if you just want count/location, super resolution techniques (https://www.science.org/doi/10.1126/science.ade2676 https://www.science.org/doi/10.1126/science.ad

if you just want count/location, super resolution techniques (https://www.science.org/doi/10.1126/science.ade2676 https://www.science.org/doi/10.1126/science.ade2676) and proximity labeling (https://www.biorxiv.org/content/10.1101/2023.10.28.564055v1 https://www.biorxiv.org/content/10.1101/2023.10.28.564055v1) may be a good starting point. cryo may be able to help with that if the direct electron detectors get better (as my understanding (and in my experience), cryo-et data is quite noisy). my guess is that multiple techniques will have to be combined and processed with sophisticated computational pipelines to make this a reality. each technique provides some information on the state of the cell, so the computational question becomes if can you figure out how to integrate information between these techniques to get the specific information you want. it may be too early to tackle this, but who knows...