These were Harry's healing crystals. This is where he trapped his nightmares, his fears, held fast till a time he felt strong enough to face them. Those dark shapes could be anything - his doubt, his self-loathing for his scar, his hatred for his enemies. All held in these prisms of stone. Hermione suddenly appreciated a whole new depth to Harry's intense life. He had such horrors in it, they were beyond his control in the conventional sense. So he had turned to ancient powers, old forms of magic ... runes and totems, ritual and ceremony ... all so that he might get through another day with his mind intact. Hermione's heart bled at the very notion that Harry needed to take such measures just to cope.