Quantification of PCR products using ImageJ

Does ImageJ measures the final or initial concentration of the PCR products?

Hi shins,

If you mean from a gel then yes, ImageJ can be used to compare the intensity of different bands. Can you be more specific as to what you need exactly? And what do you mean by final and initial concentration? You should already know the initial concentration, no?

Hi Sverre. Thank you for answering. I am just a newbie in using ImageJ and I am confused if the one it quantifies is the initial concentration or the final concentration after PCR. For example if you are quantifying samples from environment and you don’t know the initial concentration?

That depends, which are you measuring? How are you measuring it?

Why don’t you post one of the images you are trying to quantify this from, to make it more clear what you are working with and what you need from it :slight_smile:

Hi Sverre.
I am going to amplify a gene from some virus so after RT PCR, I am going to perform AGE and then quantify the PCR products using ImageJ. I am still working on my methods and still studying about the principle of how ImageJ quantifies PCR products. I didn’t conduct my experiment yet.

So I am not experienced with this protocol, do you mean qPCR? Note that ImageJ is just a tool for image analysis, it will not quantify PCR products for you, you have to employ the appropriate methods in ImageJ to analyse the data you have produced. What specifically is it that you need ImageJ to do in this protocol?

For qPCR I thought the machine did the analysis for you, but maybe this is just the fancy kinds of machines, I don’t know.

If you could be more specific about what you need from ImageJ I am sure you can get more help. How are these PCR products quantified using different software? Can you find a published paper or protocol?