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New keep here. I have had my shrimps for 3 days now. The few that were transparent started to gain some red yesterday. This morning I have woke up to this in the jar, is this a dead shrimp or is this what is left behind after they have molted?

That is a moult and looks a healthy one, very standard for them to do this when introduced to new tank parameters.

When they are established, next time you see a moult you may get eggs if lucky and the shrimp are at least 8 month + old.