Thank you for the opportunity to help you with your question!
Photon counting histogram is analysis that constitutes for a novel tool in extracting quantities from a place such as fluorescence fluctuation data. On the other hand, imhist command in matlab calculates the histogram for the intensity image. Therefore, it is true to say that they are not the same. The main reason for this is because one depends on the other for measurement.
Please let me know if you need any clarification. I'm always happy to answer your questions.