Boss stem cells are dropped by the final boss at your highest unlocked difficulty
You will get the third Boss Sterm Cell after beating the game with Three Boss Sterms active! (Expert difficulty)
On Expert difficulty Free flask recharges now only appear after the first boss and before the second. Extra ones can also be purchased from food shops.
You will be also able to collect Scroll Fragments. Upon collecting four scroll fragments, you can upgrade one of your three stats.