Imagej plot:Change x-axis units from Pixels to microns

I am trying to calculate the Radial Distribution function of some particles. In the outcome plot x-axis is in pixels although I have given the units (Analyze-> Set Scale). Do I miss something?
Is there something else I should Do?
Thanks all!!!

Hello there,
Go to Analyze > Calibrate , set your perimeters and you should be all set to go.
Bob

Hi,
Thank you for the answer!!!
Since I am not that familiar with imagej, could you please be more explicit?
Thanks again!!!

Hello again,
When you open your image use the line tool to mark a reference of a known length in the image or one side of the image if you know the ‘Image side length’ then when you use Analyze > Calibrate, the # of pixels in the reference will be indicated, you just input the known distance and it converts all data used on that image as the data points. It continues this type of action on any measurement made with that image until you change it back.
Bob

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Hi Bob,
Thank you for your kindness following back my question!
In the attached you can see what I receive when selecting …
As you can see I have selected a known distance in the image…
Sorry for bothering you…

Don’t you mean Analyze > Set Scale… instead of Analyze > Calibrate… (that’s for calibrating pixel intensities)? Please be concise to avoid any confusion for less experienced users.

As far as I can see from @Lalas_Kalas’ first post, they have tried Analyze > Set Scale… already…

@Lalas_Kalas, is inches (as displayed in your screenshot’s info bar) really the correct unit for your image? For your post title, I understand you’d like to have microns, so it seems your image scale is still not set correctly.

Hello Lalas_Kalas,
Yes, I apologize for the error.
Bob

Thanks for clarifying the situation!
I just uploaded the image to show how the calibrate menu looks on my pc… Please do not bother about the inches I know it is not correct…
In any case I thought Analyze>Set Scale would do the job which did not happen… Is there something you would suggest?
Thanks again!!!

I assume you mean this plugin (since you didn’t specify exactly the steps you took…):

http://imagejdocu.tudor.lu/macro/radial_distribution_function

If that’s what you’re using: did you see the comments in the header of the macro?

// Limitations:
// - Particle positions are rounded to full pixel nearest to particle intensity maximum
// - RDF output distances are in pixels, irrespective of any spatial calibration of the image

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You are 1000% right!!! This is the macro I used and the limitation is valid… I think this means issue is solved!!!
Thank you for your contribution!!!