my queries step by step and in detail. It really helped a lot.

Many thanks once again.
Asad :slight_smile:

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