Examples of cell and microbe sizes:
Viruses . . . . . . . . . . <= 1 um
Staphlococcus . . . . . . . . 1 um
Bacteria (E. coli) . . . . . . 2 um
Red Blood Cell . . . . . . . 8 um
Elodea epidermal cell . 65 um
Amoeba . . . . . . . . . . 700 um
These are large structures compared to atoms, which have sizes on the order of 1-4 Å, or 0.1 to 0.4 nm, or 1E-4 to 4E-4 microns. ( 1 Å = 10^-8 cm).
Now, the wavelength of visible light is in the range of 4000 (blue) to 7000 (red) Å, or 400 to 700 nm or 0.4 to 0.7 microns. The atoms, the source of photons, are much smaller than the wave length of the photons by at least 3 orders of magnitude. So we cannot 'see' atoms.
And, IIRC, one needs an electron microscope to see viruses and bacteria, because they are smaller that light wave lengths. Electrons can be accelerated to energies such that their wavelengths (de Broglie wavelength) are much smaller than those of visible light.
And nucleons and electrons are even smaller - so we definitely cannot see them either.
The only way we can detect atoms, nucleons, and electrons is by virture of their interactions. The interactions can be modeled, and those models can give us an idea of what a 'structure' might be like. For many purposes, the atom, nucleon or electron is like a point, but since it has mass, we might imagine a sphere with its pointwise symmetry.
Outside the atom, electrons behave like particles or waves. Inside the atom, electrons are thought of as waves, and their 'precise' location is meaningless. Quantum/wave mechanics gives us an idea of 'region of influence' of an electron in an atom. Scattering of electrons and X-rays by atoms gives us some idea of how the atomic structure influences them, but that does not provide an 'image' of the atom.
How might we then determine a size of an atom. Well, in solids, X-ray diffraction can give us an idea of the interatomic spacing. In addition, we can take a collection of atoms and knowing mass and density, which give us volume, and knowing Avogadro's number, we can get a size of an atom of a particular element. Introductory textbooks in chemistry and material science should have discussions on determining atomic size.