A Pyxis is a specialized box used to contain demon energies. The use of Pyxis for holding and transporting demons is actually quite old-fashioned and seems to no longer be practiced in modern times.
The Pyxis is a tall box of golden wood. It is used to safely trap and store the demons' consciousness, which is in the form of a sort of energy, as opposed to humans', whose consciousness is their souls.
The one in the London Institute in 1878 had an ouroboros burned into the front, symbolizing the different dimensions—the world they live in inside the serpent, and the rest of existence outside. The one before that, claimed by Edmund Herondale when he left, had an infinity symbol drawn upon its side.
In 1849, when Edmund Herondale was 14 years old, he slew the demon Marbas and, to celebrate his first demon slay, its spirit was kept in a Pyxis.
More than ten years later, Axel Mortmain had Nate Gray steal the Pyxis of the London Institute, intent on using demon energies to bring his automatons to life. While only Shadowhunters can open the Pyxis, Mortmain managed to open it and release the Greater Demon Armaros imprisoned in it, only to transfer it to the body of an automaton.
In 1899, the Shadowhunter Academy used Pyxis holding small, harmless demons for their training exercises. The Academy's older students scattered Pyxis in the woods, with the demons within meant to be released and engaged by the younger trainees. That particular year, a group of students put a very dangerous Vetis demon inside one of the boxes as a prank, and a student got killed in the process.
Pyxis originated from the Greak word puxos, which translates to the box-tree; the word pyxis also means "small box" in Latin. It is also a Latin name for a mariner's compass and is the name of a small and faint constellation in the southern sky, originally called Pyxis Nautica (the Nautical Box). It is another, more rarely used term for pyx and pyxidium.