You have to interact with each of the three anomalities. Initially they appear as a blue ball of energy, but interacting with them will change them in a humanoid spirit. Their locations are the following:
Medical Bay: On the lowest floor of the Medical Bay, just beneath the office in which you found the diary.
Control Room: In the Control Room, towards your right as you enter the room from the underground facility.
Particle Accelerator: In the Particle Accelerator room, next to the workbench where you have built the Aetherscope.