Can this be done in AE? (person morphs into crows)

Take footage of crows (stock video maybe or even CGI stock video), composite it. With masks and layers and perhaps some morph-style distortions (AE has a bunch of very powerful distort effects that can be used to make a morph). Won't look as good as that high-end all CGI crow shot, but if you have to ask if you can do it in AE then you don't have the skills or the budget to go that route.
 
Not sure, but I think that shot may have been made by Rythm & Hues. Hire them, perhaps? Oh, wait, they're out of business. :(

More seriously, this is basically a particle effect. When the witch gets hit with the axe (stick? sorry, haven't actually seen the movie) the VFX shop erases her to a clean plate and replaces her with a particle system where each particle is a video of a flying crow.

The crow videos may have been modeled and animated in a 3D animation program like Maya or Max- most likely modeled in one program by one artist, rigged in another by a second (lower paid) artist, maybe textured by a third artist in yet another program and then finally rendered by a (much lower paid) "render wrangler" through whatever software was used as the studio pipeline. That makes one video of one crow. you might want to make several videos that are each marginally different to really sell the effect. Or maybe hope that they cut away really fast (which they do!) so that you don't have to.

The crow video is now sent back up the pipeline to a compositor, who turns it into a particle system which originates from an object that is shaped like the witch. Each particle is a separate video of the flying crow. Someone else (who earns less money) has already rotoscoped the witch out of the shot to a clean plate (a separate shot from the same camera setup without any people in it. Which assumes that the camera was locked off on a tripod, which it does not appear to be in this case. Which means that a more expensive artist then painted in the trees where the witch was standing in the moving shot after the roto artist erased her.)

BTW, what's your budget?
 
You completely left out the development of a new feather rendering engine and feather simulation system. Maybe tied in with Houdini for the particle simulation. Crows have to look real and move real, really real. Shot may have been in 3D too. Even more development for for that. The VFX house(s) would have to scheduled time to give interviews with various industry publications where they would all talk about how these shots/this film involved tons of things no one has ever done before. They will be happy to boast about how many times the director changed their mind and how fast their team was able to turn the shot around.

Perhaps they have a Python script for that interview Q&A? I really should search Github for it. I wonder if it was developed with a Canadian subsidy?

:engel017:

Or you could just buy some stock footage of crows (Pond5 has some CGI crows on greenscreen already made). Use Particular in After Effects to do the particles (using the footage as the sprite for the particle). And get the shot done and move on.
 
Which assumes that the camera was locked off on a tripod, which it does not appear to be in this case. Which means that a more expensive artist then painted in the trees where the witch was standing in the moving shot after the roto artist erased her.)

Nobody's hand painting trees and backgrounds onto a photographic plate. It's done with motion control cameras, full CGI environments, CGI characters, etc.

Motion control can track an action shot with a set full of characters, and then re-do the same shot with the set empty. Wish I had a rig like that...
 
Something like it can definitely be done in AE. Especially if you shot the scene with this effect in mind. How close to that exact effect and how complicated and how realistic will all depend on how much time/money you want to throw at it. But it's definitely doable.
 
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