Noah Hutton already wrote an in-depth review of the neuroscience of Avatar, so I'll focus on just the brain uploading part. Would it be possible to lie down on a surface with electrochemical capabilities and somehow transfer the human mind from the cellular substrate to another form of substrate?
The Tree of Souls would need to be able to communicate with the neurons in the human's original cellular substrate at a high level of precision. There are two ways that the tree could achieve this. One would be to have some sort of biological scanner that could read at the nanometer scale in the x, y, and z directions. This would need to include penetration of at least the length of the average brain (6 inches) in the z direction. But this strikes me as highly implausible. What could possibly function as the vacuum and the electron gun?
Instead, it seems more likely that the tree would need to directly probe each of the ~ 86 +/- 8 billion neurons and ~ 85 +/- 10 billion glial cells. Perhaps by stimulating each of the brain cells individually and measuring its response curve over a number of iterations, the tree could reverse engineer a model of all of the relevant properties of that cell. In order to include learning and memory the tree would have to detect the NMDA receptor density of hippocampal neurons. It is hard to say what other details of each cell the tree would have to detect. Perhaps it would need to detect some sort of regional mRNA expression or measure of epigenetic changes to the histones and DNA of each cell. It's even possible that the tree wouldn't have to go down to that level at all and that a map of all cortical minicolumns could do the trick.
Once all of the relevant properties of the original human brain were known, the tree would have to transfer these properties to the Na'vi substrate. Since it's unlikely that the Na'vi have the same type of micro unit (the cell) as humans, this might be sort of challenging. But since most people who study the topic conclude that it'd be possible to upload the human brain in some sort of silicon substrate, there is likely to be a way to accomplish this task.
With the benefit of human technology like SSTEM (pdf) and computers, a solution to this task would be a lot easier to design. We're not so far away...