Each stage contains four crystals, two of health and two of mana, usually two crystals are on plain sight at the end of each stage, with the exception of the last one, so I’m going to ignore the visible ones and focus on the hidden rooms around
In order to enter the room simply press the up button
Chiron City (stage 1)
The second one is at 1-7 there are three vapor enemies and a machine gun one, the entry is the open window you have to jump and press up in the window
Aphros Beach (Stage 2)
The second one crystal is located at 2-8 see the small purple rectangle bellow the platform? you have to jump and press up
Asbolus Cliffs (Stage 3)
The second one is at 3-5 is at the top left, there are some star stairs in the middle top use them as height to arrive with dashes
Argeius Forest (Stage 4)
The second one is at 4-7 the bottom left side of the turret maze is the hole in the wall, besides the absorbing bullet lamp
Messus Caverns (Stage 5)
The second one is at 5-15? (not sure at the stage number) is the one with the giant drop, the room is at the right side fourth spike
Dark Temple (Stage 6)
Second one is at 6-5 this one is the stage with the drop and a lot of the vapor enemies, once you arrive at the top just drop down until you find a hole in the wall with a pillar behind
Third one is at 6-7 the room is at the right side behind pillars, you can pass through it jumping from the platform at the right