Non-destructive uploading refers to the uploading (And later WBE) of a person without killing the original, or at least without destroying the brain. With our current knowledge of brain mapping, non-destructive uploading will essentially remain science-fiction for a long time.
On the other hand, it may be that neurons are far too low-level to matter for a copy of a person (In the same way that a .pdb file of all the atoms in the body is likely to be overkill), and scanning at the level of cortical columns is just fine and dandy for uploading purposes.
MRI has a great spatial resolution for a non-invasive method, but the temporal resolution is 0.5 Hz. EEG is designed to measure neural activity, it is not exactly a scanner in the sense that you can get a map, it does not have much spatial resolution, but the temporal resolution is above 5000 Hz. Combinations of these are ongoing, and manipulations (TMS, tDCS) during the scanning, something that was not possible until quite recently, allow us to observe the causal dimension of neural activity and observe interaction. It may become possible to infer the connectome from neural activity, but if this takes far too long, neuroplasticity may have changed these connections by the time the whole map has been constructed. Moreover, a connectome alone is nothing but a circuit diagram without labels. That is to say, without chemical or physiological information, the wiring diagram may be quite useless. This is why in the non-destructive context (Or even in the destructive context, since electron micrographs don't provide direct chemical information but features from which chemistry may be inferred) chemical methods are so important, and getting chemical information turns a set of point coordinates into a brain.
It is known that all neurons in the neocortex are pyramidal, which narrows down the possibility space of morphological properties (Which may be inferred from the connections alone), but leaves behind all sorts of important properties that make a neuron an individual, special instance, as opposed to a generic neuron.
Chemical or Radioactive tracing of the connectome
The question is "Would it be possible to increase the resolution of present technology using drugs to activate specific volumes of the brain, and scanning them one by one until a whole brain has been scanned, to prevent the surrounding activity from 'blurring out' the results". The answer is that pharmacological MRI has been around for a while, and its main usage is the study of the effects of drugs in the brain, unsurprisingly. It does not a great increase the spatial resolution.
Radioactive tracing has been done by injecting peptides where one of their atoms is a radioactive isotope. The peptides are assembled into proteins which are sent from the neuron's soma to the axon by means of anterograde transport, where kinesin moves along microtubules carrying a capsule with the tracing protein. The kinesin travels along the entire axon, and radioactivity can be measured to make a map of the connectome in a particular area.
It might be possible to creating a random (Or pseudo-random) initial model of the brain (In the case of the Izhikevich model of spiking neurons, randomly initializing some matrices) and then scanning the brain with fMRI/EEG while doing a virtual equivalent of the process with the emulated, random brain. An algorithm iteratively changes the connectivity and properties of the neurons in the computer model until the "virtual EEG" data drawn from it begins to converge with that from the real brain.
This would take some yet-to-be-determined amount of time. It could be days for convergence, or years. In the latter timeframe, the properties would've changed by the time one is done with any one particular area. In most likelihood, memories will not be available.
It is possible that by expanding the mind via further external augmentation the mind can begin to operate on external mechanisms via an exocortex which can keep the brain operating even in the event of biological tissue decay as explored in the Lifetimes Infinity project.