Cell invagination effect

Hello! I'm trying to replicate the invagination of a cell that happens at 0:40 of this video , but in a more simplified way, using shape layers.
I thought about using this kind of method by ECAbrams or this one by BePerfect but both of these are not exatcly what I need, cause the cells are merging and not invaginating from the inside.
Using the tutorial from BePerfect I actually got something like I needed, and with some keying I found a way to isolate each blob. What I can't figure out is how to apply a gradient that moves with the shape and looks like the reference below.

Is there another way of doing this effect?
Is there an effect that can "detect" the shape and apply a gradient like the reference dynamically?
Any help is appreciated!
Thank you!