To help with such tasks for real chips (given the good quality images) there is Degate[1][2] open source software.

[1] https://www.degate.org/

[2] https://github.com/DegateCommunity/Degate

Degate is even a bit overkill, it is meant for when you only have images of the physical chip. This challenge has the full GDS files, which are the files that are sent to the fab for manufacturing. They still contain information about all of the separate layers. In this case they even contained the stdcell names, making even full transistor and logic function extraction unnecessary.