What does particle size means? Is it the area or the length/diameter of the particle? I mean to say in the distribution curve, the plot should be 'particle length' vs 'counts' or the 'area' vs 'counts'?
It can be particle size/length vs count but not the area.
You can measure the diameter of the obtained 2D projection of the sample.
However, generally, it is not a perfect circle. So it will be better to measure the diameter in different directions of the same particle. And the histogram will contain this diameter along the X-axis.
You have 'found' the fact that irregular particles cannot be described by a single length number unless they're spherical. See attached.
In the case of automated imaging, we normally consider a circular equivalent (as we have a 2D image of a 3D particle) and it's often the diameter of the circle that contains the same number of pixels as our real irregular particle. This is equivalent to a projected area. Note that shape is a 3D and not a 2D issue. In terms of TEM then we may have artifacts arising from the sample preparation route e.g. microtoming. If you consider slicing a cube, then all sorts of possibilities can arise and none represent the real particle. Take a look at: